Unexpected mitochondrial lineage diversity within the genus Alonella Sars, 1862 (Crustacea: Cladocera) across the Northern Hemisphere

. 2021 ; 9 () : e10804. [epub] 20210201

Status PubMed-not-MEDLINE Jazyk angličtina Země Spojené státy americké Médium electronic-ecollection

Typ dokumentu časopisecké články

Perzistentní odkaz   https://www.medvik.cz/link/pmid33585083

Representatives of the genus Alonella Sars (Crustacea: Cladocera: Chydorinae) belong to the smallest known water fleas. Although species of Alonella are widely distributed and often abundant in acidic and mountain water bodies, their diversity is poorly studied. Morphological and genetic approaches have been complicated by the minute size of these microcrustaceans. As a result, taxonomists have avoided revising these species. Here, we present genetic data on Alonella species diversity across the Northern Hemisphere with particular attention to the A. excisa species complex. We analyzed 82 16S rRNA sequences (all newly obtained), and 78 COI sequences (39 were newly obtained). The results revealed at least twelve divergent phylogenetic lineages, possible cryptic species, of Alonella, with different distribution patterns. As expected, the potential species diversity of this genus is significantly higher than traditionally accepted. The A. excisa complex is represented by nine divergent clades in the Northern Hemisphere, some of them have relatively broad distribution ranges and others are more locally distributed. Our results provide a genetic background for subsequent morphological analyses, formal descriptions of Alonella species and detailed phylogeographical studies.

Zobrazit více v PubMed

Adamowicz SJ, Purvis A. How many branchiopod crustacean species are there? Quantifying the components of underestimation. Global Ecology and Biogeography. 2005;14(5):455–468. doi: 10.1111/j.1466-822X.2005.00164.x. DOI

Alonso M, Kotov AA. A new species of Alonella Sars, 1862 (Crustacea: Cladocera: Chydoridae) from the Ecuadorian Andes. Zootaxa. 2017;4290(3):1–11. doi: 10.11646/zootaxa.4290.3.11. DOI

Baas Becking LGM. Geobiologie of inleiding tot de Milieukunde. Den Haag: W.P. Van Stockum & Zoon; 1934. DOI

Ballinger MJ, Bruenn JA, Kotov AA, Taylor DJ. Selectively maintained paleoviruses in Holarctic water fleas reveal an ancient origin for phleboviruses. Virology. 2013;446:276–282. doi: 10.1016/j.virol.2013.07.032. PubMed DOI

Bekker EI, Karabanov DP, Galimov YR, Haag CR, Neretina TV, Kotov AA. Phylogeography of Daphnia magna Straus (Crustacea: Cladocera) in Northern Eurasia: Evidence for a deep longitudinal split between mitochondrial lineages. PLOS ONE. 2018;13(3):e0194045. doi: 10.1371/journal.pone.0194045. PubMed DOI PMC

Bekker EI, Karabanov DP, Galimov YR, Kotov AA. DNA barcoding reveals high cryptic diversity in the North Eurasian Moina species (Crustacea: Cladocera) PLOS ONE. 2016;11(8):e0161737. doi: 10.1371/journal.pone.0161737. PubMed DOI PMC

Bekker EI, Kotov AA, Taylor DJ. A revision of the subgenus Eurycercus (Eurycercus) Baird, 1843 emend. nov. (Cladocera: Eurycercidae) in the Holarctic with the description of a new species from Alaska. Zootaxa. 2012;3206(1):1–40. doi: 10.11646/zootaxa.3206.1.1. DOI

Belyaeva M, Taylor DJ. Cryptic species within the Chydorus sphaericus species complex (Crustacea: Cladocera) revealed by molecular markers and sexual stage morphology. Molecular Phylogenetics and Evolution. 2009;50(3):534–546. doi: 10.1016/j.ympev.2008.11.007. PubMed DOI

Blaxter M, Mann J, Chapman T, Thomas F, Whitton C, Floyd R, Abebe E. Defining operational taxonomic units using DNA barcode data. Philosophical Transactions of the Royal Society B: Biological Sciences. 2005;360(1462):1935–1943. doi: 10.1098/rstb.2005.1725. PubMed DOI PMC

Bolstad WM. Introduction to Bayesian statistics. 2nd edition. Hoboken, New Jersey: Wiley-Interscience; 2007.

Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten W, McGinnis SD, Mereshuk Y, Raytselis Y, Sayers EW, Tao T, Ye J, Raytselis Y. BLAST: a more efficient report with usability improvements. Nucleic Acids Research. 2013;41(W1):W29–W33. doi: 10.1093/nar/gkt282. PubMed DOI PMC

Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, Du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu C-H, Xie D, Zhang C, Stadler T, Drummond AJ. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLOS Computational Biology. 2019;15(4):e1006650. doi: 10.1371/journal.pcbi.1006650. PubMed DOI PMC

Čandek K, Kuntner M. DNA barcoding gap: reliable species identification over morphological and geographical scales. Molecular Ecology Resources. 2015;15(2):268–277. doi: 10.1111/1755-0998.12304. PubMed DOI

Chiambeng GY, Dumont HJ. The genus Pleuroxus Baird, 1843 (Crustacea: Anomopoda: Chydoridae) in Cameroon, Central-West Africa. Annales de Limnologie. 2004;40(3):211–229. doi: 10.1051/limn/2004019. DOI

Chiambeng GY, Dumont HJ. The Branchiopoda (Crustacea: Anomopoda, Ctenopoda and Cyclestherida) of the rain forests of Cameroon, West Africa: low abundances, few endemics and a boreal-tropical disjunction. Journal of Biogeography. 2005;32:1611–1620. doi: 10.1111/j.1365-2699.2005.01280.x. DOI

Cieplinski A, Weisse T, Obertegger U. High diversity in Keratella cochlearis (Rotifera, Monogononta): morphological and genetic evidence. Hydrobiologia. 2017;796(1):145–159. doi: 10.1007/s10750-016-2781-z. DOI

Collins RA, Boykin LM, Cruickshank RH, Armstrong KF. Barcoding’s next top model: an evaluation of nucleotide substitution models for specimen identification. Methods in Ecology and Evolution. 2012;3(3):457–465. doi: 10.1111/j.2041-210X.2011.00176.x. DOI

Costa FO, DeWaard JR, Boutillier J, Ratnasingham S, Dooh RT, Hajibabaei M, Hebert PD. Biological identifications through DNA barcodes: the case of the Crustacea. Canadian Journal of Fisheries and Aquatic Sciences. 2007;64(2):272–295. doi: 10.1139/f07-008. DOI

Crease TJ, Omilian AR, Costanzo KS, Taylor DJ. Transcontinental phylogeography of the Daphnia pulex species complex. PLOS ONE. 2012;7(10):e46620. doi: 10.1371/journal.pone.0046620. PubMed DOI PMC

Dlouhá S, Thielsch A, Kraus RHS, Seda J, Schwenk K, Petrusek A. Identifying hybridizing taxa within the Daphnia longispina species complex: a comparison of genetic methods and phenotypic approaches. Hydrobiologia. 2010;643(1):107–122. doi: 10.1007/s10750-010-0128-8. DOI

Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLOS Biologyl. 2006;4(5):e88. doi: 10.1371/journal.pbio.0040088. PubMed DOI PMC

Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution. 2012;29(8):1969–1973. doi: 10.1093/molbev/mss075. PubMed DOI PMC

Dumont HJ. Cladocera and free-living Copepoda from the Fouta Djalon and adjacent mountain ares in West Africa. Hydrobiologia. 1981;85(2):97–116. doi: 10.1007/BF00006620. DOI

Elías-Gutiérrez M, Valdez-Moreno M, Topan J, Young MR, Cohuo-Colli JA. Improved protocols to accelerate the assembly of DNA barcode reference libraries for freshwater zooplankton. Ecology and Evolution. 2018;8(5):3002–3018. doi: 10.1002/ece3.3742. PubMed DOI PMC

Faustova M. D. Phil. Thesis. 2017. Phylogeny, phylogeography and taxonomy of selected members of the family Bosminidae.

