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Published December 23, 2021 | Version v1
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Phylogenetic analyses of a new freshwater amphipod reveal polyphyly within the Holarctic family Crangonyctidae, with revision of the genus Synurella

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Cannizzaro, Andrew G., Daniels, James D., Berg, David J. (2022): Phylogenetic analyses of a new freshwater amphipod reveal polyphyly within the Holarctic family Crangonyctidae, with revision of the genus Synurella. Zoological Journal of the Linnean Society 195: 1100-1115, DOI: 10.1093/zoolinnean/zlab092

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URL
https://www.checklistbank.org/dataset/121548
LSID
urn:lsid:zoobank.org:pub:739B6641-EC53-470C-86B8-8D27CA9E7B3E
LSID
urn:lsid:plazi.org:pub:FFB4FFC02F48DA67DE5ACE189864BA43
URL
http://publication.plazi.org/id/FFB4FFC02F48DA67DE5ACE189864BA43

Cites
Publication: 10.14284/368 (DOI)
Has part
Taxonomic treatment: 10.5281/zenodo.6986033 (DOI)
Taxonomic treatment: urn:lsid:zoobank.org:act:9E1F37D8-3DF2-458A-B7E7-3A3B43B43738 (LSID)
Taxonomic treatment: http://treatment.plazi.org/id/038D87B82F4BDA62DDBCCB3B9AA5BEB7 (URL)
Taxonomic treatment: 10.5281/zenodo.6986043 (DOI)
Taxonomic treatment: urn:lsid:zoobank.org:act:AF8DF95F-3679-4C14-B754-506892A1CED5 (LSID)
Taxonomic treatment: http://treatment.plazi.org/id/038D87B82F4DDA6BDF47CB289DE9BD04 (URL)
Dataset: http://table.plazi.org/id/DF5B66262F4ADA65DEFEC84E9C46BC2F (URL)
Figure: 10.5281/zenodo.6993750 (DOI)
Figure: 10.5281/zenodo.6993754 (DOI)
Figure: 10.5281/zenodo.6993756 (DOI)
Figure: 10.5281/zenodo.6993758 (DOI)
Figure: 10.5281/zenodo.6993760 (DOI)
Figure: 10.5281/zenodo.6993762 (DOI)
Figure: 10.5281/zenodo.6993764 (DOI)
Figure: 10.5281/zenodo.6993768 (DOI)
Figure: 10.5281/zenodo.6993770 (DOI)
Figure: 10.5281/zenodo.6993772 (DOI)
Dataset: http://table.plazi.org/id/DF5B66262F43DA6CDECBCEDC99BEBAB4 (URL)
Is source of
Dataset: https://www.gbif.org/dataset/fad80260-3167-49ea-b797-87292773a923 (URL)

