2024-03-28T12:03:49Z
https://zenodo.org/oai2d
oai:zenodo.org:1215470
2020-01-20T17:02:07Z
user-iees-paris
PEETERS Christian
2018-04-09
<p>Ant societies consist of reproductive and sterile adults that show tremendous diversity of phenotypes. These include permanently wingless queens and a soldier caste that evolved convergently in many genera. Myrmecologists describe ant castes with terminology based on form, or function, or both, moreover terms are used inconsistently in the literature. Because morphology changes less readily than behaviour, an emphasis on morphological definitions is recommended to facilitate comparative studies and understand the evolutionary origin of castes.</p>
<p>This is the english (original) version of a chapter published in Spanish in the book</p>
<p><strong>HORMIGAS DE COLOMBIA (editors F. Fernández, R. Guerrero & T. Delsinne). National University of Colombia (2019)</strong></p>
<p><strong>Capitulo 6 Castas: homología y analogía en la forma y función </strong></p>
https://doi.org/10.5281/zenodo.1215470
oai:zenodo.org:1215470
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1215469
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
morphology, queen, worker, gamergate, ergatoid queen, intercaste, soldier
Ant castes: homology and analogy in form and function
info:eu-repo/semantics/bookPart
oai:zenodo.org:10011212
2023-10-18T00:06:04Z
openaire_data
user-iees-paris
Tully, Thomas
2023-10-16
<p>This spreadsheet contains the data that has been analysed in the paper entitled </p><p> Diversity, plasticity and asynchrony of actuarial and reproductive senescence in the Collembola Folsomia candida (Willem, 1902)</p><p>Thomas Tully Original Research, Front. Ecol. Evol. - Behavioral and Evolutionary Ecology </p><p>10.3389/fevo.2023.1112045<br> </p><p>220 isolated individuals of the Collembola Folsomia candida have been raised and followed until their death. The Collembola belong to 11 clonal lineages grouped into two distinct clades (A and B, see "Clones" sheet). Half of the Collembola have been raised in an environment where food was provided ad libitum (high food, "+"), while for the other half, food was available only one day per week (low food "-").</p><p>We report the age of death in the "Lifespan" sheet, together with the Collembola size at death, and their lifetime reproductive success.</p><p>We report the clutch size (number of eggs) of each clutch laid by each individual in the "Reproduction" sheet. For each clutch we have the Collembola size and for some of the clutches the mean egg size and proportion of sterile eggs. </p><p>In the "Egg_size" sheet we put all the egg size measurements that have been made (one line per egg measured). </p><p>In the "Cumulative_Fecundity" sheet, we have the age, fecundity and cumulative fecundity for each laying event and also for the individual death ("clutch number=0 for death). </p>
https://doi.org/10.5281/zenodo.10011212
oai:zenodo.org:10011212
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10011211
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Frontiers in Ecology and Evolution, 11, 1112045, (2023-10-16)
Diversity, plasticity and asynchrony of actuarial and reproductive senescence in the Collembola Folsomia candida (Willem, 1902)
info:eu-repo/semantics/other
oai:zenodo.org:6434552
2022-04-10T13:39:26Z
user-iees-paris
Jérôme Mathieu
2022-04-10
<p>Ce document est destiné aux débutants dans le langage R et n'a aucune prétention à part aider à la prise en main du langage.</p>
<p>Le document couvre les aspects qui, d'après mon expérience, bloquent fréquemment les débutants.</p>
<p>Il fait des simplifications (abusives?) et se concentre sur les solutions les plus faciles pour les débutants.</p>
<p><br>
Le cap important est d'arriver à lire un fichier de données. Lisez bien l'intro, tout compte!</p>
<p><br>
Bon courage, cela vaut le coup!</p>
https://doi.org/10.5281/zenodo.6434552
oai:zenodo.org:6434552
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6434452
info:eu-repo/semantics/openAccess
Creative Commons Attribution Non Commercial 1.0 Generic
https://creativecommons.org/licenses/by-nc/1.0/legalcode
R language
R project
Initiation au Langage R
info:eu-repo/semantics/lecture
oai:zenodo.org:6434453
2022-04-10T13:39:26Z
user-iees-paris
Jérôme Mathieu
2022-04-10
<p>Ce document est destiné aux débutants dans le langage R et n'a aucune prétention à part aider à la prise en main du langage.</p>
<p>Le document couvre les aspects qui, d'après mon expérience, bloquent fréquemment les débutants.</p>
<p>Il fait des simplifications (abusives?) et se concentre sur les solutions les plus faciles pour les débutants.</p>
<p>Attention, il y a des coquilles dans cette version, utiliser plutôt la dernière version.</p>
<p> </p>
<p>Le cap important est d'arriver à lire un fichier de données. Lisez bien l'intro, tout compte!</p>
<p><br>
Bon courage, cela vaut le coup!</p>
https://doi.org/10.5281/zenodo.6434453
oai:zenodo.org:6434453
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6434452
info:eu-repo/semantics/openAccess
Creative Commons Attribution Non Commercial 1.0 Generic
https://creativecommons.org/licenses/by-nc/1.0/legalcode
R language
R project
Initiation au Langage R
info:eu-repo/semantics/lecture
oai:zenodo.org:3601030
2020-03-10T19:56:42Z
user-cereep-ecotron
openaire_data
user-iees-paris
Rozen-Rechels, David
Dupoué, Andréaz
Meylan, Sandrine
Qitout, Kenza
Decencière, Beatriz
Agostini, Simon
Le Galliard, Jean-François
2020-01-08
<p>Raw data of the article "Acclimation to Water Restriction Implies Different Paces for Behavioral and Physiological Responses in a Lizard Species" by Rozen-Rechels D. et al., published in Physiological and Biochemical Zoology 93(2):160-174 in 2020 (https://doi.org/10.1086/707409). These data are freely available in csv format. See the readme file for metadata explanation.</p>
<p>Data were formatted by the first author David Rozen-Rechels and collected according to standards and procedures described in the companion journal article.</p>
<p> </p>
Agence nationale de la recherche ANR-13-JSV7-0011-01
Agence nationale de la recherche ANR-17-CE02-0013
https://doi.org/10.5281/zenodo.3601030
oai:zenodo.org:3601030
eng
Zenodo
https://doi.org/10.1086/707409
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3601029
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Physiological and Biochemical Zoology, 93(2), 160-174, (2020-01-08)
body temperature
water availability
activity
evaporative water loss
exploration
metabolism
reptiles
Acclimation to water restriction implies different paces for behavioral and physiological responses in a lizard species
info:eu-repo/semantics/other
oai:zenodo.org:3757751
2020-04-22T06:59:26Z
user-cereep-ecotron
openaire_data
user-iees-paris
Badiane, Arnaud
Martin, Mélissa
Meylan, Sandrine
Richard, Murielle
Decencière Ferrandière, Beatriz
Le Galliard, Jean-François
2020-04-20
<p>This is the online dataset corresponding to the article </p>
<p><strong>Male ultraviolet reflectance and female mating history influence female mate choice and male mating success in a polyandrous lizard </strong>published in Biological Journal of Linnean Society in 2020.</p>
https://doi.org/10.5281/zenodo.3757751
oai:zenodo.org:3757751
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3757750
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Color signals
Female choice
Fertilization
Paternity
Post-copulatory selection
Sexual selection
Ultraviolet
Zootoca vivipara
Dataset: Male ultraviolet reflectance and female mating history influence female mate choice and male mating success in a polyandrous lizard
info:eu-repo/semantics/other
oai:zenodo.org:3242573
2020-01-20T12:55:00Z
user-iees-paris
Yong, Gordon
Matile-Ferrero, Danièle
Christian Peeters
2019-04-24
<p><em>Rhopalomastix</em> is a myrmicine ant distributed throughout tropical parts of Asia, with almost nothing known about its biology. Its closest relative <em>Melissotarsus</em> in Africa is the only ant genus known to live with diaspidid scale insects inside their nests, and to rely on these for food. Twelve colonies of four species of <em>Rhopalomastix</em> were sampled from seven tree genera in Singapore. Ants chewed tunnels under live bark, and these were occupied by many diaspidids belonging to five genera; at least two species are known to also live freely on the outside of trees. Inside ant nests, only a few diaspidids secreted their trademark shields. The association with the pupillarial <em>Fiorinia</em> is unexpected, since they have fewer secretions that can be used as food by the ants. <em>Rhopalomastix</em> and <em>Melissotarsus</em> workers share several morphological adaptations, including powerful mandibles and silk glands, but while the legs of <em>Melissotarsus</em> are modified for traction during tunnelling, those of <em>Rhopalomastix</em> are not. Consequently, <em>Rhopalomastix</em> workers are able to walk outside their tunnels, but they behaved timidly except in <em>R. murphyi</em>. Silk was used to repair damaged tunnels, and the spinning behaviour resembled that of <em>Melissotarsus</em>. Host trees do not gain protection from the ants against leaf herbivores, so they apparently get no benefits from this mutualism. We discuss the likely economic impact of this parasitic lifestyle, especially on fruit trees.</p>
https://doi.org/10.5281/zenodo.3242573
oai:zenodo.org:3242573
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3242572
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Insectes Sociaux, 66, 273-282, (2019-04-24)
Mutualism · Silk · Melissotarsus · Andaspis · Fiorinia · Pupillarity · Mangaspis · Pseudaulacaspis · Rhopalaspis · Aquilaria
Rhopalomastix is only the second ant genus known to live with armoured scale insects (Diaspididae)
info:eu-repo/semantics/article
oai:zenodo.org:844253
2020-01-20T16:38:43Z
user-iees-paris
user-biosyslit
Peeters, Christian
Tinaut, Alberto
2017-08-17
<p>Ergatoid (= permanently wingless) queens do not disperse individually from their natal colonies, instead they walk with nestmate workers to new nesting sites during the fission of existing colonies. Very few observations of dependent colony foundation are available, and it must often be studied with indirect data. Thirty-five colonies of <em>Monomorium algiricum</em> (BERNARD, 1955) were excavated at different times of the year. New sexuals (ergatoid queens and males) were found during a short period at the end of summer. Dissection of spermathecae in 331 queens revealed that new gynes mate soon after emergence. Ovarian activity was assessed to distinguish between "old" and newly mated queens. Both monogynous and polygynous colonies were found throughout the year; queens in the latter were less fecund. Sexuals were not produced in some polygynous colonies. The life history of M. algiricum is complex due to interactions be- tween extreme seasonality (no foraging and no egg-laying during six months of the year), coexistence between "old" and newly mated ergatoid queens, and the irregularity inherent to colony fission.</p>
https://doi.org/10.5281/zenodo.844253
oai:zenodo.org:844253
Zenodo
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.844252
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Myrmecological News, 20, 77-85, (2017-08-17)
Reproduction, polygyny, seasonality, fission, budding, yellow bodies.
Reconstructing life history in ants: Ergatoid queens, facultative monogyny and dependent colony foundation in Monomorium algiricum (Hymenoptera: Formicidae)
info:eu-repo/semantics/article
oai:zenodo.org:7772147
2023-03-27T07:28:33Z
openaire_data
user-iees-paris
Zaninotto
Fauviau
Dajoz
2023-03-26
<p>Dataset for 'Diversity of greenspace design and management impacts pollinator communities in a densely urbanized landscape: the city of Paris, France' (2023, Urban Ecosystems)</p>
https://doi.org/10.5281/zenodo.7772147
oai:zenodo.org:7772147
Zenodo
https://doi.org/10.1007/s11252-023-01351-x
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.7772146
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Urban Ecosystems, (2023-03-26)
Diversity of greenspace design and management impacts pollinator communities in a densely urbanized landscape: the city of Paris, France
info:eu-repo/semantics/other
oai:zenodo.org:1464291
2020-01-20T13:03:29Z
user-iees-paris
Christian Peeters
Mathieu Molet
Chung-Chi Ling
Johan Billen
2019-06-11
<p>The great evolutionary success of insects is partly linked to the innovation of the cuticle, which underlies a complex exoskeleton with varied functions. Cuticle development is costly because chitin and cuticular proteins require ingested nitrogen. Studying cuticle thickness on a comparative basis allows insight into the trade-off between offspring quality and quantity. This trade-off takes a particular meaning in ant workers because they are wingless, non-dispersers and generally sterile. We selected a comprehensive sample of 42 ant species (40 genera belonging to nine subfamilies) and measured cuticle thickness in workers using labour-intensive histological sectioning of the prothorax. Thickness varied substantially across genera, ranging from 1.3 to 109.8 μm. We correlated thickness with body size, measured as head width. Our results show a strong influence of body size, but also phylogeny, because workers in ‘formicoid’ species tend to have a thinner cuticle (two exceptions). The effect of body size is also obvious in species having size-polymorphic workers. We discuss the idea that a thinner cuticle is associated with miniaturization of workers, and its ecological consequences are buffered in a social environment. We reveal that the bulk of ant species have a very thin cuticle, and this represents cost savings that may partly underlie the massive increase in colony size during adaptive radiation.</p>
https://doi.org/10.5281/zenodo.1464291
oai:zenodo.org:1464291
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1464290
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Biological Journal of the Linnean Society, 121, 556-563, (2019-06-11)
allocation tradeoffs – body size – chitin – colony size – cuticle – nitrogen limitation
Evolution of cheaper workers in ants: a comparative study of exoskeleton thickness
info:eu-repo/semantics/article
oai:zenodo.org:3626903
2020-01-28T22:32:28Z
user-cereep-ecotron
user-iees-paris
Badiane, Arnaud
Martin, Mélissa
Meylan, Sandrine
Richard, Murielle
Decencière Ferrandière, Beatriz
Le Galliard, Jean-François
2020-01-25
<p>Pre-copulatory female mate choice based on male ultraviolet (UV) coloration has been demonstrated in several species of birds, fishes and lizards, but post-copulatory mechanisms have been largely overlooked. Here, we investigated female mate preference based on male UV coloration in the common lizard <em>Zootoca vivipara</em>, in which males display conspicuous UV coloration on their throat. During two successive years, we staged sequential mating trials between females and four different males with UV-reduced or control belly and throat coloration. We recorded pre-copulatory female behavior, copulation behavior and assigned paternity to all offspring. Females were more aggressive towards UV-reduced males and, in one year, UV-reduced males had a lower probability of siring at least one egg (i.e. fertilization success) during the last mating trials. However, in one year, copulation was shorter with control males. Altogether, our results suggest that females exert subtle pre-copulatory mate preference based on male UV ornaments and, conditional on the study year and female mating history, some degree of post-copulatory preference for UV-control males leading to differential male fertilization success. This study suggests that UV-based female mate choice may be more widespread than previously thought in the animal kingdom, and emphasize the importance to use a study design well adapted to the species reproductive behavior.</p>
https://doi.org/10.5281/zenodo.3626903
oai:zenodo.org:3626903
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3626902
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Color signals – Female choice – Fertilization – Paternity – Post-copulatory selection – Sexual selection – Ultraviolet – Zootoca vivipara
Male ultraviolet reflectance and female mating history influence female mate choice and male mating success in a polyandrous lizard
info:eu-repo/semantics/preprint
oai:zenodo.org:1318463
2020-01-20T16:26:53Z
user-iees-paris
user-biosyslit
Peeters, Christian
Liebig, Juergen
2009-06-01
