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Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses

Xing Guo Xin-Xin He Hong Chen Zhi-Cheng Wang Hui-Fang Li Jiang-Xian Wang Ming-Shan Wang Run-Shen Jiang

Xing Guo, Xin-Xin He, Hong Chen, Zhi-Cheng Wang, Hui-Fang Li, Jiang-Xian Wang, Ming-Shan Wang, Run-Shen Jiang. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zoological Research, 2021, 42(1): 43-50. doi: 10.24272/j.issn.2095-8137.2020.133
Citation: Xing Guo, Xin-Xin He, Hong Chen, Zhi-Cheng Wang, Hui-Fang Li, Jiang-Xian Wang, Ming-Shan Wang, Run-Shen Jiang. Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses. Zoological Research, 2021, 42(1): 43-50. doi: 10.24272/j.issn.2095-8137.2020.133

全基因组解析家鸭与野鸭进化史

doi: 10.24272/j.issn.2095-8137.2020.133

Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses

Funds: This study was supported by the Natural Science Foundation of Anhui Province (1908085QC143) and the Natural Science Foundation for Young Scholars of Anhui Agricultural University (yj2018-51)
More Information
  • 摘要: 尽管家鸭是一个重要的家禽品种,但是它们的起源问题仍然存在争议。先前研究表明绿头野鸭与斑嘴鸭都可能是家鸭的祖先。为解析家鸭起源,我们对包含家鸭、绿头野鸭以及斑嘴鸭的118个基因组进行分析。结果表明家鸭与野鸭以及两个野鸭群体之间存在广泛的基因交流。进一步分析揭示家鸭与绿头野鸭以及斑嘴鸭分歧时间在3.8与5.4万年前,这一分歧时间远超家鸭假定的训化时间。此外,群体历史模拟结果表明家鸭可能起源于一个“幽灵”野鸭群体。因此,我们认为目前的家鸭可能并不是由绿头野鸭或斑嘴鸭驯化而来,而是起源于一种目前未被发现或者本研究中没有取样的野鸭群体。该研究结果为复杂的家鸭进化史提供了一个新见解。
    #Authors contributed equally to this work
  • Figure  1.  Population relationships and structures of ducks

    A: Population nucleotide diversity. B: Principal component analysis. C: ML tree constructed based on autosomal data. MA: Mallard; CSB: Chinese spot-billed; PK: Pekin; CV: Cherry valley; MP: Maple leaf; GY: Gaoyou; JD: Jinding; SM: Shanma; SX: Shaoxing. Egg and dual-purpose type ducks (EDT), including shanma, shaoxing, jinding, and gaoyou; meat-type ducks (MET), including pekin, cherry valley, and maple leaf.

    S1.  Geographic distribution of samples used in this study.

    S2.  LD decay determined by squared correlations of allele frequencies (R2) against distance between polymorphic sites.

    Figure  2.  Admixture analysis of mallards and Chinese spot-billed ducks (A) and mallards, Chinese spot-billed ducks, and domestic ducks (B)

    MA: Mallard; CSB: Chinese spot-billed; PK: Pekin; CV: Cherry valley; MP: Maple leaf; GY: Gaoyou; JD: Jinding; SM: Shanma; SX: Shaoxing.

    S3.  CV error for ADMIXTURE analysis of two wild duck species. K values ranged from 2 to 10. K=2 is best.

    S4.  CV error for ADMIXTURE analysis of 117 ducks. K values ranged from 2 to 11. K=3 is best.

    S5.  Phylogenetic trees constructed using neighbor-joining method based on variants along autosomes. MA, mallard; CSB, Chinese spot-billed; PK, pekin; CV, cherry valley; MP, maple leaf; GY gaoyou; JD, jinding; SM; shanma; SX, shaoxing.

    S6.  FST for all possible pairwise combinations of nine duck populations.

    S7.  D-statistics for D (Muscovy duck, Mallard; Chinese spot-billed duck, P). Z<–3 indicates admixture between mallards and Chinese spot-billed ducks.

    Figure  3.  Demographic history of ducks

    A: Demographic history inferred by PSMC with a generation time=1 year and mutation rate=1.91×10–9. B: Inferred relative cross-coalescence rates between pairs of populations over time based on two individuals of spot-billed, mallard, and domestic ducks. C: Demographic scenarios simulated by ms software (X=0.25, 0.5, 1, and 1.5, representing current population sizes equal to 12.5%, 25%, 50%, and 75% of ancestral population size, respectively). D: MSMC analysis of simulated data.