References

  • Abramoff MD, Magalhaes PJ, Ram SJ. 2004. Image processing with ImageJ. Biophotonics International 11: 36-42.
  • Adams NE, Inoue K, Seidel RA, Lang BK, Berg DJ. 2018. Isolation drives increased diversification rates in freshwater amphipods. Molecular Phylogenetics and Evolution 127: 747-757.
  • Bouckaert R, Drummond AJ. 2017. bModelTest: Bayesian phylogenetic site model averaging and model comparison. BMC Evolutionary Biology 17: 42.
  • Bouckaert R, Heled J, Kuhnert D, Vaughan T, Wu C-H, Xie D, Suchard MA, Rambaut A, Drummond AJ. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology 10: e1003537.
  • Cannizzaro AG, Balding D, Lazo-Wasem EA, Sawicki TR. 2019. Morphological and molecular analyses reveal a new species of stygobitic amphipod in the genus Crangonyx (Crustacea: Crangonyctidae) from Jackson County, Florida, with a redescription of Crangonyx floridanus and notes on its taxonomy and biogeography. Journal of Natural History 53: 1-49.
  • Cannizzaro AG, Balding D, Lazo-Wasem EA, Sawicki TR. 2020. A redescription of Hobb's cave amphipod, Crangonyx hobbsi Shoemaker, 1941 (Amphipoda: Senticaudata: Crangonyctidae), including genetic sequence data for mitochondrial and nuclear genes and notes on its ecology. Proceedings of the Biological Society of Washington 132: 73-95.
  • Cannizzaro AG, Sawicki TR. 2019. Two new species of the genus Crangonyx Bate, 1859 (Amphipoda: Crangonyctidae) from the St. Marks River Basin with notes on the 'Crangonyx floridanus complex'. Zootaxa 4691: 301-332.
  • Cole GA. 1980. The mandibular palps of North American freshwater species of Gammarus. Crustaceana Supplement 4: 68-83.
  • Copilas- Ciocianu D, Sidorov D, Gontcharov A. 2019. Adrift across tectonic plates: molecular phylogenetics supports the ancient Laurasian origin of old limnic crangonyctid amphipods. Organisms Diversity & Evolution 19: 191-207.
  • Dinno A. 2012. Paran: Horn's test of principal components/ factors. Available at : https://CRAN.R-project .org / package=paran
  • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
  • Englisch U, Koenemann S. 2001. Preliminary phylogenetic analysis of selected subterranean amphipod crustacean, using small subunit rDNA gene sequences. Organisms Diversity & Evolution 1: 139-145.
  • Ezard T, Fujisawa T, Barraclough T. 2013. Splits: species' limits by threshold statistics. Available at: http://r-forge.rproject.org/projects/splits/
  • Flot JF, Worheide G, Dattagupta S. 2010. Unsuspected diversity of Niphargus amphipods in the chemoautotrophic cave ecyostems of Frasassi, central Italy. BMC Evolutionary Biology 10: 171.
  • Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology 3: 294-299.
  • Gibson R, Hutchins BT, Krejca JK, Diaz PH, Sprouse PS. 2021. Stygobromus bakeri, a new species of groundwater amphipod (Amphipoda, Crangonyctidae) associated with the Trinity and Edwards aquifers of central Texas, USA. Subterranean Biology 38: 19-45.
  • Guindon S, Dufayard JF, 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.
  • Holsinger JR. 1977. A review of the systematics of the Holarctic amphipod family Crangonyctidae. Crustaceana Supplement 4: 244-277.
  • Holsinger JR, Shafer J, Fong DW, Culver DC. 2008. Gammarus cohabitus, a new species of subterranean amphipod crustacean (Gammaridae) from groundwater habitats in central Pennsylvania, USA. Subterranean Biology 6: 31-41.
  • Horton T, Lowry J, De Broyer C, Bellan-Santini D, Coleman CO, Corbari L, Costello MJ, Daneliya M, Dauvin J-C, Fiser C, Gasca R, Grabowski M, Guerra- Garcia JM, Hendrycks E, Hughes L, Jaume D, Jazdzewski K, Kim Y-H, King R, Krapp-Schickel T, LeCroy S, Lorz AM, Mamos T, Senna AR, Serejo C, Sket B, Souza-Filho JF, Tandberg AH, Thomas JD, Thurston M, Vader W, Vainola R, Vonk R, White K, Zeidler W. 2021. World Amphipoda database. Available at: http://www. marinespecies.org/amphipoda on 2020-05-31. doi:10.14284/368.
  • Hou Z, Fu J, Li S. 2007. A molecular phylogeny of the genus Gammarus (Crustacea: Amphipoda) based on mitochondrial and nuclear gene sequences. Molecular Phylogenetics and Evolution 45: 596-611.
  • Hou Z, Sket B, Fiser C, Li S. 2011. Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification. Proceedings of the National Academy of Sciences of the United States of America 108: 14533-14538.
  • Karaman GS. 1969. XXII. Beitrag zur kenntnis der amphipoden. uber einige neue formen des genus Sarathrogammarus (Gammaridae) aus Afghanistan. Acta Musei Macedonici Scientiarium Naturalium 6: 195-208.