<p>DIVISION OF LABOR is the essence of sociality in insects and its most striking manifestation is the sterility of almost all colony members. Unequal reproduction among relatives is associated with many conflicts, and recent studies have reconciled these with kin selection (Bourke and Franks 1995). In this chapter, we examine the essential role of communication in the resolution of conflicts over reproduction. Information exchange is indeed entangled with both cooperation and conflicts. Social Hymenoptera exhibit a broad variety of colony patterns, ranging from small societies with nestmates having equivalent reproductive potentials (eg, queenless ants, Polistes wasps) to huge societies with morphologically highly specialized queens and workers. Although similar conflicts transcend this heterogeneity, the mechanisms that regulate monogyny or queen supersedure, for example, are not the same at either ends of this spectrum. We argue that seemingly dissimilar regulatory mechanisms rely all on just one type of olfactory information.</p>
https://doi.org/10.5281/zenodo.1318463
oai:zenodo.org:1318463
Harvard University Press
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1318462
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
pheromone
fecundity
queen and worker castes
Fertility signaling as a general mechanism of regulating reproductive division of labor in ants
info:eu-repo/semantics/bookPart
oai:zenodo.org:4555064
2023-03-02T13:16:28Z
user-iees-paris
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2021-02-16
<blockquote>
<p><strong>/!\ This is an old version of the official template /!\</strong></p>
<p><strong>For the current version, please go here: </strong><a href="https://doi.org/10.5281/zenodo.4543852">https://doi.org/10.5281/zenodo.4543852</a></p>
</blockquote>
https://doi.org/10.5281/zenodo.4555064
oai:zenodo.org:4555064
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
#GlobalSoilMacroFauna | Official template to report Data of Soil Macro Fauna abundance from TSBF Method
info:eu-repo/semantics/other
oai:zenodo.org:4543853
2023-03-02T13:16:28Z
user-iees-paris
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2021-02-16
<blockquote>
<p><strong>/!\ This is an old version of the official template /!\</strong></p>
<p><strong>For the current version, please go here: </strong><a href="https://doi.org/10.5281/zenodo.4543852">https://doi.org/10.5281/zenodo.4543852</a></p>
</blockquote>
<p> </p>
<p><strong>Our goals are:</strong></p>
<ol>
<li>To make a large-scale synthesis of the effects of human activity on soil macrofauna and to explore the links to ecosystem services delivery, especially primary productivity.</li>
<li>To produce maps of abundance and diversity of soil macrofauna on a global scale.</li>
<li>To produce information that will reach decision-makers and practitioners, especially farmers and land managers.</li>
</ol>
<p>We are looking for data on the abundance and biomass of 17 soil (+litter) fauna groups. The list of the taxa is given in the template.</p>
<p><strong>Ideally</strong></p>
<ul>
<li>The specimens should have been sampled in a TSBFish method, ie a monolith (25x25cmx30cm) extracted from the soil.</li>
<li>The groups should have been sampled together, but we can also integrate data focused on specific groups.</li>
<li>These data should come with data regarding habitat such as soil properties, land management, agricultural practices, primary productivity. But nothing is mandatory except
<ul>
<li>land-use type</li>
<li>sampling date</li>
<li>Geographic coordinates (in decimal degrees)</li>
</ul>
</li>
</ul>
<p><strong>Taxonomical Resolution</strong></p>
<p>The taxonomic resolution required for the database is low (typically at class or family level.</p>
<p>But please note that for a more specific part of the project, we are also looking for data at a finer resolution data, especially morphospecies or even species data, in order to compare the trends between low and high taxonomical resolution.</p>
<p><strong>Data Resolution</strong></p>
<p>When possible, we prefer data a the soil monolith level, (1 line = 1 soil monolith), or finer, when soil layers are available, but we can also work with data aggregated at the higher level (transect or plot).</p>
<p><strong>Co-authorship policy</strong></p>
<p>We intend to be inclusive in terms of co-authorship. It is difficult to give the amount of data required to become a potential co-author, but we can roughly say that the threshold can be about data from three different localities, spaced by more than 100km. But this is just an indication. Please note that co-authors are expected to contribute actively to paper writing. The credits of all data will be reported.</p>
<p><strong>Data Management Plan</strong></p>
<p>We intend to update regularly the database with new contributions.</p>
<p>We plan to publish the data on open access (with appropriate credits), but this is not mandatory for all datasets (we can remove specific datasets from the open database).</p>
<p> </p>
<p>Thank you in advance for your help. This is definitely a collaborative exercise. All contributions welcomed!</p>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.4543853
oai:zenodo.org:4543853
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
#GlobalSoilMacroFauna | Official template to report Data of Soil Macro Fauna abundance from TSBF Method
info:eu-repo/semantics/other
oai:zenodo.org:7691884
2023-03-02T13:16:29Z
user-iees-paris
Nico Eisenhauer
Ana C Antunes
Sebastien Barot
Marie L.C. Bartz
Ana E. Bonato Asato
Irene Calderon-Sanou
Thibaud Decaëns
Steven Fonte
Pierre Ganault
Benoit Gauzens
Konstantin Gongalsky
Carlos A. Guerra
Tomislav Hengl
Raphaël Marichal
Clara P.Peña Venegas
Daniel Castro
Anton Potapov
Elisa Thébault
Wilfried Thuiller
Martin Witjes
Chi Zhang
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2023-03-02
<p><strong>This is the updated official template to report soil macrofauna data produced with the TSBF sampling protocol for the #GlobalSOilMacrofauna initiative.</strong></p>
<p> </p>
<p><strong>Our goals are:</strong></p>
<ol>
<li>To make a large-scale synthesis of the effects of human activity on soil macrofauna and to explore the links to ecosystem services delivery, especially primary productivity.</li>
<li>To produce maps of abundance and diversity of soil macrofauna on a global scale.</li>
<li>To produce information that will reach decision-makers and practitioners, especially farmers and land managers.</li>
</ol>
<p>We are looking for data on the abundance and biomass of macrofauna groups. The list of the taxa is given in the template.</p>
<p><strong>Ideally</strong></p>
<ul>
<li>The specimens should have been sampled in a TSBFish method, ie a monolith (25x25cmx30cm) extracted from the soil. Soil cores are also possible.</li>
<li>The groups should have been sampled together, but we can also integrate data focused on a single group or on a subset of the groups.</li>
<li>Data should come with metadata regarding habitat such as soil properties, land management, agricultural practices, primary productivity. But nothing is mandatory except:
<ul>
<li>Land-use type</li>
<li>Sampling date (YYYY-MM-DD)</li>
<li>Geographic coordinates in decimal degrees</li>
</ul>
</li>
</ul>
<p><strong>Taxonomical Resolution</strong></p>
<p>The taxonomic resolution required for the database is low (typically at class or family level).</p>
<p>But please note that for a more specific part of the project, we are also looking for data at a finer resolution data, especially morphospecies or even species data, in order to compare the trends between low and high taxonomical resolution. Report the best you have!</p>
<p><strong>Sampling Resolution</strong></p>
<p>We prefer data a the soil monolith level, (1 line = 1 soil monolith), or finer, when soil layers are available, but we can also work with data aggregated at the higher level (transect or plot), but in this case, we need the number of samples per transect.</p>
<p><strong>Spatial and temporal Resolution</strong></p>
<p>We target a high spatial resolution, which implies that we need spatial coordinates of the samples with high accuracy, ideally around 15m. If the spatial accuracy of your data is is coarser, please advise us. Same for the sampling date: we ideally need the year, month and day of the collection of each sample.</p>
<p><strong>Co-authorship policy</strong></p>
<p>We intend to be inclusive in terms of co-authorship. Please refer to this paper for details: <a href="http://soil-organisms.org/index.php/SO/article/view/282">http://soil-organisms.org/index.php/SO/article/view/282</a></p>
<p> </p>
<p><strong>Data Management Plan</strong></p>
<p>We plan to publish the data on open access (with appropriate credits), but this is not mandatory for all datasets (we can remove specific datasets from the open database).</p>
<p> </p>
<p>Thank you in advance for your help. This is definitely a collaborative exercise. All contributions welcomed!</p>
https://doi.org/10.5281/zenodo.7691884
oai:zenodo.org:7691884
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
sOilFauna
FaunaServices
#GlobalSoilMacroFauna | Official template to report Data to the MACROFAUNA database
info:eu-repo/semantics/other
oai:zenodo.org:7711397
2024-02-29T15:02:54Z
user-cereep-ecotron
openaire_data
user-iees-paris
Bodineau Théo
Chabaud Chloé
Decencière Beatriz
Agostini Simon
Lourdais Olivier
Meylan Sandrine
Le Galliard Jean-François
2023-03-09
<p>The content of this archive includes raw data and metadata for the paper "Microhabitat humidity rather than food availability drives thermo-hydroregulation responses to drought in a terrestrial lizard" by Bodineau et al. In this experimental study, we investigated how microclimate conditions and food availability influence thermo-hydroregulation strategies and body condition of lizards (Zootoca vivipara) during a simulated drought. We found that water restriction and food deprivation caused physiological alterations such as muscle catabolism and mobilization of caudal energy reserves. Lizards developed behavioural strategy to counteract water and food deprivation like decreased thermoregulation effort, higher shelter use and increased eye closure behaviours. Hydric quality of the shelter rather than food availability was the main modulator of trade-offs between thermoregulatory and hydroregulatory activities and an important buffer against the deleterious effects of water restriction. These original findings challenge the assumptions of mechanistic models of ectotherms, which are currently calibrated on the thermal biology of ectotherms. They demonstrate the urgent need to take into account the dual effect of warming and drought events, behavioural interactions between thermoregulation and hydroregulation and the buffering role of microclimatic conditions.</p>
This work was suppported by an Agence Nationale de la Recherche grant (ANR-17-CE020013, 'AQUATHERM') to J.-F. Le Galliard. Théo Bodineau' PhD grant is funded by the Ministère de l'Enseignement Supérieur et de la Recherche. This work has benefited from human and technical resources provided by the CEREEP-Ecotron IleDeFrance (CNRS/ENS UAR 3194).
https://doi.org/10.5281/zenodo.7711397
oai:zenodo.org:7711397
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.7711396
info:eu-repo/semantics/openAccess
behaviour
food
microhabitat
shelter
thermo-hydroregulation
trade-off
water
Microhabitat humidity rather than food availability drives thermo-hydroregulation responses to drought in a terrestrial lizard
info:eu-repo/semantics/other
oai:zenodo.org:6006618
2023-06-23T09:26:27Z
openaire_data
user-iees-paris
Prosnier, Loïc
Loeuille, Nicolas
Hulot, Florence D
Renault, David
Piscart, Christophe
Bicocchi, Baptiste
Deparis, Muriel
Lam, Matthieu
Médoc, Vincent
2022-02-08
<p>Data about experimentations of DIV-1 (virus) infection on Daphnia magna.</p>
<p>Linked article: Parasites make hosts more profitable but less available to predators</p>
This work was supported by the French national program EC2CO-Biohefect/Ecodyn//Dril/MicrobiEen (Influence du parasitisme sur la distribution des flux d'énergie dans les réseaux trophiques).
https://doi.org/10.5281/zenodo.6006618
oai:zenodo.org:6006618
eng
Zenodo
https://doi.org/10.1101/2022.02.08.479552
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6006617
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Daphnia magna
white fat cell disease
optimal foraging theory
parasite-induced phenotypic alterations
European minnow
Notonecta sp.
Datasets and R source code of manuscript "Parasites make hosts more profitable but less available to predators"
info:eu-repo/semantics/other
oai:zenodo.org:10657738
2024-03-19T12:28:52Z
user-iees-paris
Jijón, Sofía
Czuppon, Peter
Blanquart, François
Débarre, Florence
2024-02-14
<h2>Abstract</h2>
<p>While the first infection by an emerging disease is often unknown, information on early cases can be used to date it, which is of great interest to trace the disease's origin and understand early infection dynamics. Here, we extend the method presented in (Czuppon et al., 2021) to estimate the time series from emergence (i.e., infection of the first human case by the focal disease or variant) to the detection of N cases. We run numerical simulations of infectious disease spreading from a single infectious individual and calibrate the model to reproduce the observed cases in two main epidemiological contexts (the emergence of the Alpha SARS-CoV-2 variant in the UK and the early cases of COVID-19 in Wuhan), but the code was built in a generic form to facilitate applications to other datasets. The main outcome of our model is the expected time to N detected cases.</p>
<p><a href="https://doi.org/10.1371/journal.pcbi.1011934">Publication</a> | <a href="https://github.com/sjijon/estimate-emergence-from-data.git">Github</a> | <a href="https://doi.org/10.5281/zenodo.10657737" target="_blank" rel="noopener">Zenodo</a></p>
<h2>Contents</h2>
<p>- <code>Data/</code> contains the files containing the time series of the early cases we use to calibrate the model for different epidemiological contexts, as well as the emergence or tMRCA estimates from previously published studies.</p>
<p>- <code>Routines/</code> contains the functions used repeatedly in each application.</p>
<p>- <code>SetParameters_EpiContext/</code> contains the parameterizations for each application of the model</p>
<p>- <code>Fig1_FirstCaseDiagrama</code> generates a diagram illustrating the notions of extinct trees, first infection of the ongoing tee and the MRCA in an epidemic outbreak.</p>
<p>- <code>Fig2-3_Emergence/</code> contains the codes to reproduce the results (<code>.jl</code>) and figures (<code>.R</code>) presented in the main text. The subfolder <code>ABC_Simulations/</code> contains the files containing the time series of the early cases to estimate the first infection in the COVID-19 example. </p>
<p>- <code>Fig4_Sensitivity Analyses/</code> contains a variation of the previous scripts to run the simulation over varying values of the main parameters.</p>
<p>- <code>Fig5_ModelDiagram/</code> plots a simplified diagram of the model (Ti<em>k</em>Z, <code>.tex</code>).</p>
<p>- <code>Figs_Appendix/</code> contain scripts to reproduce the figures presented in the article's appendix</p>
<p>See the `Readme.md` files contained in each folder for more details.</p>
<h2>Implementation details</h2>
<p>Simulations are built in <code>Julia</code> version 1.8.0. Simulations for the Approximate Bayesian Computation are built in <code>C++</code> version 17. </p>
<p>Figures are built in <code>R</code> version 4.1.2, using the <code>ggplot2</code> package version 3.3.</p>
https://doi.org/10.5281/zenodo.10657738
oai:zenodo.org:10657738
eng
Zenodo
https://github.com/sjijon/estimate-emergence-from-data/tree/v2
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10657737
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
covid-19
epidemic-model
stochastic-model
emergence
Codes and data from: Using early detection data to estimate the date of emergence of an epidemic outbreak
info:eu-repo/semantics/other
oai:zenodo.org:3900150
2020-08-10T12:41:32Z
openaire_data
user-iees-paris
Tully, Thomas
Le Galliard, Jean-François
Baron, Jean-Pierre
Tully, Thomas
Le Galliard, Jean-François
Baron, Jean-Pierre
2020-07-18
<p>This dataset gather the data used in the mansucript entitled Micro-geographic shift between negligible and actuarial senescence in a wild snake.</p>
<p>Each sheet of data refers to a specific figure from the article.</p>
https://doi.org/10.5281/zenodo.3900150
oai:zenodo.org:3900150
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3900149
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Journal of animal ecology, (2020-07-18)
senescence
ageing
snake
pace and shape
survival
Dataset on the reproductive and actuarial ageing in a population of meadow vipers (Vipera ursinii) in the Mont Serein (France)
info:eu-repo/semantics/other
oai:zenodo.org:3666172
2021-06-24T15:52:34Z
user-cereep-ecotron
openaire_data
user-iees-paris
Le Galliard, Jean-François
Chabaud, Chloé
de Andrade, Denis Otávio Vieira
Brischoux, François
Carretero, Miguel Angel
Dupoué, Andréaz
Gavira, Rodrigo
Lourdais, Olivier
Sannolo, Marco
van Dooren, Tom J. M.
