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Cited by 138Fish Biology and Ecology StudiesGenomics and Phylogenetic StudiesEvolution and Paleontology Studies

Resolving Cypriniformes relationships using an anchored enrichment approach

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Stout, Carla C., Tan, Milton, Lemmon, Alan R., Lemmon, Emily Moriarty, Armbruster, Jonathan W.·2016·BMC Evolutionary Biology
DOI 10.1186/s12862-016-0819-5PMC PMC5103605
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Abstract

BACKGROUND: Cypriniformes (minnows, carps, loaches, and suckers) is the largest group of freshwater fishes in the world (~4300 described species). Despite much attention, previous attempts to elucidate relationships using molecular and morphological characters have been incongruent. In this study we present the first phylogenomic analysis using anchored hybrid enrichment for 172 taxa to represent the order (plus three out-group taxa), which is the largest dataset for the order to date (219 loci, 315,288 bp, average locus length of 1011 bp). RESULTS: Concatenation analysis establishes a robust tree with 97 % of nodes at 100 % bootstrap support. Species tree analysis was highly congruent with the concatenation analysis with only two major differences: monophyly of Cobitoidei and placement of Danionidae. CONCLUSIONS: Most major clades obtained in prior molecular studies were validated as monophyletic, and we provide robust resolution for the relationships among these clades for the first time. These relationships can be used as a framework for addressing a variety of evolutionary questions (e.g. phylogeography, polyploidization, diversification, trait evolution, comparative genomics) for which Cypriniformes is ideally suited.

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  • C. molitorella has a sister group relationship with Labeo.

    “For C. molitorella, a sister group relationship with Labeo (103, 104) justified its replacement by the most phylogenetically proximate Labeo species in our dataset, minimizing the divergence introduced by this substitution.”

    From Convergent genome streamlining accompanies independent miniaturization in the world’s smallest fishes (2026) · cites this paper as [103]

    The Discussion > Cyprinidae passage reports that Cirrhinus is non-monophyletic, but does not identify C. molitorella or place it as sister to Labeo. Searches for “Cirrhinus molitorella Labeo sister” and “molitorella” found no passage in our copy establishing that species-specific relationship; page numbers were not provided. (LLM, conf=0.72)