  • Katoh K, Kuma K, Toh H, Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Research 33: 511-518.
  • Kornobis E, Passon S, Sidorov DA, Holsinger JR, Kristjansson BK. 2011. Molecular taxonomy and phylogenetic affinities of two groundwater amphipods, Crangonyx islandicus and Crymostygius thingvallensis, endemic to Iceland. Molecular Phylogenetics and Evolution 58: 527-539.
  • Liu K, Warnow TJ. 2014. Large-scale multiple sequence alignment and tree estimation using SATe. In: Russel DJ, ed. Multiple sequence alignment methods. Totowa: Humana Press, 219-244.
  • Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR. 2012. SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Systematic Biology 61: 90-106.
  • Macdonald KS III, Yampolsky L, Duffy JE. 2005. Molecular and morphological evaluation of the amphipod radiation of Lake Baikal. Molecular Phylogenetics and Evolution 35: 323-343.
  • Marin I, Palatov DM. 2021. Volgonyx gen. n. and Pontonyx gen. n., two new genera of the family Crangonyctidae (Crustacea: Amphipoda) from the southeastern Europe. Arthropoda Selecta 30: 43-61.
  • Michonneau F, Bolker B, Holder M, Lewis P, O'Meara B. 2016. Rncl: an interface to the nexus class library. Available at: https://CRAN.R-project.org/package=rncl
  • Minh BQ, Nguyen MA, von Haeseler A. 2013. Ultrafast approximation for phylogenetic bootstrap. Molecular Biology and Evolution 30: 1188-1195.
  • Mirarab S, Nguyen N, Guo S, Wang LS, Kim J, Warnow T. 2015. PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. Journal of Computational Biology 22: 377-386.
  • Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. 2015. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268-274.
  • Owen TM, Owen MB. 1921. History of Alabama and Dictionary of Alabama biography, Vol. 1. Chicago: S. J. Clarke Publishing Company.
  • Palatov DM, Marin IN. 2020. A new genus of the family Crangonyctidae (Crustacea,Amphipoda) from the Palaearctic, with descriptions of two new species from the foothills of the Altai mountains. Zoologicheski i Zhurnal 99: 1160-1186.
  • Paradis E, Claude J, Strimmer K. 2004. APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.
  • Price MN, Dehal PS, Arkin AP. 2010. FastTree 2 - approximately maximum-likelihood trees for large alignments. PLoS One 5: e9490.
  • Puillandre N, Brouillet S, Achaz G. 2021. ASAP: assemble species by automatic partitioning. Molecular Ecology Resources 21: 609-620.
  • Puillandre N, Lambert A, Brouillet S, Achaz G. 2012. ABGD, automatic barcode gap discovery for primary species delimitation. Molecular Ecology 21: 1864-1877.
  • Rambaut A, Suchard M, Xie W, Drummond A. 2014. Tracer v.1.6. Edinburgh: Institute of Evolutionary Biology, University of Edinburgh.
  • Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
  • Seidel RA, Lang BK, Berg DJ. 2009. Phylogeographic analysis reveals multiple cryptic species of amphipods (Crustacea: Amphipoda) in Chihuahuan Desert springs. Biological Conservation 142: 2303-2313.
  • Shimodaria H, Hasegawa M. 1999. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution 16: 1114-1116.
  • Steele DH, Steele VJ. 1991. The structure and organization of the gills of gammaridean Amphipoda. Journal of Natural History 25: 1247-1258.
  • Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Systematic Biology 56: 564-577.
  • Vaidya G, Lohman DJ, Meier R. 2011. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics 27: 171-180.
  • Vainola R, Witt JDS, Grabowski M, Bradbury JH, Jazdzewski K, Sket B. 2007. Global diversity of amphipods (Amphipoda: Crustacea) in freshwater. In: Balian EV, Leveque C, Segers H, Marten K, eds. Freshwater Animal Diversity Assessment. Dordrecht: Springer.
  • Wheeler TJ, Kececioglu JD. 2007. Multiple alignment by aligning alignments. Bioinformatics 23: i559-i568.
  • White KN. 2011. Nuclear 18S rDNA as a species-level molecular marker for Leucothoidae (Amphipoda). Journal of Crustacean Biology 31: 710-716.
  • Witt JDS, Herbert PD. 2000. Cryptic species diversity and evolution in the amphipod genus Hyalella within central glaciated North America: a molecular phylogenetic approach. Canadian Journal of Fisheries and Aquatic Science 57: 687-698.
  • Zhang J, Kapli P, Pavlidis P, Stamatakis A. 2012. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869-2976.