2020-02-13
<p><strong>Motivation: </strong>The understanding of physiological adaptations, of evolutionary radiations and of ecological responses to global change urges for global, comprehensive databases of the functional traits of extant organisms. The ability to maintain an adequate water balance is a critical functional property influencing the resilience of animal species to climate variation. In terrestrial or semi-terrestrial organisms, total water loss includes a significant contribution of evaporative water loss (EWL). The analysis of geographic and phylogenetic variation in EWL rates must however account for differences in methods and potential confounding factors which influence standard measures of whole-organism water loss. We compiled the global and standardized SquamEWL database of total, respiratory and cutaneous EWL for 325 species and sub-species of squamate reptiles (793 samples and 2536 estimates) from across the globe. An extensive set of companion data and annotations associated to the EWL measurements of potential value for future investigation, including metabolic rate data, is provided. We present preliminary descriptive statistics for the compiled data, discuss gaps and biases, and identify promising avenues to update, expand and explore this database.</p>
<p><strong>Main types of variables contained: </strong>standard water loss rates, geographic data, metabolic rates.</p>
<p><strong>Spatial location:</strong> global.</p>
<p><strong>Time period: </strong>data were obtained from extant species and were collected between 1945 and 2020.</p>
<p><strong>Major taxa: </strong>Reptilia, Squamata including lizards, snakes and amphisbaenians.</p>
<p><strong>Level of measurements: </strong>individual samples of animals from the same species, locality, age class and sex category.</p>
<p><strong>Software format: </strong>csv.</p>
<p><strong>Keyword</strong><strong>s: </strong>ectotherms, functional traits, homeostasis, hydroregulation, macrophysiology, evaporative water loss.</p>
Compilation of the database was funded by the Centre National de la Recherche Scientifique (CNRS), the Agence Nationale de la Recherche (Aquatherm: ANR-17-CE02-0013 to JFLG) and a doctoral grant from Ecole normale supérieure to CC.
https://doi.org/10.5281/zenodo.3666172
oai:zenodo.org:3666172
eng
Zenodo
https://lizardecology.org/reptile-water-loss-data-base/
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3666171
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
vertebrate macrophysiology
homeostasis
water loss
hydroregulation
ectotherms
lizards
snakes
SquamEWL: A worldwide and annotated database of evaporative water loss rates in squamate reptiles
info:eu-repo/semantics/other
oai:zenodo.org:3775431
2020-06-08T08:17:03Z
user-cereep-ecotron
openaire_data
user-iees-paris
Rozen-Rechels David
Farigoule Pauline
Agostini Simon
Badiane Arnaud
Meylan Sandrine
Le Galliard Jean-François
2020-04-29
<p>Datasets for "Short-term change in water availability influences thermoregulation behaviors in a dry-skinned ectotherm" by Rozen-Rechels et al. (2020) in Journal of Animal Ecology</p>
<p> </p>
<p><strong>Abstract</strong></p>
<p>1. Mechanistic models of terrestrial ectotherms predict that climate warming will induce activity restriction due to heat stress and loss of shade, leading to the extinction of numerous populations. Such models rely on the assumption that activity patterns are dictated by simple temperature thresholds independent of changes in water availability. However, changes in water availability may further influence thermoregulation behavior of ectotherms through dehydration risk perception, changes in water balance or changes in microclimatic conditions.</p>
<p>2. Here, we experimentally assess the interactive effects of thermal conditions and water availability on activity patterns, shade selection and thermoregulation efficiency in a model ectothermic species. 3. Thermoregulation behavior of adult common lizards (<em>Zootoca vivipara</em>) was monitored in outdoor mesocosms as we manipulated water availability, providing water as mist in the morning and free-standing water during the daytime. We recorded operative temperatures and micro-meteorological conditions to infer thermal constraints and dehydration risk.</p>
<p>4. Activity and shade selection were better predicted by continuous changes in thermal conditions and dehydration risk, respectively, than by threshold functions. In addition, water supplementation increased activity in males and reduced shade selection in both sexes, most probably as a behavioral response to the perception of a stronger dehydration risk. Water supplementation also influenced the thermal quality of the environment, which in turn altered daily activity patterns and thermoregulation statistics.</p>
<p>5. This demonstrates that dual effects of heat and water stress on activity patterns may lead to stronger activity restriction as a result of climate change than currently predicted.</p>
Fundings by Agence Nationale de la Recherche ANR-17-CE02-0013 to JFLG
https://doi.org/10.5281/zenodo.3775431
oai:zenodo.org:3775431
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3775430
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Journal of Animal Ecology, (2020-04-29)
Body temperature
water availability
activity
shade selection
dehydration
non-avian reptiles
Short-term change in water availability influences thermoregulation behaviors in a dry-skinned ectotherm
info:eu-repo/semantics/other
oai:zenodo.org:4300427
2022-06-10T05:48:14Z
openaire_data
user-iees-paris
Doré, Maël
Thébault, Elisa
Fontaine, Colin
2020-12-01
<p>This database assembles different published datasets of observed interaction networks between plants and pollinators, which were extracted from articles, theses and existing online databases.</p>
<p>Each row in the data table corresponds to an interaction between a plant and a pollinator species reported at a given site by a given publication.</p>
https://doi.org/10.5281/zenodo.4300427
oai:zenodo.org:4300427
Zenodo
https://github.com/MaelDore/Pollination_networks/tree/v.1.0.0
https://doi.org/10.5281/zenodo.4290503
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4300426
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
mutualistic network
plant-pollinator interaction
flower visitors
diversity
A database of plant-pollinator networks
info:eu-repo/semantics/other
oai:zenodo.org:3406985
2019-09-27T18:26:43Z
user-iees-paris
Economo, Evan
Keller, Roberto
Fischer, Georg
Khalife, Adam
Peeters, Christian
2019-09-13
<p>The external trochanter muscles (orange) of mid- and hindlegs originate on fused meso- and metafurcae (blue) in <em>Cataglyphis savignyi</em> queens. Depressor muscles of the petiole (light blue) originate on base of T3 furca.<br>
</p>
<p><strong>Micro-CT </strong>scans were performed at the Okinawa Institute of Science and Technology Graduate University, Japan<strong>.</strong></p>
<p><strong>Segmentation </strong>of the reconstructed image stacks was performed with ITK-SNAP 3.6.0. Structures were segmented manually.</p>
https://doi.org/10.5281/zenodo.3406985
oai:zenodo.org:3406985
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3406984
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
microCT, muscles, segmentation
Thoracic endoskeleton and posterior leg muscles in queen of ant Cataglyphis savignyi
info:eu-repo/semantics/other
oai:zenodo.org:10616154
2024-02-05T07:54:28Z
openaire_data
user-iees-paris
Bodineau, Théo
de Villemereuil, Pierre
Agostini, Simon
Decencière, Beatriz
Le Galliard, Jean-François
Meylan, Sandrine
2024-02-04
<p><span>Phenological advances are a widespread response to global warming and can contribute to determine the climate vulnerability of organisms, particularly in ectothermic species which are highly dependent on ambient temperatures to complete their life cycle. Yet, the relative contribution of breeding dates and temperature conditions during gestation on fitness of females and their offspring is poorly documented in reptiles. Here, we exposed females of the common lizard <em>Zootoca vivipara </em>to contrasting thermal scenarios (cold versus hot treatment) during gestation and quantified effects of parturition dates and thermal treatment on life-history traits of females and their offspring for one year. Overall, our results suggest that parturition date <em>per se</em> has a greater impact than parental quality or thermal conditions during gestation on the life history traits of the species. We found directional selection in favour of an earlier parturition date via positive effects on juvenile survival, growth and recruitment. Yet, an earlier parturition date compromised the energetic condition of gravid females, which suggests the existence of a mother-offspring conflict regarding the optimisation of parturition dates. Our results call for a better consideration of the effect of breeding phenology in assessing the short-term and long-term effects of global warming on the life-history traits and populations of reptiles.</span></p>
https://doi.org/10.5281/zenodo.10616154
oai:zenodo.org:10616154
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10616153
info:eu-repo/semantics/restrictedAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Data from: Breeding phenology drives variation in reproductive output, reproductive costs and offspring fitness in a viviparous ectotherm
info:eu-repo/semantics/other
oai:zenodo.org:2414184
2020-01-25T07:23:12Z
software
user-iees-paris
Schmidt, Hannes
Nunan, Naoise
Höck, Alexander
Eickhorst, Thilo
Kaiser, Christina
Woebken, Dagmar
Xavier Raynaud
2018-12-19
<p>Fiji and R codes to extract microbial cell distribution as described in Schmidt, H., Nunan, N., Höck, A., Eickhorst, T., Kaiser, C., Woebken, D., Raynaud, X., 2018. Recognizing patterns: spatial analysis of observed microbial colonization on root surfaces. Frontiers in Environmental Science 6. <a href="https://doi.org/10.3389/fenvs.2018.00061">https://doi.org/10.3389/fenvs.2018.00061</a></p>
https://doi.org/10.5281/zenodo.2414184
oai:zenodo.org:2414184
Zenodo
https://github.com/xraynaud/microbial-cell-detection/tree/1.0
https://doi.org/10.3389/fenvs.2018.00061
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.2414183
info:eu-repo/semantics/openAccess
Other (Open)
imaging
image analysis
xraynaud/microbial-cell-detection: release 1.0
info:eu-repo/semantics/other
oai:zenodo.org:10659361
2024-02-14T20:16:00Z
user-iees-paris
Jijon, Sofia
2024-02-14
<p>Deprecated data</p>
https://doi.org/10.5281/zenodo.10659361
oai:zenodo.org:10659361
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10623613
info:eu-repo/semantics/restrictedAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Empty data
info:eu-repo/semantics/other
oai:zenodo.org:1318495
2019-06-10T14:53:53Z
user-iees-paris
user-biosyslit
Economo, Evan
Peeters, Christian
Hita Garcia, Francisco
Keller, Roberto
Billen, Johan
Khalife, Adam
2018-07-21
<p>Ants of the genus<em> Melissotarsus </em>(subfamily Myrmicinae) inhabit tunnel systems excavated in the wood of living trees, where they keep large numbers of symbiotic armoured scale insects (Diaspididae). Tunnelling through healthy wood requires tremendous power. We investigated morphology of the musculoskeletal system of <em>Melissotarsus</em> using X-ray microcomputed tomography and 3D modelling (Khalife et al. 2018).</p>
<p>Segmented structures inside one half of the head of a <em>Melissotarsus </em>worker: mandible (pale green; tip cut off); closer muscles of mandible (orange); closer apodeme (red); opener muscles of mandible (light blue); opener apodeme (dark blue); brain and suboesophageal ganglion (brown); tentorium and ventromedial phragma (green).</p>
<p><strong>Micro-CT </strong>scans were performed at the Okinawa Institute of Science and Technology Graduate University, Japan<strong>.</strong></p>
<p><strong>Segmentation </strong>of the reconstructed image stacks was performed with ITK-SNAP 3.6.0<strong> </strong></p>
<p>Khalife A, Keller R, Billen J, Hita Garcia F, Economo E & Peeters C (2018) Skeletomuscular adaptations of head and legs of <em>Melissotarsus</em> ants for tunnelling through living wood. <strong>Frontiers in Zoology</strong> 15: 30. https://doi.org/10.1186/s12983-018-0277-6</p>
https://doi.org/10.5281/zenodo.1318495
oai:zenodo.org:1318495
Zenodo
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1318494
info:eu-repo/semantics/openAccess
Creative Commons Attribution Share Alike 4.0 International
https://creativecommons.org/licenses/by-sa/4.0/legalcode
queen and worker castes
mandibles
miniaturisation
Video of surface rendering of internal head structures in Melissotarsus worker ants, specialised for chewing healthy wood.