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  1. [1]Mayden RL Chen W-J The world’s smallest vertebrate species of the genus Paedocypris: a new family of freshwater fishes and the sister group to the world’s most diverse clade of freshwater fishes (Teleostei: Cypriniformes) Mol Phylogenet Evol 2010 57 152 75 10.1016/j.ympev.2010.04.008 20398777 · DOI
  2. [3]Mayden RL Chen W-J Bart HL Doosey MH Simons AM Tang KL Reconstructing the phylogenetic relationships of the earth’s most diverse clade of freshwater fishes—order Cypriniformes (Actinopterygii: Ostariophysi): A case study using multiple nuclear loci and the mitochondrial genome Mol Phylogenet Evol 2009 51 500 14 10.1016/j.ympev.2008.12.015 19141325 · DOI
  3. [4]Saitoh K Sado T Doosey MH Bart HL Jr Inoue JG Nishida M Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi) J Linn Soc London Zool 2011 161 633 62 10.1111/j.1096-3642.2010.00651.x · DOI
  4. [5]Betancur-R R, Broughton RE, Wiley EO, Carpenter K, López JA, Li C, et al. The tree of life and a new classification of bony fishes. PLoS Curr. 2013;5. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288. PMC3644299 23653398 · DOI
  5. [6]Betancur-R R, Wiley EO, Bailly N, Miya M, Lecointre G, Orti G. Phylogenetic Classification of Bony Fishes — Version 3. https://sites.google.com/site/guilleorti/home/classification. Accessed 17 Mar 2016. PMC5501477 28683774
  6. [7]Tang KL Agnew MK Hirt MV Lumbantobing DN Raley ME Sado T Limits and phylogenetic relationships of East Asian fishes in the subfamily Oxygastrinae (Teleostei: Cypriniformes: Cyprinidae) Zootaxa 2013 3681 101 10.11646/zootaxa.3681.2.1 25232592 · DOI
  7. [9]van der Laan R Eschmeyer WN Fricke R Family-group names of recent fishes Zootaxa 2014 3882 1 10.11646/zootaxa.3882.1.1 25543675 · DOI
  8. [10]Yang L Sado T Hirt MV Pasco-Viel E Arunachalam M Li J Phylogeny and polyploidy: resolving the classification of cyprinine fishes (Teleostei: Cypriniformes) Mol Phylogenet Evol 2015 85 97 116 10.1016/j.ympev.2015.01.014 25698355 · DOI
  9. [11]Mayden RL Tang KL Conway KW Phylogenetic relationships of Danio within the order Cypriniformes: a framework for comparative and evolutionary studies of a model species J Exp Biol 2007 308B 642 54 17554749
  10. [12]Schönhuth S Mayden RL Phylogenetic relationships in the genus Cyprinella (Actinopterygii: Cyprinidae) based on mitochondrial and nuclear gene sequences Mol Phylogenet Evol 2010 55 77 98 10.1016/j.ympev.2009.10.030 19903533 · DOI
  11. [13]Bufalino AP Mayden RL Molecular phylogenetics of North American phoxinins (Actinopterygii: Cypriniformes: Leuciscidae) based on RAG1 and S7 nuclear DNA sequence data Mol Phylogenet Evol 2010 55 274 83 10.1016/j.ympev.2009.12.017 20040376 · DOI
  12. [14]Tang KL Agnew MK Chen W-J Hirt MV Raley ME Sado T Phylogeny of the gudgeons (Teleostei: Cyprinidae: Gobioninae) Mol Phylogenet Evol 2011 61 103 24 10.1016/j.ympev.2011.05.022 21672635 · DOI
  13. [15]Tang Q Xiong B Yang X Liu H Phylogeny of the East Asian botiine loaches (Cypriniformes, Botiidae) inferred from mitochondrial cytochrome b gene sequences Hydrobiologia 2005 544 249 58 10.1007/s10750-005-0863-4 · DOI
  14. [16]Pramuk JB Grose MJ Clarke AL Greenbaum E Bonaccorso E Guayasamin JM Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes Mol Phylogenet Evol 2007 42 287 97 10.1016/j.ympev.2006.06.008 16876442 · DOI
  15. [17]Slechtová V Bohlen J Perdices A Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): Delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism Mol Phylogenet Evol 2008 47 812 31 10.1016/j.ympev.2007.12.018 18255319 · DOI
  16. [18]Doosey MH Bart HL Jr Saitoh K Miya M Phylogenetic relationships of catostomid fishes (Actinopterygii: Cypriniformes) based on mitochondrial ND4/ND5 gene sequences Mol Phylogenet Evol 2010 54 1028 34 10.1016/j.ympev.2009.06.006 19527790 · DOI
  17. [19]Tang KL Agnew MK Hirt MV Sado T Schneider LM Freyhof J Systematics of the subfamily Danioninae (Teleostei: Cypriniformes: Cyprinidae) Mol Phylogenet Evol 2010 57 189 214 10.1016/j.ympev.2010.05.021 20553898 · DOI
  18. [20]Britz R Conway KW Osteology of Paedocypris, a miniature and highly developmentally truncated fish (Teleostei: Ostariophysi: Cyprinidae) J Morphol 2009 270 389 412 10.1002/jmor.10698 19107939 · DOI · Paper page