Faustova M, Sacherová V, Svensson JE, Taylor DJ. Radiation of European Eubosmina (Cladocera) from Bosmina (E.) longispina - concordance of multipopulation molecular data with paleolimnology. Limnology and Oceanography. 2011;56(2):440–450. doi: 10.4319/lo.2011.56.2.0440. DOI

Frey DG. Questions concerning cosmopolitanism in Cladocera. Archiv für Hydrobiologie. 1982;93(4):484–502.

Frey DG. The non-cosmopolitanism of chydorid Cladocera: implications for biogeography and evolution. In: Gore RH, Heck KL, editors. Crustacean biogeography (Crustacean issues 4) Rotterdam: A.A.Balkema; 1987. pp. 237–256.

Fu YX. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997;147(2):915–925. doi: 10.1093/genetics/147.2.915. PubMed DOI PMC

Fujisawa T, Aswad A, Barraclough TG. A rapid and scalable method for multilocus species delimitation using Bayesian model comparison and rooted triplets. Systematic Biology. 2016;65(5):759–771. doi: 10.1093/sysbio/syw028. PubMed DOI PMC

Fujisawa T, Barraclough TG. Delimiting species using single-locus data and the Generalized Mixed Yule Coalescent approach: a revised method and evaluation on simulated data sets. Systematic Biology. 2013;62(5):707–724. doi: 10.1093/sysbio/syt033. PubMed DOI PMC

Garibian PG, Neretina AN, Klimovsky AI, Kotov AA. A new case of West-East differentiation of the freshwater fauna in Northern Eurasia: the Pleuroxus trigonellus species group (Crustacea: Cladocera: Chydoridae) Zootaxa. 2018;4532(4):451–482. doi: 10.11646/zootaxa.4532.4.1. PubMed DOI

Garrigan D, Lewontin R, Wakeley J. Measuring the sensitivity of single-locus neutrality tests using a direct perturbation approach. Molecular Biology and Evolution. 2010;27(1):73–89. doi: 10.1093/molbev/msp209. PubMed DOI PMC

Hebert PD, Ratnasingham S, De Waard JR. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences. 2003;270(suppl_1):S96–S99. doi: 10.1098/rsbl.2003.0025. PubMed DOI PMC

Hebert PD, Stoeckle MY, Zemlak TS, Francis CM. Identification of birds through DNA barcodes. PLOS Biology. 2004;2(10):e312. doi: 10.1371/journal.pbio.0020312. PubMed DOI PMC

Heled J, Drummond AJ. Bayesian inference of species trees from multilocus data. Molecular Biology and Evolution. 2009;27(3):570–580. doi: 10.1093/molbev/msp274. PubMed DOI PMC

Hiruta SF, Kobayashi N, Katoh T, Kajihara H. Molecular phylogeny of cypridoid freshwater Ostracods (Crustacea: Ostracoda), inferred from 18S and 28S rDNA sequences. Zoological Science. 2016;33(2):179–185. doi: 10.2108/zs150103. PubMed DOI

Hoang DT, Chernomor O, Von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution. 2018;35(2):518–522. doi: 10.1093/molbev/msx281. PubMed DOI PMC

Hudec I. Anomopoda, Ctenopoda, Haplopoda, Onychopoda (Crustacea: Branchiopoda). Fauna Slovenska III. Bratislava: VEDA; 2010.