info:eu-repo/semantics/other
oai:zenodo.org:10623614
2024-02-14T10:22:25Z
user-iees-paris
Jijón, Sofía
Czuppon, Peter
Blanquart, François
Florence, Débarre
2023-11-13
<h2>Abstract</h2>
<p>While the first infection by an emerging disease is often unknown, information on early cases can be used to date it, which is of great interest to trace the disease's origin and understand early infection dynamics. Here, we extend the method presented in (Czuppon et al., 2021) to estimate the time series from emergence (i.e., infection of the first human case by the focal disease or variant) to the detection of N cases. We run numerical simulations of infectious disease spreading from a single infectious individual and calibrate the model to reproduce the observed cases in two main epidemiological contexts (the emergence of the Alpha SARS-CoV-2 variant in the UK and the early cases of COVID-19 in Wuhan), but the code was built in a generic form to facilitate applications to other datasets. The main outcome of our model is the expected time to N detected cases.</p>
<p><a href="https://doi.org/10.1101/2023.01.09.23284284">Preprint</a> | <a href="https://github.com/sjijon/estimate-emergence-from-data.git">Github</a></p>
<h2>Contents</h2>
<p>- <code>Data/</code> contains the files containing the time series of the early cases we use to calibrate the model for different epidemiological contexts, as well as the emergence or tMRCA estimates from previously published studies.</p>
<p>- <code>Routines/</code> contains the functions used repeatedly in each application.</p>
<p>- <code>SetParameters_EpiContext/</code> contains the parameterizations for each application of the model</p>
<p>- <code>Fig1_FirstCaseDiagrama</code> generates a diagram illustrating the notions of extinct trees, first infection of the ongoing tee and the MRCA in an epidemic outbreak.</p>
<p>- <code>Fig2-3_Emergence/</code> contains the codes to reproduce the results (<code>.jl</code>) and figures (<code>.R</code>) presented in the main text. The subfolder <code>ABC_Simulations/</code> contains the files containing the time series of the early cases to estimate the first infection in the COVID-19 example. </p>
<p>- <code>Fig4_Sensitivity Analyses/</code> contains a variation of the previous scripts to run the simulation over varying values of the main parameters.</p>
<p>- <code>Fig5_ModelDiagram/</code> plots a simplified diagram of the model (Ti<em>k</em>Z, <code>.tex</code>).</p>
<p>- <code>Figs_Appendix/</code> contain scripts to reproduce the figures presented in the article's appendix</p>
<p>See the `Readme.md` files contained in each folder for more details.</p>
<h2>Implementation details</h2>
<p>Simulations are built in <code>Julia</code> version 1.8.0. Simulations for the Approximate Bayesian Computation are built in <code>C++</code> version 17. </p>
<p>Figures are built in <code>R</code> version 4.1.2, using the <code>ggplot2</code> package version 3.3.</p>
https://doi.org/10.5281/zenodo.10623614
oai:zenodo.org:10623614
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10623613
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
covid-19
epidemic-model
emergence
stochastic
Code - Using early detection data to estimate the date of emergence of an epidemic outbreak
info:eu-repo/semantics/other
oai:zenodo.org:3833619
2020-06-08T08:17:01Z
openaire_data
user-iees-paris
Flacher, Floriane
Raynaud, Xavier
Hansart, Amandine
Geslin, Benoit
Motard, Eric
Verstraet, Séléné
Bataillle, Manon
Dajoz, Isabelle
2020-05-19
<p>Dataset of paper "Belowground competition alters attractiveness of an insect-pollinated plant to pollinators", AOB Plants</p>
https://doi.org/10.5281/zenodo.3833619
oai:zenodo.org:3833619
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3833618
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
AOB Plants, (2020-05-19)
Belowground competition alters attractiveness of an insect-pollinated plant to pollinators
info:eu-repo/semantics/other
oai:zenodo.org:7457227
2022-12-19T14:26:35Z
openaire_data
user-iees-paris
Gineyts, Robin
Niboyet, Audrey
2022-12-19
<p>This file encompasses the data that support the findings of the study entitled "Nitrification, denitrification, and related functional genes under elevated CO<sub>2</sub>: a meta-analysis in terrestrial ecosystems" by Robin Gineyts and Audrey Niboyet in Global Change Biology.</p>
https://doi.org/10.5281/zenodo.7457227
oai:zenodo.org:7457227
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.7457226
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Nitrification, denitrification, and related functional genes under elevated CO2: a meta-analysis in terrestrial ecosystems
info:eu-repo/semantics/other
oai:zenodo.org:10479451
2024-01-10T16:14:06Z
user-iees-paris
Nico Eisenhauer
Ana C Antunes
Sebastien Barot
Marie L.C. Bartz
Ana E. Bonato Asato
Irene Calderon-Sanou
Thibaud Decaëns
Steven Fonte
Pierre Ganault
Benoit Gauzens
Konstantin Gongalsky
Carlos A. Guerra
Tomislav Hengl
Raphaël Marichal
Clara P.Peña Venegas
Daniel Castro
Anton Potapov
Elisa Thébault
Wilfried Thuiller
Martin Witjes
Chi Zhang
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2024-01-10
<p><strong>This is the updated official template to report soil macrofauna data produced with the TSBF sampling protocol for the #GlobalSOilMacrofauna initiative</strong></p>
<p> </p>
<p><strong>Our goals are:</strong></p>
<ol>
<li>To make a large-scale synthesis of the effects of human activity on soil macrofauna and to explore the links to ecosystem services delivery.</li>
<li>To produce maps of abundance and diversity of soil macrofauna on a global scale.</li>
<li>To produce information that will reach decision-makers and practitioners, especially farmers and land managers.</li>
</ol>
<p>We are looking for data on the abundance and biomass of macrofauna groups. The list of the taxa is given in the template.</p>
<p><strong>Ideally</strong></p>
<ul>
<li>The specimens should have been sampled in a TSBFish method, ie a monolith (25x25cmx30cm) extracted from the soil. Soil cores are also possible.</li>
<li>The groups should have been sampled together, but we can also integrate data focused on a single group or on a subset of the groups.</li>
<li>Data should come with metadata regarding habitat such as soil properties, land management, agricultural practices, primary productivity. But nothing is mandatory except:
<ul>
<li>Land-use type</li>
<li>Sampling date (YYYY-MM-DD)</li>
<li>Geographic coordinates in decimal degrees</li>
<li>Sample depth</li>
</ul>
</li>
</ul>
<p><strong>Taxonomical Resolution</strong></p>
<p>The taxonomic resolution required for the database is low (typically at class or family level).</p>
<p>But please note that for a more specific part of the project, we are also looking for data at a finer resolution data, especially morphospecies or even species data, in order to compare the trends between low and high taxonomical resolution. Report the best you have!</p>
<p><strong>Sampling Resolution</strong></p>
<p>Data must be at the monolith level (1 record = 1 soil monolith), or at the scale of soil layers (1 record = 1 soil layer). We can accept data aggregated at the transect or plot level, but in this case, make sur to indicate the number of samples per transect.</p>
<p><strong>Spatial and temporal Resolution</strong></p>
<p>We target a high spatial resolution, which implies that we need spatial coordinates of the samples with high accuracy, ideally around 15m. If the spatial accuracy of your data is is coarser, please advise us. Same for the sampling date: we ideally need the year, month and day of the collection of each sample.</p>
<p><strong>Co-authorship policy</strong></p>
<p>We intend to be inclusive in terms of co-authorship. Please refer to this paper for details: <a href="http://soil-organisms.org/index.php/SO/article/view/282">http://soil-organisms.org/index.php/SO/article/view/282</a></p>
<p><strong>Data Management Plan</strong></p>
<p>We plan to publish the database on open access (with appropriate credits), but specifics datasets can be removed. This should not restrain you to share the data with us.</p>
<p> </p>
<p>Thank you in advance for your help. This is definitely a collaborative exercise. All contributions welcomed!</p>
https://doi.org/10.5281/zenodo.10479451
oai:zenodo.org:10479451
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
sOilFauna
FaunaServices
#GlobalSoilMacroFauna | Official template to report soil macrofauna data
info:eu-repo/semantics/other
oai:zenodo.org:4554991
2023-03-02T13:16:30Z
user-iees-paris
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2021-02-16
<blockquote>
<p><strong>/!\ This is an old version of the official template /!\</strong></p>
<p><strong>For the current version, please go here: </strong><a href="https://doi.org/10.5281/zenodo.4543852">https://doi.org/10.5281/zenodo.4543852</a></p>
</blockquote>
https://doi.org/10.5281/zenodo.4554991
oai:zenodo.org:4554991
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
#GlobalSoilMacroFauna | Official template to report Data of Soil Macro Fauna abundance from TSBF Method
info:eu-repo/semantics/other
oai:zenodo.org:4686757
2021-07-15T13:23:48Z
openaire_data
user-iees-paris
Honorio Romain
2021-04-14
<p>Data from the overwintering study using Temnothorax nylanderi in the field. </p>
https://doi.org/10.5281/zenodo.4686757
oai:zenodo.org:4686757
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4686756
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Worker size diversity has no effect on overwintering success under natural conditions in the ant Temnothorax nylanderi.
info:eu-repo/semantics/other
oai:zenodo.org:845751
2020-01-20T15:17:11Z
user-iees-paris
user-biosyslit
Peeters, Christian
Ito, Fuminori
2015-09-15
<p>Ant colonies are organized similarly to those of wasps and bees: reproductive altruism, age polyethism, and complex communication. Yet ants exhibit more species, much higher total biomass, and their lifestyles and diet are more diverse. Hence, factors additional to sociality must be involved in this evolutionary diversification. We argue that loss of flight permitted extensive changes in body size of ant workers and queens. Wingless helpers revolutionized colonial economy because they are cheaper to manufacture. Flightlessness also removed constraints on the evolution of dwarf workers (head width 1 mm or less); these exist in 229 / 286 ant genera examined but not in social wasps and bees. Miniaturisation involves simplification of tissues and organs (compound eyes, sting apparatus, ovaries, exoskeleton), and dwarf workers are cheaper per capita. Comparison of ovariole numbers in 106 genera indicates reduction of ovaries in dwarf workers, and complete loss in six genera of Ponerinae and eight genera of Myrmicinae. Body size influences trophic ecology, but also the pattern in which a colony's finite energy budget is "packaged", allowing increases in colony size if adaptive. Dwarf workers together with big queens enabled the evolution of claustral independent colony foundation that is predominant in three large subfamilies (Dolichoderinae, Formicinae and Myrmicinae). Winglessness allows this divergence of costs between workers and queens, but also novel activity schedules and adaptations for defence. Highly dimorphic queens and workers promoted the evolution of mosaic phenotypes (soldiers and ergatoid queens), which added to colonial complexity (MOLET & al. 2012 The American Naturalist 180: 328-341). We speculate that cheaper workers caused a shift away from a carnivorous diet to carbohydrates such as honeydew. Wasp and bee workers – infertile just as in ants – need to fly and this constrained extensive divergence from queens, which prevented bigger colonies. The winglessness of ant helpers maximized the benefits of having two morphological castes.</p>
ANTEVO ANR-12-JSV7-0003-01
https://doi.org/10.5281/zenodo.845751
oai:zenodo.org:845751
Zenodo
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.845750
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Myrmecological News, 21, 117-130, (2015-09-15)
Body size, miniaturisation, morphology, colony foundation, flight, caste, queen, wasps, bees, Ponerinae
Wingless and dwarf workers underlie the ecological success of ants (Hymenoptera: Formicidae)
info:eu-repo/semantics/article
oai:zenodo.org:3744880
2021-03-02T00:27:15Z
user-cereep-ecotron
openaire_data
user-iees-paris
Le Galliard, Jean-François
Rozen-Rechels, David
Lecomte, Anjélica
Demay, Clémence
Dupoué, Andréaz
Meylan, Sandrine
2020-04-08
<p>Data sets and metadata of the paper "Short-term changes in air humidity and water availability weakly constrain thermoregulation in a dry-skinned ectotherm" by Le Galliard et al. Using experiments performed under controlled conditions in climatic chambers, we demonstrate that daytime thermal preferences of a ground-dwelling, actively foraging lizard (<em>Zootoca vivipara</em>) are significantly decreased by restriction in free-standing water availability. Air humidity during the day also influences body temperatures, but its effect is weaker than those of free standing water and depends on the time of day and the sex of the lizard. This confirms that the hydric environment leads to subtle but significant changes in thermoregulatory behaviors in lizards and further suggest that environmental humidity conditions are important methodological factors to consider in the analysis of thermal preferences.</p>
This work was suppported by an Agence Nationale de la Recherche grant (ANR-17-CE02-0013, 'AQUATHERM') to J.-F. Le Galliard. David Rozen-Rechels' PhD grant is funded by the Ministère de l'Enseignement Supérieur et de la Recherche. This work has benefited from technical and human resources provided by the CNRS IR ECOTRONS and CEREEP-Ecotron IleDeFrance (CNRS/ENS UMS 3194) as well as financial support from the Regional Council of Ile-de-France under the DIM Program R2DS bearing the references I-05-098/R and 2011-11017735 and from the European Union FEDER program 2007-2013. It has received a support under the program "Investissements d'Avenir" launched by the French government and implemented by ANR with the reference ANR-11-INBS-0001 AnaEE France.
https://doi.org/10.5281/zenodo.3744880
oai:zenodo.org:3744880
eng
Zenodo
https://doi.org/10.1371/journal.pone.0247514
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3744879
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
PLOS ONE, 16(2), e0247514, (2020-04-08)
body temperature
dehydration risk
thermoregulation
behavioral trade-off
lizards
reptiles
Short-term changes in air humidity and water availability weakly constrain thermoregulation in a dry-skinned ectotherm
info:eu-repo/semantics/other
oai:zenodo.org:10813765
2024-03-13T13:58:37Z
openaire_data
user-iees-paris
Zaninotto
Fauviau
Dajoz
2023
<p>Dataset for 'Diversity of greenspace design and management impacts pollinator communities in a densely urbanized landscape: the city of Paris, France' (2023, Urban Ecosystems)</p>
https://doi.org/10.5281/zenodo.10813765
oai:zenodo.org:10813765
Zenodo
https://doi.org/10.1007/s11252-023-01351-x
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.7772146
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Urban Ecosystems, (2023)
Diversity of greenspace design and management impacts pollinator communities in a densely urbanized landscape: the city of Paris, France
info:eu-repo/semantics/other
oai:zenodo.org:4593057
2021-03-15T08:42:26Z
user-cereep-ecotron
openaire_data
user-iees-paris
Rozen-Rechels, David
Dupoué, Andréaz
Meylan, Sandrine
Decencière, Beatriz
Guingand, Sophie
Le Galliard, Jean-François
2021-03-10
<p>Raw data of the article "Water restriction in viviparous lizards causes transgenerational effects on behavioral anxiety and immediate effects on exploration behavior" by Rozen-Rechels D. et al., published in Behavioral Ecology and Socioiology 93, 23 in 2018 (<a href="https://doi.org/10.1007/s00265-018-2443-4">https://doi.org/10.1007/s00265-018-2443-4</a>). These data are freely available in csv format. See the readme file for metadata explanation.</p>
<p>Data were formatted by the first author David Rozen-Rechels and collected according to standards and procedures described in the companion journal article.</p>
Funding: Centre National de la Recherche Scientifique (CNRS) and Agence Nationale de la Recherche grant (ANR-13-JSV7-0011-01)
https://doi.org/10.5281/zenodo.4593057
oai:zenodo.org:4593057
eng
Zenodo
https://doi.org/10.1007/s00265-018-2443-4
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.4593056
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Behavioral Ecology and Sociobiology, 72, 23, (2021-03-10)
maternal affects
exploration
thigmotaxis
stress
reptiles
water availability
Water restriction in viviparous lizards causes transgenerational effects on behavioral anxiety and immediate effects on exploration behavior
info:eu-repo/semantics/other
oai:zenodo.org:3529133
2020-01-20T16:50:01Z
user-iees-paris
Clobert, Jean
Ferrière, Régis
Le Galliard, Jean-François
2003-09-01
<p>L’hétérogénéité spatiale d’une population est engendrée à courte échelle par la portée limitée des interactions sociales et de la mobilité, à laquelle se superpose à plus longue échelle la fragmentation de l’habitat. Des facteurs intrinsèques (stochasticité démographique) et extrinsèques (fluctuations environnementales) génèrent alors de la variabilité spatio-temporelle à ces deux échelles. Cette thèse illustre certaines conséquences proximales et ultimes de cette hétérogénéité sur la dispersion et les interactions sociales. A l’échelle du voisinage social, la stochasticité démographique permet d’ouvrir l’espace nécessaire à l’expansion d’une population altruiste favorisée par la sélection de parentèle. La variation génétique et démographique qui en résulte rend aussi possible l’évolution de certaines stratégies de dispersion : évitement des interactions avec la mère, de la consanguinité, ou de la compétition pour les ressources, et préférence pour les habitats denses. Elle accroît la valeur sélective de la dispersion par la colonisation de nouveaux habitats. Interactions sociales et dispersion se retrouvent alors associées dans un processus éco-évolutif qui résume les tensions entre coopération et compétition locale.</p>
https://doi.org/10.5281/zenodo.3529133
oai:zenodo.org:3529133
fra
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3529132
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
dispersion
compétition
coopération
dynamiques adaptatives
hétérogénéité spatiale
valeur sélective
Interactions sociales et dispersion dans des populations structurées dans l'espace
info:eu-repo/semantics/doctoralThesis
oai:zenodo.org:3644247
2020-04-02T17:28:47Z
openaire_data
user-iees-paris
Gounand, Isabelle
Little, Chelsea J.
Harvey, Eric
Altermatt, Florian
2020-02-05
<p>Dataset used in the publication: " Global quantitative synthesis of ecosystem functioning across climatic zones and ecosystem types". The dataset gathers estimates of ecosystem standing stocks (biomass, organic carbon, detritus), fluxes (GPP, ER, NEP) and process rates (decomposition and carbon uptake rates) for eight broad ecosystem types (forest, grassland, agroecosystem, desert, stream, lake, pelagic and benthic marine ecosystems) in five broad climatic zones (arctic, boreal, arid, temperate, tropical, arid).</p>
https://doi.org/10.5281/zenodo.3644247
oai:zenodo.org:3644247
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3644246
info:eu-repo/semantics/openAccess
Creative Commons Attribution 1.0 Generic
https://creativecommons.org/licenses/by/1.0/legalcode
carbon cycle
climate
ecosystem functioning
multifunctionality
metabolic theory of ecology
global change
meta-ecosystem
primary production
productivity
decomposition
Data set for Global quantitative synthesis of ecosystem functioning across climatic zones and ecosystem types
info:eu-repo/semantics/other
oai:zenodo.org:7685787
2023-06-23T09:26:28Z
openaire_data
user-iees-paris
Prosnier, Loïc
Loeuille, Nicolas
Hulot, Florence D
Renault, David
Piscart, Christophe
Bicocchi, Baptiste
Deparis, Muriel
Lam, Matthieu
Médoc, Vincent
2022-02-08
<p>Data about experimentations of DIV-1 (virus) infection on Daphnia magna.</p>
<p>Linked article: Parasites make hosts more profitable but less available to predators</p>
This work was supported by the French national program EC2CO-Biohefect/Ecodyn//Dril/MicrobiEen (Influence du parasitisme sur la distribution des flux d'énergie dans les réseaux trophiques).
https://doi.org/10.5281/zenodo.7685787
oai:zenodo.org:7685787
eng
Zenodo
https://doi.org/10.1101/2022.02.08.479552
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6006617
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Daphnia magna
white fat cell disease
optimal foraging theory
parasite-induced phenotypic alterations
European minnow
Notonecta sp.