  19. [21]Britz R Conway KW Rüber L Miniatures, morphology and molecules: Paedocypris and its phylogenetic position (Teleostei, Cypriniformes) J Linn Soc London Zool 2014 172 556 615 10.1111/zoj.12184 · DOI
  20. [23]Tao W Zou M Wang X Gan X Mayden RL He S Phylogenomic analysis resolves the formerly intractable adaptive diversification of the endemic clade of east asian cyprinidae (Cypriniformes). Rankin DJ, editor PLoS One 2010 5 e13508 10.1371/journal.pone.0013508 20976012 PMC2958143 · DOI
  21. [24]Cunha C Mesquita N Dowling TE Gilles A Coelho MM Phylogenetic relationships of Eurasian and American cyprinids using cytochrome b sequences J Fish Biol 2002 61 1 16 10.1111/j.1095-8649.2002.tb01853.x · DOI
  22. [25]Liu H Chen Y Phylogeny of the East Asian cyprinids inferred from sequences of the mitochondrial DNA control region Can J Zool 2003 81 1938 46 10.1139/z03-169 · DOI
  23. [26]Saitoh K Sado T Mayden RL Hanzawa N Nakamura K Nishida M Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world’s largest freshwater fish clade based on 59 whole mitogenome sequences J Mol Evol 2006 63 826 41 10.1007/s00239-005-0293-y 17086453 · DOI
  24. [27]Thai BT Si VN Phan PD Austin CM Phylogenetic evaluation of subfamily classification of the Cyprinidae focusing on Vietnamese species Aquat Living Resour 2007 20 143 53 10.1051/alr:2007025 · DOI
  25. [28]Wang X Li J He S Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences Mol Phylogenet Evol 2007 42 157 70 10.1016/j.ympev.2006.06.014 16919973 · DOI
  26. [30]Chen W-J Mayden RL Molecular systematics of the Cyprinoidea (Teleostei: Cypriniformes), the world’s largest clade of freshwater fishes: Further evidence from six nuclear genes Mol Phylogenet Evol 2009 52 544 9 10.1016/j.ympev.2009.01.006 19489125 · DOI
  27. [31]Fang F Norén M Liao TY Källersjö M Kullander SO Molecular phylogenetic interrelationships of the south Asian cyprinid genera Danio, Devario and Microrasbora (Teleostei, Cyprinidae, Danioninae) Zool Scr 2009 38 237 56 10.1111/j.1463-6409.2008.00373.x · DOI
  28. [32]Gaubert P Denys G Oberdorff T Genus-level supertree of Cyprinidae (Actinopterygii: Cypriniformes), partitioned qualitative clade support and test of macro-evolutionary scenarios Biol Rev 2009 84 653 89 10.1111/j.1469-185X.2009.00091.x 19857213 · DOI
  29. [33]Wang X Gan X Li J Mayden RL He S Cyprinid phylogeny based on Bayesian and maximum likelihood analyses of partitioned data: implications for Cyprinidae systematics Sci China Life Sci 2012 55 761 73 10.1007/s11427-012-4366-z 23015124 · DOI
  30. [34]Rüber L Kottelat M Tan H Ng PK Britz R Evolution of miniaturization and the phylogenetic position of Paedocypris, comprising the world’s smallest vertebrate BMC Evol Biol 2007 7 38 10.1186/1471-2148-7-38 17355618 PMC1838906 · DOI · Paper page
  31. [35]Faircloth BC McCormack JE Crawford NG Harvey MG Brumfield RT Glenn TC Ultraconserved elements anchor thousands of genetic markers spanning multiple evolutionary timescales Syst Biol 2012 61 717 26 10.1093/sysbio/sys004 22232343 · DOI
  32. [36]Lemmon AR Emme SA Lemmon EM Anchored hybrid enrichment for massively high-throughput phylogenomics Syst Biol 2012 61 727 44 10.1093/sysbio/sys049 22605266 · DOI
  33. [37]Lemmon EM Lemmon AR High-throughput genomic data in systematics and phylogenetics Annu Rev Ecol Evol Syst 2013 44 99 121 10.1146/annurev-ecolsys-110512-135822 · DOI
  34. [38]He S Liu H Yiyu C Kuwahara M Nakajima T Zhong Y Molecular phylogenetic relationships of Eastern Asian Cyprinidae (Pisces: Cypriniformes) inferred from cytochrome b sequences Sci China Ser C 2004 47 130 8 10.1360/03yc0034 15379245 · DOI
  35. [39]Chen WJ Lheknim V Mayden RL Molecular phylogeny of the Cobitoidea (Teleostei: Cypriniformes) revisited: position of enigmatic loach Ellopostoma resolved with six nuclear genes J Fish Biol 2009 75 2197 208 10.1111/j.1095-8649.2009.02398.x 20738682 · DOI
  36. [40]Tang KL Lumbantobing DN Mayden RL The phylogenetic placement of Oxygaster van Hasselt, 1823 (Teleostei: Cypriniformes: Cyprinidae) and the taxonomic status of the family-Group Name Oxygastrinae Bleeker, 1860 Copeia 2013 2013 13 22 10.1643/CG-10-121 · DOI
  37. [41]Eytan RI Evans BR Dornburg A Lemmon AR Lemmon EM Wainwright PC Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment BMC Evol Biol 2015 15 113 10.1186/s12862-015-0415-0 26071950 PMC4465735 · DOI