Huemer P, Mutanen M, Sefc KM, Hebert PD. Testing DNA barcode performance in 1000 species of European Lepidoptera: large geographic distances have small genetic impacts. PLOS ONE. 2014;9(12):e115774. doi: 10.1371/journal.pone.0115774. PubMed DOI PMC

Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Systematic Biology. 2012;61(6):1061–1067. doi: 10.1093/sysbio/sys062. PubMed DOI

Ishida S, Kotov AA, Taylor DJ. A new divergent lineage of Daphnia (Cladocera: Anomopoda) and its morphological and genetical differentiation from Daphnia curvirostris Eylmann, 1887. Zoological Journal of the Linnean Society. 2006;146(3):385–405. doi: 10.1111/j.1096-3642.2006.00214.x. DOI

Ishida S, Taylor DJ. Quaternary diversification in a sexual Holarctic zooplankter, Daphnia galeata. Molecular Ecology. 2007;16:569–582. doi: 10.1111/j.1365-294X.2006.03160.x. PubMed DOI

Jeffery NW, Elías-Gutiérrez M, Adamowicz SJ. Species diversity and phylogeographical affinities of the Branchiopoda (Crustacea) of Churchill, Manitoba, Canada. PLOS ONE. 2011;6(5):e18364. doi: 10.1371/journal.pone.0018364. PubMed DOI PMC

Jones G. Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent. Journal of Mathematical Biology. 2017;74(1–2):447–467. doi: 10.1007/s00285-016-1034-0. PubMed DOI

Kalyaanamoorthy S, Minh BQ, Wong TK, Haeseler Avon, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods. 2017;14(6):587–589. doi: 10.1038/nmeth.4285. PubMed DOI PMC

Kapli P, Lutteropp S, Zhang J, Kobert K, Pavlidis P, Stamatakis A, Flouri T. Multi-rate Poisson tree processes for single-locus species delimitation under maximum likelihood and Markov chain Monte Carlo. Bioinformatics. 2017;33(11):1630–1638. doi: 10.1093/bioinformatics/btx025. PubMed DOI PMC

Karabanov DP, Bekker EI, Shiel RJ, Kotov AA. Invasion of a Holarctic planktonic cladoceran Daphnia galeata Sars (Crustacea: Cladocera) in the Lower Lakes of South Australia. Zootaxa. 2018;4402(1):136–148. doi: 10.11646/zootaxa.4402.1.6. PubMed DOI

Karanovic T, Cooper SJ. Explosive radiation of the genus Schizopera on a small subterranean island in Western Australia (Copepoda: Harpacticoida): unravelling the cases of cryptic speciation, size differentiation and multiple invasions. Invertebrate Systematics. 2012;26(2):115–192. doi: 10.1071/IS11027. DOI

Kartavtsev YP. Barcode index number, taxonomic rank and modes of speciation: examples from fish. Mitochondrial DNA Part A. 2018;29(4):535–542. doi: 10.1080/24701394.2017.1315570. PubMed DOI

Katoh K, Standley DM. A simple method to control over-alignment in the MAFFT multiple sequence alignment program. Bioinformatics. 2016;32(13):1933–1942. doi: 10.1093/bioinformatics/btw108. PubMed DOI PMC

Kotov AA. Morphology and phylogeny of the Anomopoda (Crustacea: Cladocera) KMK Scientific Press Ltd; Moscow: 2013.

Kotov AA. Faunistic complexes of the Cladocera (Crustacea, Branchiopoda) of Eastern Siberia and the Far East of Russia. Biology Bulletin. 2016;43(9):970–987. doi: 10.1134/S1062359016090041. DOI

Kotov AA, Garibian PG, Bekker EI, Taylor DJ, Karabanov DP. 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, On-line First. 2020:zlaa046. doi: 10.1093/zoolinnean/zlaa046. DOI

Kotov AA, Ishida S, Taylor DJ. Revision of the genus Bosmina (Cladocera: Bosminidae), based on evidence from male morphological characters and molecular phylogenies. Zoological Journal of the Linnean Society. 2009;156(1):1–51. doi: 10.1111/j.1096-3642.2008.00475.x. DOI

Kotov AA, Karabanov DP, Bekker EI, Neretina TV, Taylor DJ. Phylogeography of the Chydorus sphaericus group (Cladocera: Chydoridae) in the Northern Palearctic. PLOS ONE. 2016;11(12):e0168711. doi: 10.1371/journal.pone.0168711. PubMed DOI PMC