Datasets and R source code of manuscript "Parasites make hosts more profitable but less available to predators"
info:eu-repo/semantics/other
oai:zenodo.org:4430455
2021-01-15T00:27:17Z
user-cereep-ecotron
openaire_data
user-iees-paris
Kawamoto, Anna
Le Galliard, Jean-François
Badiane, Arnaud
2021-01-10
<p>Here are the data associated with the study entitled "The role of social costs as a mechanism enforcing the honesty of ultraviolet-reflecting signals in a lizard<strong>"</strong> authored by Anna Kawamoto, Jean-François Le Galliard, and Arnaud Badiane and published in <em>Biological Journal of the Linnean Society</em>.</p>
<p>Four different data sets are provided and the Notes.xlsx file explains the content of these data sets.</p>
<p>We also added three short videos showing typical lizards' behaviours scored in this study.</p>
<p> </p>
https://doi.org/10.5281/zenodo.4430455
oai:zenodo.org:4430455
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.4430454
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Animal communication
Deception
Male competition
Ultraviolet
Zootoca vivipara
Dataset: The role of social costs as a mechanism enforcing the honesty of ultraviolet-reflecting signals in a lizard
info:eu-repo/semantics/other
oai:zenodo.org:7199844
2023-08-15T02:27:09Z
openaire_data
user-iees-paris
Pruvost, Charlotte
Mathieu, Jérome
Muratet, Audrey
Vallet, Jeanne
Dubs, Florence
Gigon, Agnes
Lerch, Thomas
Blouin, Manuel
2022-10-16
<p>Dataset of the Paper "Successful recycling of construction wastes into multifunctional soil for green infrastructures" by Pruvost et al. 2023.</p>
<p>macrofauna.csv</p>
<p>soil_properties.csv</p>
<p>vegetation.csv</p>
<p>vegetation_biomass.csv</p>
https://doi.org/10.5281/zenodo.7199844
oai:zenodo.org:7199844
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.7199843
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Artificial soil, Technosol, Soil macrofauna, Vegetation, Excavated soil, Ecological restoration, Ecological engineering
Data from : Successful recycling of construction wastes into multifunctional soil for green infrastructures, Pruvost & al 2022
info:eu-repo/semantics/other
oai:zenodo.org:8073920
2024-02-04T10:52:30Z
openaire_data
user-iees-paris
Prosnier, Loïc
Loeuille, Nicolas
Hulot, Florence D
Renault, David
Piscart, Christophe
Bicocchi, Baptiste
Deparis, Muriel
Lam, Matthieu
Médoc, Vincent
2022-02-08
<p>Data about experimentations of DIV-1 (virus) infection on Daphnia magna.</p>
<p>Linked article: Parasites make hosts more profitable but less available to predators</p>
This work was supported by the French national program EC2CO-Biohefect/Ecodyn//Dril/MicrobiEen (Influence du parasitisme sur la distribution des flux d'énergie dans les réseaux trophiques).
https://doi.org/10.5281/zenodo.8073920
oai:zenodo.org:8073920
eng
Zenodo
https://doi.org/10.1101/2022.02.08.479552
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6006617
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Daphnia magna
white fat cell disease
optimal foraging theory
parasite-induced phenotypic alterations
European minnow
Notonecta sp.
Datasets and R source code of manuscript "Parasites make hosts more profitable but less available to predators"
info:eu-repo/semantics/other
oai:zenodo.org:3246981
2020-01-24T19:25:26Z
user-cereep-ecotron
openaire_data
user-iees-paris
Names, Gabrielle
Martin, Mélissa
Badiane, Arnaud
Le Galliard, Jean-François
2019-06-16
<p>This is the dataset of the paper "The relative importance of body size and UV coloration in influencing male-male competition in a Lacertid lizard" published in Behavioral Ecology and Sociobiology by Names et al. (2019). It includes a metadata statement and five data spreadsheets.</p>
<p><strong>Abstract of the paper</strong></p>
<p>Communication via color signals is common in natural systems. Ultraviolet (UV)-blue patches located on the outer-ventral scales of some Lacertid lizards are thought to be involved in male-male competition. However, the mechanisms that maintain their honesty remain unknown. Here, we use the common wall lizard <em>Podarcis muralis</em> to<br>
test whether the lateral UV-blue spots are conventional signals, the honesty of which is guaranteed by receiver-dependent costs, and discuss their potential role as an amplifier of body size. We first described the morphology and reflectance properties of lateral blue spots in common wall lizards and investigated how they influence male-<br>
male competition. Spot size and number, UV chroma, and conspicuousness (calculated using vision models) were significantly greater in adult males relative to adult females and adult males relative to juveniles. Total spot area (and not spot number) of adult males was positively correlated with body size. We conducted staged competition encounters between focal males and smaller or larger rivals with control or manipulated spots. Spots were enlarged in small rivals and reduced in large rivals to disrupt the phenotypic correlation between spot area and body size. Aggressiveness and dominance were positively influenced by body size in control encounters. Spot manipulations resulted in greater submission and less aggressiveness in focal males. These results contradict the predictions associated with conventional signals and amplifiers, but suggest that spots contributed to opponent evaluation during short-distance encounters between competing males.</p>
https://doi.org/10.5281/zenodo.3246981
oai:zenodo.org:3246981
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3246980
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Behavioral Ecology and Sociobiology, (2019-06-16)
Intrasexual competition
Podarcis muralis
UV coloration
Territorial conflict
Dataset The relative importance of body size and UV coloration in influencing male-male competition in a Lacertid lizard
info:eu-repo/semantics/other
oai:zenodo.org:4569489
2021-03-02T00:27:15Z
user-cereep-ecotron
openaire_data
user-iees-paris
Artacho, Paulina
Saravia, Julia
Perret, Samuel
Bartheld, José Luis
Le Galliard, Jean-François
2021-03-01
<p>Populations at the warm range margins of the species distribution may be at the greatest risks of extinction from global warming unless they can tolerate extreme environmental conditions. Yet, some studies suggest that the thermal behavior of some lizard species is evolutionarily rigid. During two successive years, we compared the thermal biology of two populations of <em>Liolaemus pictus</em> living at the northern (warmer) and one population living at the southern (colder) range limits, thus spanning an 800 km latitudinal distance. Populations at the two range margins belong to two deeply divergent evolutionary clades. We quantified field body temperatures (T<sub>b</sub>), laboratory preferred body temperatures (PBT), and used operative temperature data (T<sub>e</sub>) to calculate the effectiveness of thermoregulation (<em>E</em>). During one year in all populations, we further exposed half of the lizards to a cold or a hot acclimation treatment to test for plasticity in the thermal behavior. The environment at the southern range limit was characterized by cooler weather and lower T<sub>e</sub>. Despite that, females had higher T<sub>b</sub> and both males and females had higher PBT in the southernmost population (or clade) than in the northernmost populations. Acclimation to cold conditions led to higher PBT in all populations suggesting that plastic responses to thermal conditions, instead of evolutionary history, may contribute to geographic variation. Lizards regulated moderately well their body temperature (<em>E≈</em>0.7): they avoided warm microhabitats in the northern range but capitalized on warm microhabitats in the southern range. We review literature data to show that <em>Liolaemus</em> species increase their thermoregulation efficiency in thermally challenging environments. Altogether, this indicates that habitats of low thermal quality generally select against thermoconformity in these lizards.</p>
This study was funded by a research project Fondecyt no 11121365 from the Comision Nacional de Investigación Científica y Tecnológica de Chile (CONICYT) to P. Artacho. All protocols were approved by the National Agency of Agriculture and Livestock (SAG, Servicio Agrícola y Ganadero) and the Bioethics Committee of the Austral University of Chile (permit 2833). D.L. Moreno Azócar kindly provided unpublished operative temperature data.
https://doi.org/10.5281/zenodo.4569489
oai:zenodo.org:4569489
eng
Zenodo
https://doi.org/10.1016/j.jtherbio.2016.11.001
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.4024403
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Journal of Thermal Biology, 63, 78-87, (2021-03-01)
Body temperature
Effectiveness of thermoregulation
Lizards
Thermal precision Reptiles
Reptiles
Acclimation
Data supplement to "Geographic variation and acclimation effects on thermoregulation behavior in the widespread lizard Liolaemus pictus"
info:eu-repo/semantics/other
oai:zenodo.org:6421014
2022-06-27T11:44:09Z
openaire_data
user-iees-paris
Jerome Mathieu
Carlos Fragoso
John W. Reynods
Jérôme Mathieu
2022-04-07
<p><strong>EWINA_RICH</strong> gathers data on observed and predicted native and alien species richness of earthworms species across geographical units of North America (Mexico, US and Canada), based on data from 1850 to 2021.</p>
<p>Please refer to [REF pub to update] for the details about the process to produce the predictions and the general interpretation of the results.</p>
<p>Data are given at two spatial resolutions</p>
<blockquote>
<p><strong>Data at resolution of counties or equivalent</strong></p>
<ul>
<li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_counties.geojson">EWINA_counties.geojson: </a>Spatial layer of all counties or alike geographical units, with environmental covariates. Used to map geographical units and to predict RASR.</li>
<li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_2000_counties_obs.csv">EWINA_2000_counties_obs.csv</a>: Observed earthworm species richness and RASR (Relative Alien Species Richness) in the geographical units with earthworm data, since year 2000, together with the environmtal covariates. Used to fit the model. Use the GEOID field to merge with the spatial layer.</li>
<li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_2000_counties_pred.csv">EWINA_2000_counties_pred.csv</a>: Predicted earthworm RASR (Relative Alien Species Richness) and its uncertainty, in all counties or equivalent, based on a model fitted on data after the year 2000. Use the GEOID field to merge with the spatial layer.</li>
</ul>
<p><strong>Data at resolution of TDWG4 geographical units</strong></p>
<p>see <a href="https://www.tdwg.org/">the Biodiversity Information Facility Website</a> for more info about the definition of the geographical units</p>
<ul>
<li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_TDWG4_aboveground.geojson">EWINA_TDWG4_aboveground.geojson</a><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_counties.geojson">: </a>Spatial layers of TDWG4 geographical units, with above ground alien taxa richness from Dawson 2017 <a href="https://doi.org/10.1038/s41559-017-0186">https://doi.org/10.1038/s41559-017-0186</a></li>
<li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_TDWG4_earthworms.csv">EWINA_TDWG4_earthworms.csv:</a> Observed earthworm native and exotic species richness in the TDWG4 units, data cumulated from 1850 to 2021.</li>
</ul>
</blockquote>
<p>All data files are provided with a readme file, with the suffix "_variables", that explains the meaning of the variables</p>
https://doi.org/10.5281/zenodo.6421014
oai:zenodo.org:6421014
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6421013
info:eu-repo/semantics/restrictedAccess
earthworm
oligochaeta
macroecology
biogeography
soil biodiversity
species richness
native species
alien species
biological invasions
EWINA_RICH : a database of EarthWorm native and alien species richness In North America
info:eu-repo/semantics/other
oai:zenodo.org:6728385
2023-12-01T12:26:59Z
openaire_data
user-iees-paris
Jerome Mathieu
Carlos Fragoso
John W. Reynods
Jérôme Mathieu
2022-04-07
<p><strong>EWINA_RICH</strong> gathers data on observed and predicted native and alien species richness of earthworms species across geographical units of North America (Mexico, US and Canada), based on data from 1850 to 2021.</p><p>Please refer to the published paper for the details about the process to produce the predictions and the general interpretation of the results.</p><p>Data are given at two distinct spatial resolutions</p><blockquote><p><strong>- Data at the resolution of counties or equivalent</strong></p><ul><li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_counties.geojson">EWINA_counties.geojson: </a>Spatial layer of all counties or alike geographical units, with environmental covariates. Used to map geographical units and to predict RASR.</li><li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_2000_counties_obs.csv">EWINA_2000_counties_obs.csv</a>: Observed earthworm species richness and RASR (Relative Alien Species Richness) in the geographical units with earthworm data, since year 2000, together with the environmtal covariates.(Coverage based estimates, used in the paper, will be released soon, feel free to reach out if you need them).</li><li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_2000_counties_pred.csv">EWINA_2000_counties_pred.csv</a>: Predicted earthworm RASR (Relative Alien Species Richness) and its uncertainty, in all counties or equivalent, based on a model fitted on data after the year 2000.</li></ul><p><strong>- Data at the resolution of TDWG4 geographical units (≈ states)</strong></p><p>see <a href="https://www.tdwg.org/">the Biodiversity Information Facility Website</a> for more info about the definition of TDWG4 geographical units</p><ul><li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_TDWG4_aboveground.geojson">EWINA_TDWG4_aboveground.geojson</a><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_counties.geojson">: </a>Spatial layer of TDWG4 geographical units, with above ground alien taxa richness from Dawson 2017 <a href="https://doi.org/10.1038/s41559-017-0186">https://doi.org/10.1038/s41559-017-0186</a>.</li><li><a href="https://zenodo.org/api/files/61402820-f567-48fb-b030-2353b156a676/EWINA_TDWG4_earthworms.csv">EWINA_TDWG4_earthworms_YYYY.csv:</a> Observed earthworm native and exotic species richness in the TDWG4 units, data cumulated from 1850 to YYYY.</li><li><a href="https://zenodo.org/api/files/dea6f9e3-c6b3-488a-85ea-a9c6d63799c4/EWINA_TDWG4_fun.csv">EWINA_TDWG4_fun.csv</a>: Observed native and alien earthworm species functionnal role in the TDWG4 units, data cumulated from 1850 to 2021.</li></ul></blockquote><p>All data files are provided with a readme file that explains the meaning of the variables.</p><p>Scripts to use the data are stored on GitHub: <a href="https://github.com/JeromeMathieuEcology/GlobalWorming">https://github.com/JeromeMathieuEcology/GlobalWorming</a></p>
https://doi.org/10.5281/zenodo.6728385
oai:zenodo.org:6728385
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6421013
info:eu-repo/semantics/openAccess
earthworm
oligochaeta
macroecology
biogeography
soil biodiversity
species richness
native species
alien species
biological invasions
EWINA_RICH : a database of EarthWorm native and alien species richness accross North America
info:eu-repo/semantics/other
oai:zenodo.org:4024404
2021-03-01T10:13:50Z
user-cereep-ecotron
openaire_data
user-iees-paris
Artacho, Paulina
Saravia, Julia
Perret, Samuel
Bartheld, José Luis
Le Galliard, Jean-François
2020-09-11
<p>Populations at the warm range margins of the species distribution may be at the greatest risks of extinction from global warming unless they can tolerate extreme environmental conditions. Yet, some studies suggest that the thermal behavior of some lizard species is evolutionarily rigid. During two successive years, we compared the thermal biology of two populations of <em>Liolaemus pictus</em> living at the northern (warmer) and one population living at the southern (colder) range limits, thus spanning an 800 km latitudinal distance. Populations at the two range margins belong to two deeply divergent evolutionary clades. We quantified field body temperatures (T<sub>b</sub>), laboratory preferred body temperatures (PBT), and used operative temperature data (T<sub>e</sub>) to calculate the effectiveness of thermoregulation (<em>E</em>). During one year in all populations, we further exposed half of the lizards to a cold or a hot acclimation treatment to test for plasticity in the thermal behavior. The environment at the southern range limit was characterized by cooler weather and lower T<sub>e</sub>. Despite that, females had higher T<sub>b</sub> and both males and females had higher PBT in the southernmost population (or clade) than in the northernmost populations. Acclimation to cold conditions led to higher PBT in all populations suggesting that plastic responses to thermal conditions, instead of evolutionary history, may contribute to geographic variation. Lizards regulated moderately well their body temperature (<em>E≈</em>0.7): they avoided warm microhabitats in the northern range but capitalized on warm microhabitats in the southern range. We review literature data to show that <em>Liolaemus</em> species increase their thermoregulation efficiency in thermally challenging environments. Altogether, this indicates that habitats of low thermal quality generally select against thermoconformity in these lizards.</p>
This study was funded by a research project Fondecyt no 11121365 from the Comision Nacional de Investigación Científica y Tecnológica de Chile (CONICYT) to P. Artacho. All protocols were approved by the National Agency of Agriculture and Livestock (SAG, Servicio Agrícola y Ganadero) and the Bioethics Committee of the Austral University of Chile (permit 2833). D.L. Moreno Azócar kindly provided unpublished operative temperature data.