  38. [42]Glasauer SMK Neuhauss SCF Whole-genome duplication in teleost fishes and its evolutionary consequences Mol Genet Genomics 2014 289 1045 60 10.1007/s00438-014-0889-2 25092473 · DOI
  39. [43]Li C Ortí G Zhang G Lu G A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study BMC Evol Biol 2007 7 44 10.1186/1471-2148-7-44 17374158 PMC1838417 · DOI
  40. [45]Kent WJ Sugnet CW Furey TS Roskin KM Pringle TH Zahler AM The human genome browser at UCSC Genome Res 2002 12 996 1006 10.1101/gr.229102.ArticlepublishedonlinebeforeprintinMay2002 12045153 PMC186604 · DOI
  41. [46]Katoh K Standley DM MAFFT multiple sequence alignment software version 7: improvements in performance and usability Mol Biol Evol 2013 30 772 80 10.1093/molbev/mst010 23329690 PMC3603318 · DOI · Paper page
  42. [47]Schartl M Walter RB Shen Y Garcia T Catchen J Amores A The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits Nat Genet 2013 45 567 72 10.1038/ng.2604 23542700 PMC3677569 · DOI
  43. [48]Loh Y-HE Katz LS Mims MC Kocher TD Yi SV Streelman JT Comparative analysis reveals signatures of differentiation amid genomic polymorphism in Lake Malawi cichlids Genome Biol 2008 9 R113 10.1186/gb-2008-9-7-r113 18616806 PMC2530870 · DOI
  44. [49]Meyer M Kircher M Illumina sequencing library preparation for highly multiplexed target capture and sequencing Cold Spring Harb Protoc 2010 6 t5448 10.1101/pdb.prot5448 20516186 · DOI
  45. [50]Rokyta DR Lemmon AR Margres MJ Aronow K The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus) BMC Genomics 2012 13 312 10.1186/1471-2164-13-312 23025625 PMC3472243 · DOI
  46. [51]Liu L Yu L Pearl DK Edwards SV Estimating species phylogenies using coalescence times among sequences Syst Biol 2009 58 468 77 10.1093/sysbio/syp031 20525601 · DOI
  47. [52]Shaw TI Ruan Z Glenn TC Liu L STRAW: species tree analysis web server Nucleic Acids Res 2013 41 W238 41 10.1093/nar/gkt377 23661681 PMC3692081 · DOI
  48. [53]Mirarab S Warnow T ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes Bioinformatics 2015 31 i44 52 10.1093/bioinformatics/btv234 26072508 PMC4765870 · DOI
  49. [56]Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. Version 3.04 http://mesquiteproject.org. 2015. pp. 1–3.
  50. [57]Ronquist F Teslenko M van der Mark P Ayres DL Darling A Hohna S mrbayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space Syst Biol 2012 61 539 42 10.1093/sysbio/sys029 22357727 PMC3329765 · DOI
  51. [58]Wright AM Hillis DM Bayesian analysis using a simple likelihood model outperforms parsimony for estimation of phylogeny from discrete morphological data PLoS One 2014 9 e109210 10.1371/journal.pone.0109210 25279853 PMC4184849 · DOI
  52. [60]Gatesy J Springer MS Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum Mol Phylogenet Evol 2014 80 231 66 10.1016/j.ympev.2014.08.013 25152276 · DOI
  53. [61]Tonini J Moore A Stern D Shcheglovitova M Orti G Concatenation and species tree methods exhibit statistically indistinguishable accuracy under a range of simulated conditions PLoS Curr 2015 25901289 PMC4391732
  54. [62]Alfaro ME Holder MT The posterior and the prior in Bayesian phylogenetics Annu Rev Ecol Evol Syst 2006 37 19 42 10.1146/annurev.ecolsys.37.091305.110021 · DOI
  55. [64]Yang L Arunachalam M Sado T Levin BA Golubtsov AS Freyhof J Molecular phylogeny of the cyprinid tribe Labeonini (Teleostei: Cypriniformes) Mol Phylogenet Evol 2012 65 362 79 10.1016/j.ympev.2012.06.007 22728909 · DOI
  56. [65]Lothongkham A Arbsuwan S Musikasinthorn P Garra waensis, a new cyprinid fish (Actinopterygii: Cypriniformes) from the Nan River basin of the Chao Phraya River system, northern Thailand Zootaxa 2014 3790 543 54 10.11646/zootaxa.3790.4.3 24869886 · DOI
  57. [67]Liao TY Kullander SO Fang F Phylogenetic position of rasborin cyprinids and monophyly of major lineages among the Danioninae, based on morphological characters (Cypriniformes: Cyprinidae) J Zool Syst Evol Res 2011 49 224 32 10.1111/j.1439-0469.2011.00621.x · DOI
  58. [68]Liao TY Kullander SO Phylogenetic significance of the kinethmoid-associated Y-shaped ligament and long intercostal ligaments in the Cypriniformes (Actinopterygii: Ostariophysi) Zool Scr 2013 42 71 87 10.1111/j.1463-6409.2012.00565.x · DOI
