Biodiversity Literature Repository

Submit to community
Liberated Data
Published December 8, 2025 | Version v1
Journal article Open

Mitogenome of an endemic Andean Daphnia titicacensis Birge, 1909 in the context of evolutionary history of the D. pulex complex (Cladocera: Daphniidae)

Authors/Creators

  • 1. Laboratory of Ecology of Aquatic Communities and Invasions, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia; https://orcid.org/0009-0004-8194-7585; https://orcid.org/0000-0003-1153-9995; https://orcid.org/0000-0002-8863-6438
  • 2. Department of Hydrobiology, Faculty of Biology, University of Bialystok, Białystok, Poland; https://orcid.org/0000-0003-0711-5903 *Corresponding author. E-mail: alexey-a-kotov@yandex.ru

Description

Pereboev, Dmitry D., Karpowicz, Maciej, Efeykin, Boris D., Kotov, Alexey A. (2025): Mitogenome of an endemic Andean Daphnia titicacensis Birge, 1909 in the context of evolutionary history of the D. pulex complex (Cladocera: Daphniidae). Ecologica Montenegrina 92: 81-92, DOI: 10.37828/em.2025.92.7, URL: https://doi.org/10.37828/em.2025.92.7

Files

source.pdf

Files (2.5 MB)

Name Size Download all
md5:f6c09c6b36c41fea8c68cfba8832f419
2.5 MB Preview Download

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:FFC09C6BFFC4FFEA8C68FFBA8832F419

Related works

Has part
Figure: 10.5281/zenodo.20168561 (DOI)
Figure: 10.5281/zenodo.20168565 (DOI)
Figure: 10.5281/zenodo.20168569 (DOI)
Figure: 10.5281/zenodo.20168573 (DOI)