    Figure  4.  Demographic scenarios tested by fastsimcoal2

    A, B: Ducks domesticated from Chinese spot-billed ducks or mallards. C, D: Ducks domesticated from "ghost" duck population. MA: Mallard; CSB: Chinese spot-billed; GH: Ghost; DO: Domestic. Model C is best.

    S8.  Boxplot of AIC values for four demographic scenarios (Model C is best).

    S1.   Summary of genomic data for 118 ducks.

    Accession numbersBreedData sourceAverage depth
    SRR6323925CherryvalleyEBI5.2
    SRR6323934CherryvalleyEBI3.9
    SRR6323936CherryvalleyEBI4.3
    SRR6323938CherryvalleyEBI8
    SRR6323940CherryvalleyEBI4.5
    SRR6323941CherryvalleyEBI4.5
    SRR6323943CherryvalleyEBI4.7
    SRR6323945CherryvalleyEBI4.5
    SRR6323885GaoyouEBI5.2
    SRR6323891GaoyouEBI4.2
    SRR6323915GaoyouEBI9.7
    SRR6323916GaoyouEBI5.4
    SRR6323917GaoyouEBI4.3
    SRR6323920GaoyouEBI5.1
    SRR6323937GaoyouEBI4.8
    SRR6323944GaoyouEBI5.2
    SRR7091480GaoyouEBI8.8
    SRR7091481GaoyouEBI7.9
    SRR7091482GaoyouEBI11.4
    SRR6323880JindingEBI4.9
    SRR6323881JindingEBI5.5
    SRR6323884JindingEBI10.5
    SRR6323887JindingEBI5.2
    SRR6323911JindingEBI4.5
    SRR6323912JindingEBI5.1
    SRR6323913JindingEBI5.2
    SRR6323914JindingEBI5.7
    SRR7091483JindingEBI6.5
    SRR7091484JindingEBI7.9
    SRR7091485JindingEBI9.2
    SRR6323877MapleleafEBI5.1
    SRR6323886MapleleafEBI4.9
    SRR6323888MapleleafEBI4.5
    SRR6323889MapleleafEBI4.6
    SRR6323892MapleleafEBI4.9
    SRR6323893MapleleafEBI4.4
    SRR6323897MapleleafEBI4.2
    SRR6323898MapleleafEBI5.3
    SRR6323868PekinEBI4.6
    SRR6323869PekinEBI8.1
    SRR6323872PekinEBI4.3
    SRR6323873PekinEBI5.2
    SRR6323874PekinEBI5.1
    SRR6323875PekinEBI4.1
    SRR6323878PekinEBI5.3
    SRR6323879PekinEBI4.2
    SRR7091411PekinEBI10.3
    SRR7091412PekinEBI10.8
    SRR7091413PekinEBI4.8
    SRR7091414PekinEBI6.5
    SRR7091417PekinEBI6.7
    SRR7091418PekinEBI5.7
    SRR7091419PekinEBI6.4
    SRR7091432PekinEBI11.8
    SRR7091487PekinEBI7.4
    SRR7091488PekinEBI7.9
    SRR7091500PekinEBI9
    SRR7091501PekinEBI12
    SRR7091505PekinEBI10.6
    SRR7091506PekinEBI9.5
    SRR6323882ShanmaEBI4.9
    SRR6323883ShanmaEBI5.5
    SRR6323907ShanmaEBI5.2