  59. [69]Chen W-J Lavoué S Mayden RL Evolutionary origin and early biogeography of otophysan fishes (Ostariophysi: Teleostei) Evolution 2013 67 2218 39 10.1111/evo.12104 23888847 · DOI
  60. [70]Tao W Mayden RL He S Remarkable phylogenetic resolution of the most complex clade of Cyprinidae (Teleostei: Cypriniformes): A proof of concept of homology assessment and partitioning sequence data integrated with mixed model Bayesian analyses Mol Phylogenet Evol 2013 66 603 16 10.1016/j.ympev.2012.09.024 23044401 · DOI
  61. [71]Yang J He S Freyhof J Witte K Liu H The phylogenetic relationships of the Gobioninae (Teleostei: Cyprinidae) inferred from mitochondrial cytochrome b gene sequences Hydrobiologia 2006 553 255 66 10.1007/s10750-005-1301-3 · DOI
  62. [72]Briolay J Galtier N Brito RM Bouvet Y Molecular phylogeny of cyprinidae inferred from cytochrome b DNA sequences Mol Phylogenet Evol 1998 9 100 8 10.1006/mpev.1997.0441 9479699 · DOI
  63. [73]Wang C Wang J Yang J Lu G Song X Chen Q Complete mitogenome sequence of black carp (Mylopharyngodon piceus) and its use for molecular phylogeny of leuciscine fishes Mol Biol Rep 2012 39 6337 42 10.1007/s11033-012-1455-9 22350152 · DOI
  64. [74]Cavender TM, Coburn MM. Phylogenetic relationships of North American Cyprinidae. In: Mayden RL, ed. Systematics, historical ecology, and North American freshwater fishes. Palo Alto, CA: Stanford University Press; 1992. p. 293–327.
  65. [75]Sakai H Ito Y Shedko SV Safronov SN Frolov SV Chereshnev IA Phylogenetic and taxonomic relationships of northern Far Eastern phoxinin minnows, Phoxinus and Rhynchocypris (Pisces, Cyprinidae), as inferred from allozyme and mitochondrial 16S rRNA sequence analyses Zool Sci 2006 23 323 31 10.2108/zsj.23.323 16702765 · DOI
  66. [76]Sasaki T Kartavtsev YP Chiba SN Uematsu T Sviridov VV Hanzawa N Genetic divergence and phylogenetic independence of Far Eastern species in subfamily Leuciscinae (Pisces: Cyprinidae) inferred from mitochondrial DNA analyses Genes Genet Syst 2007 82 329 40 10.1266/ggs.82.329 17895584 · DOI
  67. [77]Zhang X Yue B Jiang W Song Z The complete mitochondrial genome of rock carp Procypris rabaudi (Cypriniformes: Cyprinidae) and phylogenetic implications Mol Biol Rep 2008 36 981 91 10.1007/s11033-008-9271-y 18496768 · DOI
  68. [78]Strange RM Mayden RL Phylogenetic relationships and a revised taxonomy for North American cyprinids currently assigned to Phoxinus (Actinopterygii: Cyprinidae) Copeia 2009 2009 494 501 10.1643/CI-07-070 · DOI
  69. [79]Bufalino AP Mayden RL Phylogenetic relationships of North American phoxinins (Actinopterygii: Cypriniformes: Leuciscidae) as inferred from S7 nuclear DNA sequences Mol Phylogenet Evol 2010 55 143 52 10.1016/j.ympev.2009.11.001 19909821 · DOI
  70. [80]Bufalino AP Mayden RL Phylogenetic evaluation of North American Leuciscidae (Actinopterygii: Cypriniformes: Cyprinoidea) as inferred from analyses of mitochondrial and nuclear DNA sequences Syst Biodivers 2010 8 493 505 10.1080/14772000.2010.516029 · DOI
  71. [81]Imoto JM Saitoh K Sasaki T Yonezawa T Adachi J Kartavtsev YP Phylogeny and biogeography of highly diverged freshwater fish species (Leuciscinae, Cyprinidae, Teleostei) inferred from mitochondrial genome analysis Gene 2013 514 112 24 10.1016/j.gene.2012.10.019 23174367 · DOI
  72. [82]Meng F Braasch I Phillips JB Lin X Titus T Zhang C Evolution of the eye transcriptome under constant darkness in Sinocyclocheilus cavefish Mol Biol Evol 2013 30 1527 43 10.1093/molbev/mst079 23612715 PMC3684860 · DOI
  73. [83]Yang L Wang Y Zhang Z He S Comprehensive transcriptome analysis reveals accelerated genic evolution in a Tibet fish, Gymnodiptychus pachycheilus Genome Biol Evol 2015 7 251 61 10.1093/gbe/evu279 PMC4316632 25543049 · DOI
  74. [84]Xu P Zhang X Wang X Li J Liu G Kuang Y Genome sequence and genetic diversity of the common carp, Cyprinus carpio Nat Genet 2014 46 1212 9 10.1038/ng.3098 25240282 · DOI
  75. [85]Burns FR Cogburn AL Ankley GT Villeneuve DL Waits E Chang Y-J Sequencing and de novo draft assemblies of a fathead minnow (Pimephales promelas) reference genome Environ Toxicol Chem 2015 35 212 7 10.1002/etc.3186 26513338 · DOI
  76. [86]Yang J Chen X Bai J Fang D Qiu Y Jiang W The Sinocyclocheilus cavefish genome provides insights into cave adaptation BMC Biol 2016 14 1 13 10.1186/s12915-015-0223-4 26728391 PMC4698820 · DOI