References

  • Adamowicz, S.J., Hebert, P.D.N. & Marinone, M.C. (2004) Species diversity and endemism in the Daphnia of Argentina: a genetic investigation. Zoological Journal of the Linnean Society, 140, 171-205.
  • Adamowicz, S.J., Petrusek, A., Colbourne, J.K., Hebert, P.D.N. & Witt, J.D.S. (2009) The scale of divergence: a phylogenetic appraisal of intercontinental allopatric speciation in a passively dispersed freshwater zooplankton genus. Molecular phylogenetics and evolution, 50, 423-436.
  • Agnarsson, I. & Kuntner, M. (2007) Taxonomy in a changing world: seeking solutions for a science in crisis. Systematic biology, 56, 531-539.
  • Aguilera, X., Mergeay, J., an Wollebrants, Declerck, S. & Meester, L. de (2007) Asexuality and polyploidy in Daphnia from the tropical Andes. Limnology and oceanography, 52, 2079-2088.
  • Birge, E.A. (1909) 2-Cladoceros. Diaz Romero N. (ed.), Los lagos de los altiplanos de la America del Sud. La Paz: Tipografia commercial de Ismael Argote, 137-142.
  • Capella-Gutierrez, S., Silla-Martinez, J.M. & Gabaldon, T. (2009) trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics (Oxford, England), 25, 1972-1973.
  • Castellucci, F., Luchetti, A. & Mantovani, B. (2022) Exploring mitogenome evolution in Branchiopoda (Crustacea) lineages reveals gene order rearrangements in Cladocera. Scientific reports, 12, 4931.
  • Chen, S. (2023) Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2, e107.
  • Clement, M., Posada, D. & Crandall, K.A. (2000) TCS: a computer program to estimate gene genealogies. Molecular ecology, 9, 1657-1659.
  • Colbourne, J.K., Pfrender, M.E., Gilbert, D., Thomas, W.K., Tucker, A., Oakley, T.H., Tokishita, S., Aerts, A., Arnold, G.J., Basu, M.K., Bauer, D.J., Caceres, C.E., Carmel, L., Casola, C., Choi, J.-H., Detter, J.C., Dong, Q., Dusheyko, S., Eads, B.D., Frohlich, T., Geiler-Samerotte, K.A., Gerlach, D., Hatcher, P., Jogdeo, S., Krijgsveld, J., Kriventseva, E.V., Kultz, D., Laforsch, C., Lindquist, E., Lopez, J., Manak, J.R., Muller, J., Pangilinan, J., Patwardhan, R.P., Pitluck, S., Pritham, E.J., Rechtsteiner, A., Rho, M., Rogozin, I.B., Sakarya, O., Salamov, A., Schaack, S., Shapiro, H., Shiga, Y., Skalitzky, C., Smith, Z., Souvorov, A., Sung, W., Tang, Z., Tsuchiya, D., Tu, H., Vos, H., Wang, M., Wolf, Y.I., Yamagata, H., Yamada, T., Ye, Y., Shaw, J.R., Andrews, J., Crease, T.J., Tang, H., Lucas, S.M., Robertson, H.M., Bork, P., Koonin, E.V., Zdobnov, E.M., Grigoriev, I.V., Lynch, M. & Boore, J.L. (2011) The ecoresponsive genome of Daphnia pulex. Science, 331, 555-561.
  • Colbourne, J.K., Wilson, C.C. & Hebert, P.D.N. (2006) The systematics of Australian Daphnia and Daphniopsis (Crustacea: Cladocera) : a shared phylogenetic history transformed by habitatspecific rates of evolution. Biological Journal of the Linnean Society, 89, 469-488.
  • Crease, T.J., Floyd, R., Cristescu, M.E. & Innes, D. (2011) Evolutionary factors affecting Lactate dehydrogenase A and B variation in the Daphnia pulex species complex. BMC evolutionary biology, 11, 212.
  • Crease, T.J., Omilian, A.R., Costanzo, K.S. & Taylor, D.J. (2012) Transcontinental phylogeography of the Daphnia pulex species complex. PloS one, 7, e46620.
  • Daday, E. (1902) Mikroskopische Susswasserthiere aus Patagonien, gesammelt von Dr. Filippo Sylvestri. Termeszetrajzi Fuzetek, 25, 201-310.
  • Ekman, S. (1900) Cladoceren aus Patagonien, gesammelt von der schwedischen Expedition nach Patagonien 1899. Zoologische Jahrbucher. Abteilung fur Systematik, Geographie und Biologie der Tiere, 14, 62-84.
  • Elguweidi, A. & Crease, T. (2024) Copy number and sequence variation in rDNA of Daphnia pulex from natural populations: insights from whole-genome sequencing. G3 (Bethesda, Md.), 14.
  • Galimov, Y., Walser, B. & Haag, C.R. (2011) Frequency and inheritance of non-male producing clones in Daphnia magna: Evolution towards sex specialization in a cyclical parthenogen? Journal of evolutionary biology, 24, 1572-1583.
  • Grant, J.R., Enns, E., Marinier, E., Mandal, A., Herman, E.K., Chen, C.-Y., Graham, M., van Domselaar, G. & Stothard, P. (2023) Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic acids research, 51, W484-W492.
  • Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W. & Gascuel, O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Systematic biology, 59, 307-321.
  • Hebert, P. (1987) Genetics of Daphnia. Memorie dell' Istituto Italiano di ldrobiologia, 45, 439-460.
  • Hebert, P.D.N., Witt, J.D.S. & Adamowicz, S.J. (2003) Phylogeographical patterning in Daphnia ambigua: Regional divergence and intercontinental cohesion. Limnology and oceanography, 48, 261-268.
  • Hoang, D.T., Chernomor, O., Haeseler, A. von, Minh, B.Q. & Le Vinh, S. (2018) UFBoot2: Improving the ultrafast bootstrap approximation. Molecular biology and evolution, 35, 518-522.
  • International Commission on Zoological Nomenclature (ICZN) (2000) International code of zoological nomenclature. Fourth edition. The Natural History Museum, London.
  • Jin, J.-J., Yu, W.-B., Yang, J.-B., Song, Y., dePamphilis, C.W., Yi, T.-S. & Li, D.-Z. (2020) GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome biology, 21, 241.