https://doi.org/10.5281/zenodo.4024404
oai:zenodo.org:4024404
eng
Zenodo
https://doi.org/10.1016/j.jtherbio.2016.11.001
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.4024403
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Journal of Thermal Biology, 63, 78-87, (2020-09-11)
Body temperature
Effectiveness of thermoregulation
Lizards
Thermal precision Reptiles
Reptiles
Acclimation
Data supplement to "Geographic variation and acclimation effects on thermoregulation behavior in the widespread lizard Liolaemus pictus"
info:eu-repo/semantics/other
oai:zenodo.org:1039952
2020-09-21T14:21:14Z
software
user-iees-paris
Jerome Mathieu
2017-10-31
<p>The <strong>EGrowth</strong> database contains 1073 growth curves of 51 species of earthworms, representing 16002 measures of body mass. It covers publications on earthworm body size from 1900 to 2016. The environmental conditions in which the growth curves were produced are also reported (e.g. temperature, pesticides).</p>
<p>The database is open access and can be explored directly from R:</p>
<pre><code># R code to type in console
if (!require('shiny ')) install.packages('shiny')
library(shiny)
runGitHub("EGrowth", "JeromeMathieuEcology")</code></pre>
<p>For further explanations, please go to the publication:</p>
<p><a href="https://doi.org/10.1016/j.soilbio.2018.04.004">https://doi.org/10.1016/j.soilbio.2018.04.004</a></p>
<p> </p>
<p>The database can also be browsed from a graphical user interface. See :</p>
<p><a href="http://www.jerome-mathieu.com/egrowth">http://www.jerome-mathieu.com/egrowth</a></p>
https://doi.org/10.5281/zenodo.1039952
oai:zenodo.org:1039952
eng
Zenodo
https://github.com/JeromeMathieuEcology/EGrowth/tree/v1.0.1
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1039951
info:eu-repo/semantics/openAccess
Other (Open)
Soil Biology and Biochemistry, 122, 71-80, (2017-10-31)
Database
Earthworm
Ontogeny
Life History Traits
Body size
EGrowth: a global database of earthworm body growth curves
info:eu-repo/semantics/other
oai:zenodo.org:6759725
2022-06-28T12:57:38Z
openaire_data
user-iees-paris
Mathieu, Jérome
2022-06-27
<p>Year of the first record of each native and exotic earthworm species (Oligochaeta) present in North America. Stops in 2021.</p>
<p>More details here: <a href="https://github.com/JeromeMathieuEcology/GlobalWorming">https://github.com/JeromeMathieuEcology/GlobalWorming</a>.</p>
https://doi.org/10.5281/zenodo.6759725
oai:zenodo.org:6759725
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6759724
info:eu-repo/semantics/openAccess
Creative Commons Attribution Non Commercial 1.0 Generic
https://creativecommons.org/licenses/by-nc/1.0/legalcode
earthworm
oligochaeta
exotic
invasion biology
first observation
biogeography
EWINA_1st_RECORDS: Year of the first record of observation of each native and exotic earthworm species present in North America
info:eu-repo/semantics/other
oai:zenodo.org:3530450
2020-01-20T17:02:12Z
user-cereep-ecotron
user-iees-paris
Le Galliard, Jean-François
Montoya, Jose M
2017-09-01
<p>L’expérimentation dans le large domaine des sciences de l’environnement a vécu au cours des dernières années une véritable révolution technologique impliquant des changements majeurs dans la dimension spatiale des outils, la complexité des systèmes étudiés, la précision du contrôle et de la mesure, et la diversité et la complexité de l’instrumentation analytique. Dans les laboratoires, des enjeux de recherche spécifiques ont justifié le développement de nouvelles approches expérimentales sur des objets d’étude et des thématiques de recherche variés : expérimentation à l’échelle des paysages naturels et des agro-écosystèmes, évolution expérimentale dans des milieux confinés, expérimentation globale coopérative sur les écosystèmes ou expérimentations en ingénierie écologique, par exemple. Ces nouvelles approches expérimentales nous permettent d’appréhender les passages d’échelles, dans leurs dimensions biologique et culturelle, spatiale et temporelle. Elles offrent une vaste gamme de possibilités de forçage des paramètres biotiques et abiotiques sur une diversité d’écosystèmes soit analogues aux <br>
systèmes naturels soit complètement artificiels. Le développement actuel de ces outils expérimentaux ainsi que celui de grandes infrastructures de recherche nationales et internationales dédiées à l’étude du fonctionnement des écosystèmes et socio-écosystèmes est à programmer dans un contexte dynamique d’évolution constante et rapide des objectifs de recherche ainsi que des moyens et des techniques. Organisé dans le cadre de la prospective du CNRS-INEE, l’atelier « Expérimentation en écologie et environnement » a réuni plus d’une trentaine de participants et visait à faire le point sur toutes ces avancées afin d’impliquer les acteurs de la communauté du CNRS-INEE dans l’identification des enjeux, des perspectives et des verrous majeurs de développement de l’expérimentation en écologie et environnement à court et moyen termes.</p>
https://doi.org/10.5281/zenodo.3530450
oai:zenodo.org:3530450
fra
Centre national de la recherche scientifique
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3530449
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
expérimentation
écologie
Expérimentation en écologie et environnement
info:eu-repo/semantics/conferencePaper
oai:zenodo.org:1318465
2019-06-11T13:21:40Z
user-iees-paris
Adam Khalife
Christian Peeters
Evan Economo
2018-08-01
<p>This is additional material to understand space constraint inside the heads of <em>Melissotarsus</em> workers (see Khalife et al. 2018) </p>
https://doi.org/10.5281/zenodo.1318465
oai:zenodo.org:1318465
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1318464
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Drishti video inside the head of Melissotarsus workers, showing mandible muscles and brain
info:eu-repo/semantics/other
oai:zenodo.org:1194640
2020-01-25T07:21:55Z
software
user-iees-paris
Xavier Raynaud
2018-03-09
<p>First release</p>
https://doi.org/10.5281/zenodo.1194640
oai:zenodo.org:1194640
Zenodo
https://github.com/xraynaud/svg2psp/tree/v1.0
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1194639
info:eu-repo/semantics/openAccess
Other (Open)
xraynaud/svg2psp: v1.0
info:eu-repo/semantics/other
oai:zenodo.org:10219671
2024-02-05T07:54:21Z
openaire_data
user-iees-paris
Le Galliard, Jean-François
Baron, Jean-Pierre
Tully, Thomas
Jaffré, Malo
2023-11-29
<p>Here, we used more than three decades of mark-recapture data in a natural population of the endangered meadow viper (<i>Vipera ursinii ursinii</i>) to unravel the patterns of temporal variation in reproductive traits, local climatic determinants of inter-annual variation in reproduction and the potential buffering effects of life cycle on population growth rate. We found significant inter-annual variation in annual body growth, gestation length, post-parturition body condition, clutch success and offspring traits at birth, but little temporal effects in reproductive effort. Temperature during gestation was the most influential local climatic determinant by shortening gestation length, and increasing clutch success and post-parturition body condition. Neither air humidity nor insolation was found to influence reproduction.</p>
https://doi.org/10.5281/zenodo.10219671
oai:zenodo.org:10219671
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10219670
info:eu-repo/semantics/restrictedAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Climate warming and temporal variation in reproduction strategies in the endangered meadow viper
info:eu-repo/semantics/other
oai:zenodo.org:3066005
2020-01-20T16:58:18Z
user-iees-paris
PEETERS Christian
2019-05-03
<p>Ant societies consist of reproductive and sterile adults that show tremendous diversity of phenotypes. These include permanently wingless queens and a soldier caste that evolved convergently in many genera. Myrmecologists describe ant castes with terminology based on form, or function, or both, moreover terms are used inconsistently in the literature. Because morphology changes less readily than behaviour, an emphasis on morphological definitions is recommended to facilitate comparative studies and understand the evolutionary origin of castes.</p>
<p>This is the english (original) version of a chapter published in Spanish in the book</p>
<p><strong>HORMIGAS DE COLOMBIA (editors F. Fernández, R. Guerrero & T. Delsinne). National University of Colombia (2019)</strong></p>
<p><strong>Capitulo 6 Castas: homología y analogía en la forma y función </strong></p>
https://doi.org/10.5281/zenodo.3066005
oai:zenodo.org:3066005
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.1215469
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
morphology, queen, worker, gamergate, ergatoid queen, intercaste, soldier
Ant castes: homology and analogy in form and function
info:eu-repo/semantics/bookPart
oai:zenodo.org:844223
2020-01-20T13:33:52Z
user-iees-paris
user-biosyslit
Peeters Christian
Fisher Brian Lee
2016-03-16
<p>Most ponerine ants have flying queens that monopolise sexual reproduction, but in a minority of species, workers can also mate and lay fertilised eggs. Such ‘gamergates' reproduce in addition to queens in some species but have replaced queens entirely in other species. The occurrence of a functional spermatheca in workers often appears associated with a slight difference in body size relative to winged queens, as is the case in <em>Euponera sikorae</em> (Forel) studied here. Eight colonies (19.9±8.7 workers and 0–2 dealate queens) were collected in humid forests of Madagascar. A mated queen reproduced in most colonies, but ovarian dissections indicated that 1–3 workers were also inseminated, and one of these laid eggs if the original founding queen was missing or no longer fecund. Exoskeleton remains (including 29 heads) of a staphylinid beetle were found in one nest of <em>E. sikorae</em>, pointing to specialised predation. We review the occurrence of non-flying reproductives (gamergates and ergatoid queens) in <em>Odontomachus</em> genus-group.</p>
https://doi.org/10.4001/003.024.0180
oai:zenodo.org:844223
Zenodo
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
African Entomology, 24, 180-187, (2016-03-16)
monogyny, reproduction, mating, inbreeding, independent colony foundation, gamergate
Gamergates (mated egg-laying workers) and queens both reproduce in Euponera sikorae ants from Madagascar.
info:eu-repo/semantics/article
oai:zenodo.org:852717
2020-01-20T14:50:31Z
user-iees-paris
user-biosyslit
Peeters, Christian
Aron, Serge
2017-08-29
<p>Sexual activity is only a brief moment in the life of ant colonies, but it determines several characteristics of life history. Mating behaviour, distance of female dispersal and mode of colony foundation are interlinked. In species exhibiting ‘male aggregation’ (males and queens fly and mate away from natal nests), newly mated queens have no option but to found a colony alone (independent colony founding, ICF). In contrast, in ‘female calling’ species, queens mate close to the natal nests, then either fly or walk away for dispersal. In several species, they can also disperse on foot accompanied by nestmate workers (dependent colony founding, DCF). Here, we review field observations and genetic data to untangle dispersal strategies across the genus <em>Cataglyphis</em>. We complement these existing informations with queen thorax morphology and dissection of wing muscles. Our comparative study includes 18 species belonging to six species-groups. We found that female calling occurs across all clades, with only two species showing male aggregation. Although most species have normal flying queens specialized for ICF, species in three out of the six species-groups show DCF. Remarkably, species with DCF evolved short-winged ‘brachypterous’ queens that lack wing muscles. Relative size of their thorax sclerites can be used to predict lack of flight ability. Altogether, these results show a marked deviation from the breeding behaviour typical of most species in subfamily Formicinae. We discuss how reduction of female dispersal may be linked to harsh desert conditions.</p>
See Supporting Material
https://doi.org/10.1093/biolinnean/blx052
oai:zenodo.org:852717
Zenodo
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Biological Journal of the Linnean Society, 122, 58-70, (2017-08-29)
Brachyptery – colony foundation – flight – functional morphology – mating – wing muscles.