Kotov AA, Taylor DJ. A new African lineage of the Daphnia obtusa group (Cladocera: Daphniidae) disrupts continental vicariance patterns. Journal of Plankton Research. 2010;32(6):937–949. doi: 10.1093/plankt/fbq018. DOI

Kotov AA, Taylor DJ. Contrasting endemism in pond-dwelling cyclic parthenogens: the Daphnia curvirostris species group (Crustacea: Cladocera) Scientific Reports. 2019;9(1):1–10. doi: 10.1093/plankt/fbq018. PubMed DOI PMC

Kotov AA, Van Damme K, Bekker EI, Siboualipha S, Silva-Briano M, dabache Ortiz AA, Galvándela Rosa R, Sanoamuang L. Cladocera (Crustacea: Branchiopoda) of Vientiane province and municipality, Laos. Journal of Limnology. 2013;72(s2):81–108. doi: 10.4081/jlimnol.2013.s2.e6. DOI

Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution. 2018;35(6):1547–1549. doi: 10.1093/molbev/msy096. PubMed DOI PMC

Lampert W. Daphnia: development of a model organism in ecology and evolution. Excellence in Ecology. 2011;21:1–250.

Lohse K. Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006) Systematic Biology. 2009;58(4):439–442. doi: 10.1093/sysbio/syp039. PubMed DOI

Maddison WP, Wiens JJ. Gene trees in species trees. Systematic Biology. 1997;46:523–536. doi: 10.1093/sysbio/46.3.523. DOI

Marková S, Dufresne F, Rees DJ, Černý M, Kotlík P. Cryptic intercontinental colonization in water fleas Daphnia pulicaria inferred from phylogenetic analysis of mitochondrial DNA variation. Molecular Phylogenetics and Evolution. 2007;44(1):42–52. doi: 10.1016/j.ympev.2006.12.025. PubMed DOI

Meier R, Shiyang K, Vaidya G, Ng PK. DNA barcoding and taxonomy in Diptera: a tale of high intraspecific variability and low identification success. Systematic Biology. 2006;55(5):715–728. doi: 10.1080/10635150600969864. PubMed DOI

Millette KL, Xu S, Witt JD, Cristescu ME. Pleistocene-driven diversification in freshwater zooplankton: Genetic patterns of refugial isolation and postglacial recolonization in Leptodora kindtii (Crustacea, Cladocera) Limnology and Oceanography. 2011;56(5):1725–1736. doi: 10.4319/lo.2011.56.5.1725. DOI

Mills S, Alcántara-Rodríguez JA, Ciros-Pérez J, Gómez A, Hagiwara A, Galindo KH, Jersabek C, Malekzadeh-Viayeh R, Leasi F, Lee J, Mark Welch D, Papakostas S, Riss S, Segers H, Serra M, Shiel R, Smolak R, Snell T, Stelzer C, Tang CQ, Wallace RL, Fontaneto D, Walsh EJ, Welch DBM. Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy. Hydrobiologia. 2017;796(1):39–58. doi: 10.1007/s10750-016-2725-7. DOI

Molloy EK, Warnow T. To include or not to include: the impact of gene filtering on species tree estimation methods. Systematic Biology. 2018;67(2):285–303. doi: 10.1093/sysbio/syx077. PubMed DOI

Montoliu-Elena L, Elías-Gutiérrez M, Silva-Briano M. Moina macrocopa (Straus, 1820): a species complex of a common Cladocera, highlighted by morphology and DNA barcodes. Limnetica. 2019;38(1):253–277. doi: 10.23818/limn.38.19. DOI

Nei M, Kumar S. Molecular evolution and phylogenetics. Oxford university press; 2000.