  • Kalyaanamoorthy, S., Minh, B.Q., Wong, T.K.F., Haeseler, A. von & Jermiin, L.S. (2017) ModelFinder: Fast model selection for accurate phylogenetic estimates. Nature methods, 14, 587-589.
  • Katoh, K. & Standley, D.M. (2013) MAFFT multiple sequence alignment software version 7 : Improvements in performance and usability. Molecular biology and evolution, 30, 772-780.
  • Korovchinsky, N.M. & Kotov, A.A. (Eds.) (2021) Water fleas (Crustacea: Cladocera) of North Eurasia. In two volumes. KMK Press, Moscow, Vol. 1: 481 pp, Vol. 2: 544 pp.
  • Kotov, A.A. (2015) A critical review of the current taxonomy of the genus Daphnia O. F. Muller, 1785 (Anomopoda, Cladocera). Zootaxa, 3911, 184-200.
  • Kotov, A.A. & Ferrari, F.D. (2010) The taxonomic research of Jules Richard on Cladocera (Crustacea: Branchiopoda) and his collection at the National Museum of Natural History, USA. Zootaxa, 2551, 37.
  • Kotov, A.A., Garibian, P.G., Bekker, E.I., Taylor, D.J. & Karabanov, D.P. (2021) A new species group from the Daphnia curvirostris species complex (Cladocera: Anomopoda) from the eastern Palaearctic: taxonomy, phylogeny and phylogeography. Zoological journal of the Linnean Society, 191, 772-822.
  • Lampert, W. (2011) Daphnia: Development of a model organism in ecology and evolution. International Ecology Institute, Oldendorf/Luhe, XIX + 250.
  • Ma, X., Petrusek, A., Wolinska, J., Gieβler, S., Zhong, Y., Yang, Z., Hu, W. & Yin, M. (2015) Diversity of the Daphnia longispina species complex in Chinese lakes: a DNA taxonomy approach. Journal of plankton research, 37, 56-65.
  • Ma, X., Petrusek, A., Wolinska, J., Hu, W. & Yin, M. (2019) Lineage diversity and reproductive modes of the Daphnia pulex group in Chinese lakes and reservoirs. Molecular phylogenetics and evolution, 130, 424-433.
  • Markova, S., Dufresne, F., Manca, M. & Kotlik, P. (2013) Mitochondrial capture misleads about ecological speciation in the Daphnia pulex complex. PLoS one, 8, e69497.
  • Meng, G., Li, Y., Yang, C. & Liu, S. (2019) MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization. Nucleic acids research, 47, e63.
  • Mergeay, J., Aguilera, X., Declerck, S., Petrusek, A., Huyse, T. & Meester, L. de (2008) The genetic legacy of polyploid Bolivian Daphnia: the tropical Andes as a source for the North and South American D. pulicaria complex. Molecular ecology, 17, 1789-1800.
  • Mergeay, J., Verschuren, D. & Meester, L. de (2006) Invasion of an asexual American water flea clone throughout Africa and rapid displacement of a native sibling species. Proceedings. Biological sciences, 273, 2839-2844.
  • Moniez, R. (1889) Sur quelques Cladoceres et sur un Ostracode nouveaux du lac Titicaca. Revue Biologique du Nord de la France, 1, 419-429.
  • Paggi, J.C. (1996) Daphnia (Cienodaphnia) menucoensis (Anomopoda; Daphniidae): a new species from athalassic saline waters in Argentina. Hydrobiologia, 319, 137-147.
  • Paggi, J.C. (1999) Status and phylogenetic relationships of Daphnia sarsi Daday, 1902 (Crustacea: Anomopoda). Hydrobiologia, 403, 27-38.
  • Pereboev, D.D., Garibian, P.G., Karabanov, D.P., Efeykin, B.D., Galimov, Y.R., Petrusek, A. & Kotov, A.A. (2025) A non-monophyly of 'crowned' Daphnia (Ctenodaphnia) Dybowski et Grochowski, 1895 (Cladocera: Daphniidae): From genomes to morphology. Zoologica scripta, 54, 69-90.
  • Petrusek, A., Hobaek, A., Nilssen, J.P., Skage, M., Cerny, M., Brede, N. & Schwenk, K. (2008) A taxonomic reappraisal of the European Daphnia longispina complex (Crustacea, Cladocera, Anomopoda). Zoologica scripta, 37, 507-519.
  • Petrusek, A., Tollrian, R., Schwenk, K., Haas, A. & Laforsch, C. (2009) A "crown of thorns" is an inducible defense that protects Daphnia against an ancient predator. Proceedings of the National Academy of Sciences of the United States of America, 106, 2248-2252.
  • Sars, G.O. (1901) Contributions to the knowledge of the fresh-water Entomostraca of South America, as shown by artificial hatching from dried material. 1. Cladocera. Archiv for Mathematik og Naturvidenskab, 23, 1-102.
  • Seda, J. & Petrusek, A. (2011) Daphnia as a model organism in limnology and aquatic biology: some aspects of its reproduction and development. Journal of Limnology, 70, 335.
  • Smirnov, N.N. (2017) Physiology of the Cladocera. Second edition. Academic Press, Amsterdam, 1- 418.
  • Taylor, D.J., Finston, T.L. & Hebert, P.D.N. (1998) Biogeography of a widespread freshwater crustacean: Pseudocongruence and cryptic endemism in the North American Daphnia laevis complex. Evolution, 52, 1648-1670.
  • Wong, T.K., Ly-Trong, N., Ren, H., Banos, H., Roger, A.J., Susko, E., … & Minh, B.Q. (2025) IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models. Ecoevorxiv.org.
  • Ye, Z., Pfrender, M.E. & Lynch, M. (2023) Evolutionary Genomics of Sister Species Differing in Effective Population Sizes and Recombination Rates. Genome biology and evolution, 15.
  • Ye, Z., Williams, E., Zhao, C., Burns, C.W. & Lynch, M. (2021) The rapid, mass invasion of New Zealand by North American Daphnia "pulex". Limnology and oceanography, 66(7), 2672- 2683.