Evolutionary reduction of female dispersal in Cataglyphis desert ants
info:eu-repo/semantics/article
oai:zenodo.org:3993032
2020-08-30T19:23:00Z
openaire_data
user-iees-paris
Zaninotto Vincent
Raynaud Xavier
Gendreau Emmanuel
Kraepiel Yvan
Motard Eric
Babiar Olivier
Hansart Amandine
Hignard Cécile
Dajoz Isabelle
2020-08-24
<p>Datasets for 'Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one' by Zaninotto et al. (2020) in Ecology and Evolution.</p>
https://doi.org/10.5281/zenodo.3993032
oai:zenodo.org:3993032
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3993031
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
plant-pollinator interactions
urbanization
phenology
plant reproductive success
Sinapis alba
Lotus corniculatus
Broader phenology of pollinator activity and higher plant reproductive success in an urban habitat compared to a rural one
info:eu-repo/semantics/other
oai:zenodo.org:6462831
2023-12-01T12:17:57Z
openaire_data
user-iees-paris
Jerome Mathieu
John Reynolds
Carlos Fragoso
2022-04-24
<p>This is a list of the earthworm species known in North America (Mexico, USA, Canada) before 2021, together with their ecological profile: geographical range, diet, and reproduction type.</p>
<p>There are two files:</p>
<ul>
<li><a href="https://zenodo.org/api/files/1ea17cf1-f5fd-4023-8b72-a58ffc149acb/EWINA_SP.csv">EWINA_SP.csv</a>: the dataset itself (308 species)</li>
<li><a href="https://zenodo.org/api/files/1ea17cf1-f5fd-4023-8b72-a58ffc149acb/EWINA_SP_variables.csv">EWINA_SP_variables.csv </a>: a file that explains the variables in the dataset</li>
</ul>
<p> </p>
https://doi.org/10.5281/zenodo.6462831
oai:zenodo.org:6462831
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6462830
info:eu-repo/semantics/openAccess
earthworm
ecological niche
biological invasions
geographical range
diet
functionnal group
reproduction
life history
traits
EWINA_SP: Ecological profile of earthworm species found in North America
info:eu-repo/semantics/other
oai:zenodo.org:7118362
2022-12-06T14:26:59Z
openaire_data
user-iees-paris
Dezetter, Mathias
Le Galliard, Jean-François
Lourdais, Olivier
2022-09-28
<p>This dataset contains raw data and associated metadata as well as R scripts to analyze the data of our paper "Behavioural hydroregulation protects against acute effects of drought in a dry-skinned ectotherm" published in Oecologia.</p>
<p>Abstract:</p>
<p>During extreme climate events, behavioural thermoregulation may buffer ectotherms from thermal stress and overheating. However, heatwaves are also combined with dry spells and limited water availability, and how much individuals can behaviourally mitigate dehydration risks through microclimate selection remains largely unknown. Herein, we investigated the behavioural and physiological responses to changes in air and microhabitat humidity in a terrestrial ectotherm, the asp viper (<em>Vipera aspis</em>). We exposed individuals to a simulated heatwave together with water deprivation for 3 weeks, and manipulated air water vapour density (wet air vs. dry air) and microclimate (wet shelter vs. dry shelter) in a two-by-two factorial design. Dry air conditions led to substantial physiological dehydration and muscle wasting. Vipers exposed to dry air more often used a shelter that provided a moist micro-climate, which reduced dehydration and muscle wasting at the individual level. These results provide the first experimental evidence that active behavioural hydroregulation can mitigate specific physiological stress responses caused by a dry spell in an ectotherm. Future studies investigating organismal responses to climate change should consider moisture gradient in the habitat and integrate both hydroregulation and thermoregulation behaviours.</p>
https://doi.org/10.5281/zenodo.7118362
oai:zenodo.org:7118362
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.7118361
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Oecologia, (2022-09-28)
behaviour
humidity gradient
hydroregulation
microclimate selection
water
vipers
Behavioural hydroregulation protects against acute effects of drought in a dry-skin ectotherm
info:eu-repo/semantics/other
oai:zenodo.org:3242590
2020-01-20T14:17:10Z
user-iees-paris
Christian Peeters
Fuminori Ito
Decha Wiwatwitaya
Roberto A. Keller
Rosli Hashim
Mathieu Molet
2017-07-01
<p><em>Gesomyrmex</em> (subfamily Formicinae) is a poorly known arboreal ant from the Oriental tropics. We sampled colonies in three localities (NE Thailand, peninsular Malaysia, and Sabah) and examined inhabitants of ten nests inside living branches. None of the nests had a reproductive dealate queen, indicating colonies are polydomous. We distinguished three sterile castes using discrete morphological traits, morphometry and total body size. Observations of behaviour are challenging in tree canopies, and we use functional morphology to predict the specialised functions of different castes. Disproportionately large eyes and piercing mandibles are consistent with workers being agile hunters. Soldiers and supersoldiers share robust mandibles, but the latter have a rectangular head and substantially larger body size, like the queens. This suggests both supersoldiers and queens have the muscular power necessary to chew entrance tunnels in healthy wood. Queens and supersoldiers also share frontal lobes (protection for antennal bases), suggesting that they block nest entrances with their heads. When founding a nest, newly mated queens need to chew an entrance tunnel that reaches the innermost soft pith. Supersoldiers are mostly restricted inside nests where they store nutrients in their gaster, but they may also chew the entrance tunnels of additional nests as the colony expands.</p>
https://doi.org/10.5281/zenodo.3242590
oai:zenodo.org:3242590
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3242589
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Asian Myrmecology, 9(e009015), (2017-07-01)
functional morphology, soldiers, supersoldiers, repletes, phragmotic, ovaries, mandibles, mosaics
Striking polymorphism among infertile helpers in the arboreal ant Gesomyrmex
info:eu-repo/semantics/article
oai:zenodo.org:7488942
2023-01-25T09:31:52Z
openaire_data
user-iees-paris
Zaninotto
Thebault
Dajoz
2023-01-11
<p>Datasets for 'Native and exotic plants play different roles in urban pollination networks across seasons' by Zaninotto et al. (2023) in Oecologia.</p>
https://doi.org/10.5281/zenodo.7488942
oai:zenodo.org:7488942
eng
Zenodo
https://doi.org/10.1007/s00442-023-05324-x
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.7488941
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Oecologia, (2023-01-11)
green spaces
nestedness
specialization
phenology
invasive species
Native and exotic plants play different roles in urban pollination networks across seasons
info:eu-repo/semantics/other
oai:zenodo.org:3529308
2020-01-20T17:20:07Z
user-cereep-ecotron
openaire
user-iees-paris
Rozen-Rechels, David
Dupoué, Andréaz
Lourdais, Olivier
Chamaillé-James, Simon
Meylan, Sandrine
Clobert, Jean
Le Galliard, Jean-François
2019-11-05
<p>The regulation of body temperature (thermoregulation) and water balance (hydroregulation) are key processes underlying ecological and evolutionary responses to climatic conditions in animal populations. Despite a long standing tradition of biophysical models of joint water and temperature regulation, the ecological and evolutionary implications of thermoregulation and hydroregulation have so far mostly been studied independently. In terrestrial or semi-terrestrial animals, thermoregulation and hydroregulation however closely interact and combined temperature and water constraints should directly influence individual performances. We emphasize the unifying concept of thermo-hydroregulation to address the functional integration of body temperature and water balance regulation. This concept refines our mechanistic understanding of the physiological and behavioral flexibility of animals in a changing world dominated by concurrent trends in temperature and water availability. This integrative approach has implications on a range of ecological and evolutionary processes such as space use and dispersal, resource-based trade-offs and optimal life history tactics.</p>
https://doi.org/10.5281/zenodo.3529308
oai:zenodo.org:3529308
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3529307
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
FEC 2018, Functional Ecology Conference 2018, Nancy, 10-13 December 2018
behavioral decisions
body temperature
water balance
physiological adjustments
When water meets temperature: ecological and evolutionary implications of thermo-hydroregulation
info:eu-repo/semantics/lecture
oai:zenodo.org:3739151
2020-04-06T09:00:27Z
user-cereep-ecotron
user-iees-paris
Kawamoto, Anna
Badiane, Arnaud
Le Galliard, Jean-François
2020-04-03
<p>According to animal signalling theory, various mechanisms can maintain signal honesty in the face of deception. Conventional signals are usually cheap to produce but socially imposed costs, often taking the form of aggression from conspecifics, can enforce their honesty. While our understanding of signal evolution and honesty has much improved for some pigment-based colour signals, the mechanisms maintaining the honesty of structural colour signals, such as ultraviolet (UV), remain elusive. Here, we used the common lizard <em>Zootoca vivipara</em> to test whether or not the honesty of UV signals displayed on male throats is under social control. To do so, we staged dyadic agonistic interactions between non-manipulated focal males and opponents of either larger or smaller body size, and with either control or manipulated UV signals so as to create small cheaters with UV-enhanced throats, large cheaters with UV-reduced throats, and their respective controls. Focusing on control interactions, we first confirmed that male UV coloration and bite force were good predictors of contest outcomes in this species. Furthermore, in support of a conventional signal hypothesis, focal males were more aggressive towards large cheaters and became more submissive when these large cheaters retaliated, and were less submissive against small cheaters. However, that focal males were not more aggressive towards small cheaters contradicts our initial predictions. Overall, we provide some evidence suggesting that socially imposed costs may enforce the honesty of UV signals in common lizards.</p>
https://doi.org/10.5281/zenodo.3739151
oai:zenodo.org:3739151
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3739150
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Animal communication – Deception – Social costs - Signals – Ultraviolet – Male competition – Lizards – Zootoca vivipara
The role of social costs as a mechanism enforcing the honesty of ultraviolet signals in a lizard
info:eu-repo/semantics/preprint
oai:zenodo.org:10621236
2024-02-06T09:52:46Z
openaire_data
user-iees-paris
Jeantet, Aurélie
Audebert, Fabienne
Agostini, Simon
Decencière, Beatriz
Lorang, Camille
Jamet, Laura
Giner, Clarisse
Flandi, Emma
Nardou, Nora
Lemaire, Baptiste
Federici, Pierre
Rozen-Rechels, David
Gasparini, Julien
2024-02-05
<p><span>Living organisms are exposed to multiple environmental factors that can affect their fitness. The effects of these simultaneous stressors can be additive or can interact in negative synergistic or antagonistic ways to affect the health of exposed individuals. Parasites can accumulate pollutants in their own tissues and have been shown to increase the tolerance of their hosts to different pollutants (antagonistic interaction between parasites and pollutants). We tested the existence of combined antagonistic effects between intestinal parasites and lead exposure on urban feral pigeons (<em>Columba livia</em>) which are known to be exposed to trace metal pollution and harbor a wide variety of internal and external parasites. </span><span>We experimentally exposed feral pigeons to two treatments: an anthelmintic treatment to eliminate intestinal nematode parasites; an exposure to lead for a period of 6 months. We tested the effects of these crossed treatments on several components of fitness: immunocompetence, reproduction, and body mass. </span><span>Our findings suggest that the overall effects of lead exposure, either alone or in combination with the presence of intestinal parasites (without </span><span>anthelmintic </span><span>treatment) were negative, through either additive or synergistic means. </span><span>In the absence of putative antagonistic effects between lead exposure and with helminths, the detoxification hypothesis could not be confirmed. </span><span>Our results reveal the existence of negative combined effects between pollutant exposure and intestinal parasites, highlighting the importance of accounting for multiple stress factors when studying the effects of exposure to pollutants and/or other environmental stressors on the fitness of organisms.</span></p>
https://doi.org/10.5281/zenodo.10621236
oai:zenodo.org:10621236
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10621235
info:eu-repo/semantics/restrictedAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Data from: Crossed effects of helminth infection and lead exposure on fitness: an experimental study in feral pigeons (Columba livia)
info:eu-repo/semantics/other
oai:zenodo.org:4564319
2021-02-26T12:27:14Z
openaire_data
user-iees-paris
Zaninotto Vincent
Perrard Adrien
Babiar Olivier
Hansart Amandine
Hignard Cécile
Dajoz Isabelle
2021-02-26
<p>Dataset for "Seasonal Variations of Pollinator Assemblages among Urban and Rural Habitats: A Comparative Approach Using a Standardized Plant Community" by Zaninotto et al. (2021), in Insects.</p>
https://doi.org/10.5281/zenodo.4564319
oai:zenodo.org:4564319
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4564318
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
urbanization
plant-pollinator interactions
pollinator communities
Sinapis alba
Lotus corniculatus
Seasonal Variations of Pollinator Assemblages among Urban and Rural Habitats: A Comparative Approach Using a Standardized Plant Community
info:eu-repo/semantics/other
oai:zenodo.org:3601023
2020-03-10T19:56:43Z
user-cereep-ecotron
openaire_data
user-iees-paris
Rozen-Rechels, David
Badiane, Arnaud
Agostini, Simon
Meylan, Sandrine
Le Galliard, Jean-François
2020-01-08
<p>Raw data of the article "Water restriction induces behavioral fight but impairs thermoregulation in a dry‐skinned ectotherm" by Rozen-Rechels D. et al., published in Oikos in 2020 (https://doi.org/10.1111/oik.06910). These data are freely available and are provided as csv files. Check the readme file for information on metadata.</p>
<p>Data were formatted by David Rozen-Rechels and produced according to standards and protocols described in the companion paper.</p>
Agence nationale de la recherche contract ANR-17-CE02-0013
https://doi.org/10.5281/zenodo.3601023
oai:zenodo.org:3601023
eng
Zenodo
https://doi.org/10.1111/oik.06910
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.3601022
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Oikos, (2020-01-08)
activity
body temperature
dehydration
micro-habitat selection
non-avian reptiles
water availability
Water restriction induces behavioral fight but impairs thermoregulation in a dry-skinned ectotherm
info:eu-repo/semantics/other
oai:zenodo.org:844241
2020-01-20T16:10:52Z
user-iees-paris
user-biosyslit
Peeters, Christian
2012-01-10
<p>Flight is a one-off event in ants, hence after mating, the wing muscles of winged queens can function as protein reserves during independent colony foundation (ICF). Another strategy occurring in many unrelated lineages is dependent colony foundation (DCF). DCF does not require queens with expensive wing muscles because dispersal is on foot, and a found- ress relies on nestmate workers to feed her first brood of workers. The shift to DCF seems the reason why wingless reproductives (ergatoid queens, short-winged queens, and gamergates) evolved independently in more than 50 genera belonging to 16 subfamilies. In various species they occur together with winged queens (in the same or different popu- lations), in other species winged queens were replaced completely. Because wingless reproductives are the product of convergence, there is tremendous heterogeneity in morphological characteristics as well as selective contexts. These novel reproductive phenotypes cannot function without nestmate workers (foundresses forage in only few species), hence addi- tional investment in workers is needed.</p>
https://doi.org/10.5281/zenodo.844241
oai:zenodo.org:844241
Zenodo
https://zenodo.org/communities/biosyslit
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.844240
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Myrmecological News, 16, 75-91, (2012-01-10)
Colony foundation, flight, reproduction, dispersal, brachyptery, ergatoid queens, gamergates
Convergent evolution of wingless reproductives across all subfamilies of ants, and sporadic loss of winged queens (Hymenoptera: Formicidae)
info:eu-repo/semantics/article
oai:zenodo.org:6683661
2022-07-01T08:04:51Z
user-cereep-ecotron
openaire_data
user-iees-paris
user-eu
Badiane, Arnaud
Dupoué, Andréaz
Blaimont, Pauline
Miles, Donald B
Gilbert, Anthony L
Leroux-Coyau, Mathieu
Kawamoto, Anna
Rozen-Rechels, David
Meylan, Sandrine
Clobert, Jean
Le Galliard, Jean-François
2022-06-22
<p>Dataset and R code associated with the following publication:</p>
<p>Badiane et al. (2022), Environmental conditions and male quality traits simultaneously explain variation of multiple colour signals in male lizards. Journal of Animal Ecology, in press</p>
<p>This dataset includes the following files:</p>
<p>- An excel file containing the reflectance spectra of all individuals from all the study populations</p>
<p>- An excel file containing the variables collected at the individual and population levels</p>
<p>- Two R scripts corresponding to the analyses performed in the publication</p>
https://doi.org/10.5281/zenodo.6683661
oai:zenodo.org:6683661
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://zenodo.org/communities/eu
https://doi.org/10.5281/zenodo.6683660
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Animal communication
Coloration
Palearctic
Reptile
Visual signalling
Zootoca vivipara
Dataset: Environmental conditions and male quality traits simultaneously explain variation of multiple colour signals in male lizards
info:eu-repo/semantics/other
oai:zenodo.org:4586044
2023-03-02T13:16:28Z
user-iees-paris
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2021-02-16
<blockquote>
<p><strong>/!\ This is an old version of the official template /!\</strong></p>
<p><strong>For the current version, please go here: </strong><a href="https://doi.org/10.5281/zenodo.4543852">https://doi.org/10.5281/zenodo.4543852</a></p>
</blockquote>
https://doi.org/10.5281/zenodo.4586044
oai:zenodo.org:4586044
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
#GlobalSoilMacroFauna | Official template to report Data of Soil Macro Fauna abundance from TSBF Method
info:eu-repo/semantics/other
oai:zenodo.org:7469111
2023-03-02T13:16:29Z
user-iees-paris
Nico Eisenhauer
Ana C Antunes
Sebastien Barot
Marie L.C. Bartz
Ana E. Bonato Asato
Irene Calderon-Sanou
Thibaud Decaëns
Steven Fonte
Pierre Ganault
Benoit Gauzens
Konstantin Gongalsky
Carlos A. Guerra
Tomislav Hengl
Raphaël Marichal
Clara P.Peña Venegas
Daniel Castro
Anton Potapov
Elisa Thébault
Wilfried Thuiller
Martin Witjes
Chi Zhang
Mathieu, Jérôme
Lavelle, Patrick
Brown, George
2021-02-16
<blockquote>
<p><strong>/!\ This is an old version of the official template /!\</strong></p>
<p><strong>For the current version, please go here: </strong><a href="https://doi.org/10.5281/zenodo.4543852">https://doi.org/10.5281/zenodo.4543852</a></p>
</blockquote>
https://doi.org/10.5281/zenodo.7469111
oai:zenodo.org:7469111
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4543852
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Soil Invertebrates
Soil Macro Fauna
Soil Biodiversity
Soil Fertility
Agricultural Practices
Data Template
Earthworm
Ant
Termite
Diplopoda
Chilopoda
Hemiptera
Orthoptera
Aranae
sOilFauna
#GlobalSoilMacroFauna | Official template to report Data to the MACROFAUNA database
info:eu-repo/semantics/other
oai:zenodo.org:6408609
2022-04-07T12:56:50Z
openaire_data
user-iees-paris
Jérôme Mathieu
2022-04-02
<p><strong>This dataset centralizes data of earthworm interception events at the US borders between 1945 and 1975.</strong></p>
<p>These data come from the U.S. Bureau of Plant Quarantine, U.S. Department of Agriculture and were compiled by E. Gates in a list of papers (see references).</p>
<p>Each record in the EWINA_IPATHS database relates an interception event of introduced earthworms.</p>
<p>Interception events are described by the name of the intercepted species, its abundance, the date and place of interception, the geographical point of origin, the transportation mode (boat, plane, car), and the substrate in which the earthworms were found (e.g. soil, leaves, fish bait).</p>
<p>EWINA_IPATHS contains 1 016 events of earthworm interceptions.</p>
<p>Files:</p>
<ul>
<li><strong>EWINAPATH.csv </strong>: dataset itself</li>
<li><strong>EWINAPATH_references.csv</strong> : list of references where the data come from. Merge to EWINAPATH.csv with the field source_ID.</li>
<li><strong>EWINAPATH_variables.csv</strong>: list of variables and their meaning.</li>
</ul>
<p> </p>
<p> </p>
https://doi.org/10.5281/zenodo.6408609
oai:zenodo.org:6408609
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.6408608
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Biological invasions
Earthworms
Introductions
Colonization
Transportations
EWINA_IPATHS : a global database of earthworm introductions' pathways into the US from 1945 to 1975
info:eu-repo/semantics/other
oai:zenodo.org:4030491
2020-09-21T12:20:34Z
user-cereep-ecotron
openaire_data
user-iees-paris
Rozen-Rechels David
Rutschmann Alexis
Dupoué Andréaz
Blaimont Pauline
Chauveau Victor
Miles Donald B.