    SRR6323908ShanmaEBI4.9
    SRR6323909ShanmaEBI9.7
    SRR6323910ShanmaEBI4.8
    SRR6323921ShanmaEBI5.4
    SRR6323922ShanmaEBI5
    SRR6064551ShaoxingEBI3.3
    SRR6064694ShaoxingEBI3.2
    SRR6064695ShaoxingEBI3.6
    SRR6064867ShaoxingEBI3.2
    SRR6064869ShaoxingEBI3.4
    SRR6064893ShaoxingEBI3.4
    SRR6064902ShaoxingEBI3.6
    SRR6064934ShaoxingEBI3.3
    SRR6323876ShaoxingEBI4.8
    SRR6323890ShaoxingEBI5.2
    SRR6323894ShaoxingEBI5.2
    SRR6323918ShaoxingEBI5.2
    SRR6323919ShaoxingEBI7.9
    SRR6323923ShaoxingEBI5.3
    SRR6323935ShaoxingEBI4.4
    SRR6323942ShaoxingEBI4.8
    CRR056777Chinese spot-billedGSA27.7
    CRR056784Chinese spot-billedGSA21.4
    CRR056778Chinese spot-billedGSA15.3
    CRR056779 Chinese spot-billedGSA13.5
    CRR056780Chinese spot-billedGSA13.8
    CRR056782Chinese spot-billedGSA12.1
    CRR056783Chinese spot-billedGSA13.7
    SRR6040147Chinese spot-billedEBI34.5
    SRR6040148
    SRR6040149
    SRR6040150
    SRR6040151
    SRR6040167MallardEBI33.9
    SRR6040168
    SRR6040169
    SRR6040170
    SRR6040171
    SRR6323870MallardEBI9.7
    SRR6323871MallardEBI9.9
    SRR6323899MallardEBI4.8
    SRR6323900MallardEBI9
    SRR6323901MallardEBI4.7
    SRR6323902MallardEBI10.6
    SRR6323904MallardEBI9.1
    SRR6323905MallardEBI10.4
    SRR6323906MallardEBI9.3
    SRR6323924MallardEBI8.3
    SRR6323926MallardEBI5.3
    SRR6323928MallardEBI17.5
    SRR6323929MallardEBI5.2
    SRR6323930MallardEBI5.2
    SRR6323931MallardEBI4.8
    SRR6323932MallardEBI5.2
    SRR6323933MallardEBI5.4
    SRR6323939MallardEBI8.5
    SRR7091437MallardEBI7.9
    SRR7091438MallardEBI7.9
    SRR7091439MallardEBI8
    SRR7091440MallardEBI9.3
    SRR7091445MallardEBI12
    SRR7091473MallardEBI8.6
    SRR6364413Muscovy duck(Out group)EBI49.2
    SRR6364567
    SRR6364773
    SRR6364908
    SRR6364950
    SRR6365122
    SRR6367586
    SRR6381606
    SRR6382379
    SRR6382409
    SRR6382410
    SRR6382435
    SRR6382515
    SRR6382580
    SRR6382581
    SRR6382585
    SRR6382586
    SRR6382587
    SRR6382594
    SRR6383594
    SRR6383681
    SRR6383682
    SRR6383801
    SRR6383802
    SRR6383834
    1Samples that hightlight in yellow were used for PSMC and MSMC analysis
    下载: 导出CSV