Neretina AN, Garibian PG, Romero M, Mondragón DM, Silva-Briano M. A record of Disparalona hamata (Birge, 1879) (Cladocera: Chydoridae) in phytotelmata of Tillandsia aguascalentensis Gardner, 1984 (Poales: Bromeliaceae) Zootaxa. 2019;4567(2):347–357. doi: 10.11646/zootaxa.4567.2.7. PubMed DOI

Neretina AN, Garibian PG, Sinev AY, Kotov AA. Diversity of the subgenus Disparalona (Mixopleuroxus) Hudec, 2010 (Crustacea: Cladocera) in the new and old world. Journal of Natural History. 2018;52(3–4):155–205. doi: 10.1080/00222933.2017.1411987. DOI

Neretina AN, Kotov AA. A new species of Acroperus Baird, 1843 (Cladocera: Chydoridae) from Africa. Zootaxa. 2015;4039(4):516–528. doi: 10.11646/zootaxa.4039.4.2. PubMed DOI

Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution. 2015;32(1):268–274. doi: 10.1093/molbev/msu300. PubMed DOI PMC

Ni Y, Ma X, Hu W, Blair D, Yin M. New lineages and old species: lineage diversity and regional distribution of Moina (Crustacea: Cladocera) in China. Molecular Phylogenetics and Evolution. 2019;134:87–98. doi: 10.1016/j.ympev.2019.02.007. PubMed DOI

Petrusek A, Černy M, Audenaert E. Large intercontinental differentiation of Moina micrura (Crustacea: Anomopoda): one less cosmopolitan cladoceran? Hydrobiologia. 2004;526:73–81. doi: 10.1023/B:HYDR.0000041612.08425.f0. DOI

Petrusek A, Hobæk A, Nilssen JP, Skage M, Černý M, Brede N, Schwenk K. A taxonomic reappraisal of the European Daphnia longispina complex (Crustacea, Cladocera, Anomopoda) Zoologica Scripta. 2008;37:507–519. doi: 10.1111/j.1463-6409.2008.00336.x. DOI

Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, Hazell S, Kamoun S, Sumlin WD, Vogler AP. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology. 2006;55(4):595–609. doi: 10.1080/10635150600852011. PubMed DOI

Popova EV, Petrusek A, Kořínek V, Mergeay J, Bekker EI, Karabanov DP, Galimov YR, Neretina TV, Taylor DJ, Kotov AA. Revision of the Old World Daphnia (Ctenodaphnia) similis group (Cladocera: Daphniidae) Zootaxa. 2016;4161(1):1–40. doi: 10.11646/zootaxa.4161.1.1. PubMed DOI

Posada D, Buckley TR. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology. 2004;53(5):793–808. doi: 10.1080/10635150490522304. PubMed DOI

Posada D, Crandall KA. Selecting the best-fit model of nucleotide substitution. Systematic Biology. 2001;50(4):580–601. doi: 10.1080/10635150118469. PubMed DOI

Powell JR. Accounting for uncertainty in species delineation during the analysis of environmental DNA sequence data. Methods in Ecology and Evolution. 2012;3(1):1–11. doi: 10.1111/j.2041-210X.2011.00122.x. DOI

Prosser S, Martínez-Arce A, Elías-Gutiérrez M. A new set of primers for COI amplification from freshwater microcrustaceans. Molecular Ecology Resources. 2013;13(6):1151–1155. doi: 10.1111/1755-0998.12132. PubMed DOI

Puillandre N, Lambert A, Brouillet S, Achaz G. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology. 2012;21(8):1864–1877. doi: 10.1111/j.1365-294X.2011.05239.x. PubMed DOI

Rambaut A, Drummond AJ, Xie D, Baele G, Suchard MA. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Systematic Biology. 2018;67(5):901–904. doi: 10.1093/sysbio/syy032. PubMed DOI PMC

Ramírez-Soriano A, Ramos-Onsins SE, Rozas J, Calafell F, Navarro A. Statistical power analysis of neutrality tests under demographic expansions, contractions and bottlenecks with recombination. Genetics. 2008;179(1):555–567. doi: 10.1534/genetics.107.083006. PubMed DOI PMC

Ramos-Onsins SE, Rozas J. Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution. 2002;19(12):2092–2100. doi: 10.1093/oxfordjournals.molbev.a004034. PubMed DOI

Ratnasingham S, Hebert PD. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLOS ONE. 2013;8(7):e66213. doi: 10.1371/journal.pone.0066213. PubMed DOI PMC

Reid NM, Carstens BC. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evolutionary Biology. 2012;12(1):196. doi: 10.1186/1471-2148-12-196. PubMed DOI PMC

Rey J, Saint-Jean L. Les Cladocères (Crustacés, Branchiopodes) du Tchad. Cahiers ORSTOM. série Serie Hydrobiologie. 1968;2(3/4):79–118.