Guillon Michael
Richard Murielle
Badiane Arnaud
Meylan Sandrine
Clobert Jean
Le Galliard Jean-François
2020-09-15
<p>Raw data and scripts of the article "Interaction of hydric and thermal conditions drive geographic variation in thermoregulation in a widespread lizard" by Rozen-Rechels D. et al., in Ecological Monographs. These data are freely available in csv format. See the readme file for metadata explanation.</p>
<p>Data were formatted by the first author David Rozen-Rechels and collected according to standards and procedures described in the companion journal article.</p>
<p> </p>
<p>Abstract of the paper:</p>
<p>Behavioral thermoregulation is an efficient mechanism to buffer the physiological effects of climate change. Thermal ecology studies have traditionally tested how thermal constraints shape thermoregulatory behaviors without accounting for the potential major effects of landscape structure and water availability. Thus, we lack a general understanding of the multifactorial determinants of thermoregulatory behaviors in natural populations. In this study, we quantified the relative contribution of elevation, thermal gradient, moisture gradient and landscape structure in explaining geographic variation in thermoregulation strategies of a terrestrial ectotherm species. We measured field active body temperature, thermal preferences and operative environmental temperatures to calculate thermoregulation indices, including thermal quality of the habitat and thermoregulation efficiency for a very large sample of common lizards (<em>Zootoca vivipara</em>) from 21 populations over 3 years across the Massif Central mountain range in France. We used an information-theoretic approach to compare eight <em>a priori</em> thermo-hydroregulation hypotheses predicting how behavioral thermoregulation should respond to environmental conditions. Environmental characteristics exerted little influence on thermal preference with the exception that females from habitats with permanent access to water had lower thermal preferences. Field body temperatures and accuracy of thermoregulation were best predicted by the interaction between air temperature and a moisture index. In mesic environments, field body temperature and thermoregulation inaccuracy increased with air temperature, but they decreased in drier habitats. Thermoregulation efficiency (difference between thermoregulation inaccuracy and the thermal quality of the habitat) was maximized in cooler and more humid environments and was mostly influenced by the thermal quality of the habitat. Our study highlights complex patterns of variation in thermoregulation strategies, which are mostly explained by the interaction between temperature and water availability, independent of the elevation gradient or thermal heterogeneity. Although changes in landscape structure were expected to be the main driver of extinction rate of temperate zone ectotherms with ongoing global change, we conclude that changes in water availability coupled with rising temperatures might have a drastic impact on the population dynamics of some ectotherm species.</p>
https://doi.org/10.5281/zenodo.4030491
oai:zenodo.org:4030491
Zenodo
https://zenodo.org/communities/iees-paris
https://zenodo.org/communities/cereep-ecotron
https://doi.org/10.5281/zenodo.4030490
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Ecological Monographs, (2020-09-15)
Body temperature
Elevational gradient
Moisture gradient
Landscape heterogeneity
Non-avian reptiles
Interaction of hydric and thermal conditions drive geographic variation in thermoregulation in a widespread lizard
info:eu-repo/semantics/other
oai:zenodo.org:3738546
2020-04-02T20:20:13Z
openaire_data
user-iees-paris
Gounand, Isabelle
Little, Chelsea J.
Harvey, Eric
Altermatt, Florian
2020-04-02
<p>Dataset used in the publication: " Global quantitative synthesis of ecosystem functioning across climatic zones and ecosystem types". The dataset gathers estimates of ecosystem standing stocks (biomass, organic carbon, detritus), fluxes (GPP, ER, NEP) and process rates (decomposition and carbon uptake rates) for eight broad ecosystem types (forest, grassland, agroecosystem, desert, stream, lake, pelagic and benthic marine ecosystems) in five broad climatic zones (arctic, boreal, arid, temperate, tropical, arid).</p>
<p>The scripts to produce the figures and the statistics of the publication are released along with the txt version of the data, which file is uploaded when running the script.</p>
https://doi.org/10.5281/zenodo.3738546
oai:zenodo.org:3738546
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3644246
info:eu-repo/semantics/openAccess
Creative Commons Attribution 1.0 Generic
https://creativecommons.org/licenses/by/1.0/legalcode
carbon cycle
climate
ecosystem functioning
multifunctionality
metabolic theory of ecology
global change
meta-ecosystem
primary production
productivity
decomposition
Data set for Global quantitative synthesis of ecosystem functioning across climatic zones and ecosystem types
info:eu-repo/semantics/other
oai:zenodo.org:5105734
2021-07-15T13:48:17Z
openaire_data
user-iees-paris
Romain Honorio
Lauren Jacquier
Claudie Doums
Mathieu Molet
2021-07-15
<p>Data from the paper 'Disentangling the roles of social and individual effects on cadmium tolerance in the ant Temnothorax nylanderi.'</p>
https://doi.org/10.5281/zenodo.5105734
oai:zenodo.org:5105734
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.5105733
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Disentangling the roles of social and individual effects on cadmium tolerance in the ant Temnothorax nylanderi.
info:eu-repo/semantics/other
oai:zenodo.org:6630184
2022-06-10T13:50:47Z
openaire_data
user-iees-paris
Doré, Maël
Parra, Santiago
Thébault, Elisa
Fontaine, Colin
2022-06-10
<p>This database assembles different published datasets of observed interaction networks between plants and pollinators, which were extracted from articles, theses and existing online databases.</p>
<p>Each row in the data table corresponds to an interaction between a plant and a pollinator species reported at a given site by a given publication.</p>
https://doi.org/10.5281/zenodo.6630184
oai:zenodo.org:6630184
Zenodo
https://github.com/MaelDore/Pollination_networks/tree/v.1.0.0
https://doi.org/10.5281/zenodo.4290503
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.4300426
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
mutualistic network
plant-pollinator interaction
flower visitors
diversity
A database of plant-pollinator networks
info:eu-repo/semantics/other
oai:zenodo.org:10212829
2023-11-29T08:09:04Z
openaire_data
user-iees-paris
Jacques Pédron
Sylvia Thieffry
Christelle Gomes de Faria
Elisa Thebault
Marie-Anne Barny
2023-11-28
<p>Illumina gapA sequences of synthetic communities of plant bacterial pathogens: Pectobacterium and Dickeya genus. Sequencing was performed after growth on TSB synthetic medium (2 days post inoculation) or growth on potato tubers (5 days post infection).</p><p> </p><p>The following files are available:</p><p>PT_table.txt: description of the potato tubers samples</p><p>TSB_table.txt: description of samples in synthetic medium (TSB)</p><p>gapA_PT.fasta.gz: Illumina fasta sequences after potato tubers infection (35,000 reads)</p><p>gapA_TSB.fasta.gz: Illumina fasta sequences after synthetic medium inoculation (35,000 reads)</p><p>gapA_without_primers.fasta: gapA sequences (without primers) of Pectobacterium and Dickeya strains used in this study (27 strains)</p><p>species.txt: list of bacterial species used in this study (9 species)</p><p>strains.txt: list of bacterial strains used in this study (27 strains)</p><p>count.py: python3 script used to analyse the output of blastn</p><p> </p><p>Method (examplified with the gapA_TSB sequences at the species level):</p><p>• gapA sequences were blasted (blastn) against gapA sequences of Pectobacterium and Dickeya strains used in this study:</p><p>makeblastdb -in gapA_without_primers.fasta -dbtype nucl -out dbblastn</p><p>blastn -db dbblastn -query gapA_TSB.fasta -outfmt 6 -out blast.blastn -num_threads 12 -evalue 0.00001 -num_alignments 1</p><p>• Reads count. Reads matching (100% identity) with gapA sequences of Pectobacterium and Dickeya strains used in this study were counted using the count.py python script. The output is a tab-separated values (.tsv) file:</p><p>python3 count.py species.txt blast.blastn</p>
https://doi.org/10.5281/zenodo.10212829
oai:zenodo.org:10212829
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10212828
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Bacterial pathogens dynamic during multi-species infections
info:eu-repo/semantics/other
oai:zenodo.org:10404740
2023-12-19T09:55:51Z
openaire_data
user-iees-paris
Jacques Pédron
Sylvia Thieffry
Christelle Gomes de Faria
Elisa Thebault
Marie-Anne Barny
2023-12-19
<p>Illumina gapA sequences of synthetic communities of plant bacterial pathogens: Pectobacterium and Dickeya genus. Sequencing was performed after growth on TSB synthetic medium (2 days post inoculation) or growth on potato tubers (5 days post infection).</p>
<p> </p>
<p>The following files are available:</p>
<p>PT_table.txt: description of the potato tubers samples</p>
<p>TSB_table.txt: description of samples in synthetic medium (TSB)</p>
<p>gapA_PT.fasta.gz: Illumina fasta sequences after potato tubers infection (35,000 reads)</p>
<p>gapA_TSB.fasta.gz: Illumina fasta sequences after synthetic medium inoculation (35,000 reads)</p>
<p>gapA_without_primers.fasta: gapA sequences (without primers) of Pectobacterium and Dickeya strains used in this study (27 strains)</p>
<p>species.txt: list of bacterial species used in this study (9 species)</p>
<p>strains.txt: list of bacterial strains used in this study (27 strains)</p>
<p>count.py: python3 script used to analyse the output of blastn</p>
<p>R_script_FigureS1.R: R script for statistical analysis</p>
<p>R_script_Figure2b.R: R script for statistical analysis</p>
<p>R_script_Figure2a.R: R script for statistical analysis</p>
<p> </p>
<p>Method (examplified with the gapA_TSB sequences at the species level):</p>
<p>• gapA sequences were blasted (blastn) against gapA sequences of Pectobacterium and Dickeya strains used in this study:</p>
<p>makeblastdb -in gapA_without_primers.fasta -dbtype nucl -out dbblastn</p>
<p>blastn -db dbblastn -query gapA_TSB.fasta -outfmt 6 -out blast.blastn -num_threads 12 -evalue 0.00001 -num_alignments 1</p>
<p>• Reads count. Reads matching (100% identity) with gapA sequences of Pectobacterium and Dickeya strains used in this study were counted using the count.py python script. The output is a tab-separated values (.tsv) file:</p>
<p>python3 count.py species.txt blast.blastn</p>
https://doi.org/10.5281/zenodo.10404740
oai:zenodo.org:10404740
eng
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.10212828
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
Bacterial pathogens dynamic during multi-species infections
info:eu-repo/semantics/other
oai:zenodo.org:3226979
2019-06-08T11:59:40Z
user-iees-paris
Jerome Mathieu
2019-05-23
<ul>
<li><strong>ArcGis</strong> est un SIG (Système d'Information Géographique) payant très utilisé dans le domaine de la cartographie et des analyses spatiales.</li>
</ul>
<ul>
<li><strong>Fragstats </strong>est un logiciel libre qui permet de calculer des métriques de description du paysage (connectivité, fragmentation, etc).</li>
</ul>
<p> </p>
<blockquote>
<p><strong>Dans ce tutoriel vous apprendrez à faire les opérations de base avec un SIG :</strong></p>
<ul>
<li>Cartes</li>
<li>Jointures spatiales</li>
<li>Analyse spatiales élémentaires (intersection, union etc)</li>
<li>Description d'un paysage par des métriques</li>
<li>Automatisation des analyses avec Model Builder</li>
</ul>
</blockquote>
<p> </p>
<p>Personnellement je recommande plutôt d'utiliser Qgis et R pour du SIG en recherche en écologie.</p>
<p>ArcGis est néanmoins très utilisé dans les bureaux d'étude en environnement/Biodiversité.</p>
<p> </p>
<p>Les applications sont centrées sur des problématiques d'écologie.</p>
Ce tutoriel a été fait pour le module de SIG en M1 du parcours BEE (Biodiversité Ecologie et Evolution) de Sorbonne Université
https://doi.org/10.5281/zenodo.3226979
oai:zenodo.org:3226979
fra
Zenodo
https://zenodo.org/communities/iees-paris
https://doi.org/10.5281/zenodo.3226978
info:eu-repo/semantics/openAccess
Creative Commons Attribution 4.0 International
https://creativecommons.org/licenses/by/4.0/legalcode
GIS
SIG
spatial analyses
raster
shapefile
fragmentation
landscape ecology
spatial data
Tutoriel ArcGis (10.1) et Fragstats pour l'écologie
info:eu-repo/semantics/lecture