Cited by

Sorted by citations

Authors
Stout, C. C., Tan, M., Lemmon, A. R., Lemmon, E. M., & Armbruster, J. W.
Affiliations
  • Auburn University (US)
  • Florida State University (US)
Corresponding author
Stout, Carla C.
ORCID
Venue
BMC Evolutionary Biology
Publisher
Springer Science and Business Media LLC
Published
2016-11-09
Volume
16
Issue
1
Pages
244-244
ISSN
1471-2148 (ISSN-L)
DOI
10.1186/s12862-016-0819-5
PMC
PMC5103605
OpenAlex
W2552892314
Cited by
138
References
1
Citations by year
2026: 12 · 2025: 10 · 2024: 12 · 2023: 11 · 2022: 21 · 2021: 18 · 2020: 13 · 2019: 13 · 2018: 19 · 2017: 7 · 2016: 2
FWCI
17.24
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Evolutionary Biology (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
National Science Foundation (DEB-0315963, IIP 1313554, DEB-1120516)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Aquatic Science › Fish Biology and Ecology Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
Keywords
Cypriniformes, phylogenomics, anchored hybrid enrichment, freshwater fish, Danionidae, monophyly, species tree, clade relationships, fish evolution
MeSH terms
Animals, Cypriniformes, Phylogeny, Species Specificity, Likelihood Functions, Sequence Analysis, DNA, Evolution, Molecular, Databases as Topic, Base Pairing, Genomics, Genetic Loci

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