Rokas A, Williams BL, King N, Carroll SB. Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature. 2003;425(6960):798–804. doi: 10.1038/nature02053. PubMed DOI

Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, Librado P, Ramos-Onsins SE, Sánchez-Gracia A. DnaSP 6: DNA sequence polymorphism analysis of large data sets. Molecular Biology and Evolution. 2017;34(12):3299–3302. doi: 10.1093/molbev/msx248. PubMed DOI

Sacherová V, Hebert PDN. The evolutionary history of the Chydoridae (Crustacea: Cladocera) Biological Journal of the Linnean Society. 2003;79:629–643. doi: 10.1046/j.1095-8312.2003.00216.x. DOI

Sarver BA, Pennell MW, Brown JW, Keeble S, Hardwick KM, Sullivan J, Harmon LJ. The choice of tree prior and molecular clock does not substantially affect phylogenetic inferences of diversification rates. PeerJ. 2019;7:e6334. doi: 10.7717/peerj.6334. PubMed DOI PMC

Schwenk K, Sand A, Boersma M, Brehm M, Mader E, Offerhaus D, Spaak P. Genetic markers, genealogies and biogeographic patterns in the Cladocera. Aquatic Ecology. 1998;32(1):37–51. doi: 10.1023/A:1009939901198. DOI

Schwentner M, Rabet N, Richter S, Giribet G, Padhye S, Cart JF, et al. Rogers DC. Phylogeny and Biogeography of Spinicaudata (Crustacea: Branchiopoda) Zoological Studies. 2020;59(44):2020–2059. doi: 10.6620/ZS.2020.59-44. PubMed DOI PMC

Scornavacca C, Zickmann F, Huson DH. Tanglegrams for rooted phylogenetic trees and networks. Bioinformatics. 2011;27(13):i248–i256. doi: 10.1093/bioinformatics/btr210. PubMed DOI PMC

Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Flook P. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals of the entomological Society of America. 1994;87(6):651–701. doi: 10.1093/aesa/87.6.651. DOI

Sinev AY, Karabanov DP, Kotov AA. A new North Eurasian species of the Alona affinis complex (Cladocera: Chydoridae) Zootaxa. 2020;4767(1):115–137. doi: 10.11646/zootaxa.4767.1.5. PubMed DOI

Smirnov NN. Chydoridae fauni mira. Fauna SSSR. Rakoobraznie. 1971;1(2):1–531.

Smirnov NN. Cladocera: the Chydorinae and Sayciinae (Chydoridae) of the world. Guides to the identification of the microivertebrates of the Continental Waters of the world. SPB Academic Publishing, Amsterdam. 1996;11:1–197.

Smirnov NN, Kotov AA. The morphological radiation of setae in the Cladocera (Crustacea) and their potential for morphogenesis. International Review of Hydrobiology. 2010;95(6):482–519. doi: 10.1002/iroh.201011244. DOI

Steel M, McKenzie A. Properties of phylogenetic trees generated by Yule-type speciation models. Mathematical Biosciences. 2001;170(1):91–112. doi: 10.1016/S0025-5564(00)00061-4. PubMed DOI

Sukumaran J, Knowles LL. Multispecies coalescent delimits structure, not species. Proceedings of the National Academy of Sciences of the United States of America. 2017;114(7):1607–1612. doi: 10.1073/pnas.1607921114. PubMed DOI PMC

Sweet AD, Boyd BM, Allen JM, Villa SM, Valim MP, Rivera-Parra JL, Wilson RE, Johnson KP. Integrating phylogenomic and population genomic patterns in avian lice provides a more complete picture of parasite evolution. Evolution. 2018;72(1):95–112. doi: 10.1111/evo.13386. PubMed DOI