    S2.   D-statistics for D (Muscovy duck, mallard; P1, P2) or D (Muscovy duck, Chinese spot-billed duck; P1, P2). P1 and P2 represent different domestic duck groups. Z<–3 indicates admixture between mallards or Chinese spot-billed ducks and P1.

    Muscovyduckmallard or spot-billedP1P2Z value
    Muscovyduckmallardcherryvalleypekin7.857371
    Muscovyduckmallardcherryvalleymapleleaf6.914372
    Muscovyduckmallardcherryvalleyjinding6.541389
    Muscovyduckmallardcherryvalleyshanma-7.55236
    Muscovyduckmallardcherryvalleyshaoxing-12.8254
    Muscovyduckmallardcherryvalleygaoyou-0.18837
    Muscovyduckmallardpekincherryvalley-7.85736
    Muscovyduckmallardpekinmapleleaf3.147368
    Muscovyduckmallardpekincherryvalley-7.85736
    Muscovyduckmallardpekinshanma-12.2904
    Muscovyduckmallardpekinshaoxing-19.2684
    Muscovyduckmallardpekingaoyou-8.26936
    Muscovyduckmallardmapleleafcherryvalley-6.91435
    Muscovyduckmallardmapleleafpekin-3.14736
    Muscovyduckmallardmapleleafjinding-0.76638
    Muscovyduckmallardmapleleafshanma-12.0633
    Muscovyduckmallardmapleleafshaoxing-16.3974
    Muscovyduckmallardmapleleafgaoyou-8.28535
    Muscovyduckmallardjindingcherryvalley-6.54137
    Muscovyduckmallardjindingpekin-2.22636
    Muscovyduckmallardjindingmapleleaf0.76638
    Muscovyduckmallardjindingshanma-13.6674
    Muscovyduckmallardjindingshaoxing-20.1153
    Muscovyduckmallardjindinggaoyou-7.88537
    Muscovyduckmallardshanmacherryvalley7.552381
    Muscovyduckmallardshanmapekin12.29039
    Muscovyduckmallardshanmamapleleaf12.06339
    Muscovyduckmallardshanmajinding13.66739
    Muscovyduckmallardshanmashaoxing-4.65336
    Muscovyduckmallardshanmagaoyou8.018384
    Muscovyduckmallardshaoxingcherryvalley12.8254
    Muscovyduckmallardshaoxingpekin19.26841
    Muscovyduckmallardshaoxingmapleleaf16.39741
    Muscovyduckmallardshaoxingjinding20.1154
    Muscovyduckmallardshaoxinggaoyou15.0484
    Muscovyduckmallardshaoxingshanma4.653375
    Muscovyduckmallardgaoyoushaoxing-15.0484
    Muscovyduckmallardgaoyoucherryvalley0.188367
    Muscovyduckmallardgaoyoupekin8.269376
    Muscovyduckmallardgaoyoumapleleaf8.285376
    Muscovyduckmallardgaoyoujinding7.885386
    Muscovyduckmallardgaoyoushanma-8.01836
    Muscovyduckspot-billedcherryvalleymallard1.220391
    Muscovyduckspot-billedcherryvalleypekin28.13342
    Muscovyduckspot-billedcherryvalleymapleleaf9.066393
    Muscovyduckspot-billedcherryvalleyjinding40.2225
    Muscovyduckspot-billedcherryvalleyshanma-3.34938
    Muscovyduckspot-billedcherryvalleyshaoxing0.670404
    Muscovyduckspot-billedcherryvalleygaoyou9.4924
    Muscovyduckspot-billedpekinmallard-27.0174
    Muscovyduckspot-billedpekincherryvalley-28.1334
    Muscovyduckspot-billedpekinmapleleaf-11.6024
    Muscovyduckspot-billedpekincherryvalley-28.1334
    Muscovyduckspot-billedpekinshanma-20.3224
    Muscovyduckspot-billedpekinshaoxing-18.9394
    Muscovyduckspot-billedpekingaoyou-17.6114
    Muscovyduckspot-billedmapleleafmallard-9.28538
    Muscovyduckspot-billedmapleleafcherryvalley-9.06636
    Muscovyduckspot-billedmapleleafpekin11.6024
    Muscovyduckspot-billedmapleleafjinding29.82049
    Muscovyduckspot-billedmapleleafshanma-9.54237
    Muscovyduckspot-billedmapleleafshaoxing-6.76139
    Muscovyduckspot-billedmapleleafgaoyou-1.99738
    Muscovyduckspot-billedjindingcherryvalley-40.2223
    Muscovyduckspot-billedjindingpekin-31.2744
    Muscovyduckspot-billedjindingmapleleaf-29.8204
    Muscovyduckspot-billedjindingshanma-44.7563
    Muscovyduckspot-billedjindingshaoxing-48.0563
    Muscovyduckspot-billedjindinggaoyou-37.9684
    Muscovyduckspot-billedshanmacherryvalley3.349393
    Muscovyduckspot-billedshanmapekin20.32244
    Muscovyduckspot-billedshanmamapleleaf9.54241
    Muscovyduckspot-billedshanmajinding44.75651
    Muscovyduckspot-billedshanmashaoxing4.666403
    Muscovyduckspot-billedshanmagaoyou10.66641
    Muscovyduckspot-billedshaoxingcherryvalley-0.6704
    Muscovyduckspot-billedshaoxingpekin18.93944
    Muscovyduckspot-billedshaoxingmapleleaf6.761423
    Muscovyduckspot-billedshaoxingjinding48.0565
    Muscovyduckspot-billedshaoxinggaoyou7.474418
    Muscovyduckspot-billedshaoxingshanma-4.66639
    Muscovyduckspot-billedgaoyoucherryvalley-9.49238
    Muscovyduckspot-billedgaoyoupekin17.61142
    Muscovyduckspot-billedgaoyoumapleleaf1.997389
    Muscovyduckspot-billedgaoyoujinding37.96849
    Muscovyduckspot-billedgaoyoushanma-10.6664
    下载: 导出CSV
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  • 收稿日期:  2020-09-23
  • 录用日期:  2020-11-30
  • 网络出版日期:  2020-12-03
  • 刊出日期:  2021-01-18

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