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SCIENCE CHINA Life Sciences, Volume 62, Issue 4: 553-565(2019) https://doi.org/10.1007/s11427-019-9480-3

Phylogenetic relationships of Cypriniformes and plasticity of pharyngeal teeth in the adaptive radiation of cyprinids

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  • ReceivedOct 5, 2018
  • AcceptedNov 1, 2018
  • PublishedMar 25, 2019

Abstract

The Cypriniformes comprise approximately 4,200 species accounting for 25% of the diversity of all freshwater fish, which is widely distributed across the world’s continents except Antarctica, South America, and Australia. The highest species diversity is found in Southeastern Asia. Despite its remarkable species diversity and broad-scale geographic patterns of distribution, the evolutionary history of this major freshwater fish group remains largely unresolved. To gain insight of the evolutionary history of Cypriniformes, we present a phylogeny of this group using 1 mitochondrial gene and 15 nuclear genes comprising a total of 14,061 bp. Bayesian inference using all gene fragments yielded a well resolved phylogeny, which is mostly consistent with topologies obtained from Maximum Likelihood analyses. Our results further confirmed the monophyly of Cypriniformes and seven constituent subclades including Cyprinidae, Catostomidae, Gyrinocheilidae, Balitoridae, Cobitidae, Nemacheilidae, and Botiidae. Bayesian divergence time analysis indicated that the origin of the Cypriniformes was about 193 Mya during the early Jurassic, coinciding with the onset of the Pangaea breakup. The basal divergence of Cypriniformes is 154 Mya during the late Jurassic. Our findings from molecular divergence and biogeographical analysis indicate the most likely initial geographical range of the ancient Cypriniformes was both East and South Asia (Southeastern area of Mesozoic Laurasia). Moreover, the burst in species diversity in Cyprinidae afforded by the nearly worldwide colonization is possibly in response to the plasticity of pharyngeal dentition. The present study demonstrates that the Cypriniformes was about 193 Mya during the early Jurassic, coinciding with the onset of the Pangaea breakup. The plasticity of pharyngeal dentition of cyprinids might contribute to the burst and radiation of this lineage. The phylogenetic and biogeographic analyses in this study help to improve our understanding of the evolutionary history of this diverse and important freshwater fish group.


Funded by

the National Natural Science Foundation of China(31372190,91131014,31502147)

the Pilot projects(XDB13020100)

the Fundamental Research Funds for the Central Universities(Ministry,of,Education,of,China)


Acknowledgment

We are grateful to the people who provided help with the field work. Special thanks go to Chuanjiang Zhou and Liandong Yang for their participation in sample collection. We are also indebted to Lihong Guan and Meiling Yu for their laboratory assistance. This work was supported by the Pilot projects (XDB13020100), the National Natural Science Foundation of China (31372190, 91131014, 31502147), the Fundamental Research Funds for the Central Universities (Ministry of Education of China) (XDJK2018B025). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


Interest statement

The author(s) declare that they have no conflict of interest.


Supplement

SUPPORTING INFORMATION

Table S1ƒSpecies, catalog numbers, and sampling location of cypriniform fishes in this study

The supporting information is available online at http://life.scichina.com and https://link.springer.com. The supporting materials are published as submitted, without typesetting or editing. The responsibility for scientific accuracy and content remains entirely with the authors.


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  • Figure 1

    The Maximum Likelihood tree (–lnL=289,432.237912) from partitioned maximum likelihood analysis conducted based on the combination of mitochondrial and nuclear dataset. Numbers above nodes indicate the bootstrap supported values (1,000 replicates).

  • Figure 2

    The Bayesian tree resulting from partitioned Bayesian analysis conducted based on the combination of mitochondrial and nuclear dataset. Numbers above nodes indicate the posterior probabilities values.

  • Figure 3

    Maximum clade credibility chronogram inferred from a BEAST dating analysis. A posterior distribution of divergence times with 95% credibility intervals (shaded rectangles) was obtained from the concatenated data.

  • Figure 4

    Geographic evolution of cypriniform fishes from S-DIVA. Present-day distributions of individual groups are indicated by letters. Pie charts at nodes show probabilities of alternative ancestral ranges. The six geographical regions are (A) Europe, (B) Sibera, (C) North America, (D) Africa, (E) East Asia, and (F) South Aisa.

  • Figure 5

    Pharyngeal teeth of Cyprinidae, Cobitidae, Gyrinocheilidae and Catostomidae (He et al., 1997; Nakajima, 1977).

  • Table 1   Length, variable sites, parsimony sites, average p-distance and ratio of ti/tv of sampled genes and concatenated data

    Gene

    Length (bp)

    Variable sites (bp)

    Variable site %

    Parsimorny

    sites (bp)

    Parsimony sites %

    Average p-distance

    ti/tv

    TBR

    657

    359

    0.494

    190

    0.257

    0.055

    1.336

    ND4

    1,029

    747

    0.732

    599

    0.591

    0.264

    1.595

    ZNF503

    1,251

    792

    0.591

    533

    0.395

    0.089

    1.395

    UBE3A

    621

    301

    0.478

    246

    0.383

    0.086

    2.528

    RH

    849

    492

    0.580

    402

    0.473

    0.153

    1.731

    RAG1

    1,479

    810

    0.548

    665

    0.450

    0.139

    2.005

    ENC1

    780

    475

    0.609

    339

    0.435

    0.122

    2.483

    GYLT

    807

    592

    0.734

    458

    0.568

    0.135

    1.668

    IRBP

    798

    526

    0.659

    446

    0.559

    0.165

    1.533

    PLAGI2

    837

    494

    0.590

    347

    0.415

    0.086

    2.329

    RYR3

    810

    522

    0.644

    444

    0.548

    0.164

    1.505

    BACH

    525

    339

    0.646

    247

    0.470

    0.102

    2.009

    EGR3

    867

    404

    0.466

    314

    0.362

    0.092

    2.291

    RAG2

    1,233

    836

    0.678

    625

    0.507

    0.162

    2.034

    KIAA

    720

    441

    0.613

    300

    0.417

    0.085

    2.390

    EGR2B

    798

    404

    0.506

    313

    0.392

    0.120

    1.613

    Con_1st

    4,692

    2,758

    0.588

    2,062

    0.440

    0.118

    1.807

    Con_2nd

    4,692

    2,828

    0.603

    2,131

    0.455

    0.131

    1.885

    Con_3rd

    4,692

    2,766

    0.590

    2,075

    0.443

    0.082

    1.879

    Con_genes

    14,076

    8,352

    0.594

    6,268

    0.446

    0.128

    1.81

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