Tang CQ, Humphreys AM, Fontaneto D, Barraclough TG. Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data. Methods in Ecology and Evolution. 2014;5(10):1086–1094. doi: 10.1111/2041-210X.12246. PubMed DOI PMC

Taylor DJ, Hebert PDN. Cryptic intercontinental hybridization in Daphnia (Crustacea): the ghost of introductions past. Proceedings of the Royal Society of London, Series B-Biological Sciences. 1993;254:163–168. doi: 10.1098/rspb.1993.0141. DOI

Trifinopoulos J, Nguyen LT, Von Haeseler A, Minh BQ. W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Research. 2016;44(W1):W232–W235. doi: 10.1093/nar/gkw256. PubMed DOI PMC

Vaidya G, Lohman DJ, Meier R. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics. 2011;27(2):171–180. doi: 10.1111/j.1096-0031.2010.00329.x. PubMed DOI

Van Damme K, Eggermont H. The Afromontane Cladocera (Crustacea: Branchiopoda) of the Rwenzori (Uganda–DR Congo): taxonomy, ecology and biogeography. Hydrobiologia. 2011;676(1):57–100. doi: 10.1007/s10750-011-0892-0. DOI

Vitecek S, Kučinić M, Previšić A, Živić I, Stojanović K, Keresztes L, Bálint M, Hoppeler F, Waringer J, Graf W, Pauls SU. Integrative taxonomy by molecular species delimitation: multi-locus data corroborate a new species of Balkan Drusinae micro-endemics. BMC Evolutionary Biology. 2017;17(1):129. doi: 10.1186/s12862-017-0972-5. PubMed DOI PMC

Warren DL, Geneva AJ, Lanfear R. RWTY (R We There Yet): an R package for examining convergence of Bayesian phylogenetic analyses. Molecular Biology and Evolution. 2017;34(4):1016–1020. doi: 10.1093/molbev/msw279. PubMed DOI

Xu L, Han BP, Van Damme K, Vierstraete A, Vanfleteren JR, Dumont HJ. Biogeography and evolution of the Holarctic zooplankton genus Leptodora (Crustacea: Branchiopoda: Haplopoda) Journal of Biogeography. 2011;38(2):359–370. doi: 10.1111/j.1365-2699.2010.02409. DOI

Xu S, Hebert PDN, Kotov AA, Cristescu ME. The noncosmopolitanism paradigm of freshwater zooplankton: insights from the global phylogeography of the predatory cladoceran Polyphemus pediculus (Linnaeus, 1761) (Crustacea, Onychopoda) Molecular Ecology. 2009;18(24):5161–5179. doi: 10.1111/j.1365-294X.2009.04422.x. PubMed DOI

Yin M, Wan X, Ma X, Gießler S, Petrusek A, Griebel J, Hu W, Wolinska J. Cytonuclear diversity and shared mitochondrial haplotypes among Daphnia galeata populations separated by seven thousand kilometres. BMC Evolutionary Biology. 2018;18(1):130. doi: 10.1186/s12862-018-1256-4. PubMed DOI PMC

Zhang J, Kapli P, Pavlidis P, Stamatakis A. A general species delimitation method with applications to phylogenetic placements. Bioinformatics. 2013;29(22):2869–2876. doi: 10.1093/bioinformatics/btt499. PubMed DOI PMC

Zhang C, Rabiee M, Sayyari E, Mirarab S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinformatics. 2018;19(6):153. doi: 10.1186/s12859-018-2129-y. PubMed DOI PMC

Zuykova EI, Simonov EP, Bochkarev NA, Abramov SA, Sheveleva NG, Kotov AA. Contrasting phylogeographic patterns and demographic history in closely related species of Daphnia longispina group (Crustacea: Cladocera) with focus on North-Eastern Eurasia. PLOS ONE. 2018;13(11):e0207347. doi: 10.1371/journal.pone.0207347. PubMed DOI PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...