Revisiting the evolutionary history of domestic and wild ducks based on genomic analyses
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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。Abstract: Although domestic ducks have been important poultry species throughout human history, their origin remains enigmatic, with mallards and/or Chinese spot-billed ducks being proposed as the direct wild ancestor(s) of domestic ducks. Here, we analyzed 118 whole genomes from mallard, Chinese spot-billed, and domestic ducks to reconstruct their evolutionary history. We found pervasive introgression patterns among these duck populations. Furthermore, we showed that domestic ducks separated from mallard and Chinese spot-billed ducks nearly 38 thousand years ago (kya) and 54 kya, respectively, which is considerably outside the time period of presumed duck domestication. Thus, our results suggest that domestic ducks may have originated from another wild duck population that is currently undefined or unsampled, rather than from present-day mallard and/or Chinese spot-billed ducks, as previously thought. Overall, this study provides new insight into the complex evolution of ducks.
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Key words:
- Duck /
- Population structure /
- Demographic histories /
- Domestication
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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.
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.
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.
S1. Summary of genomic data for 118 ducks.
Accession numbers Breed Data source Average depth SRR6323925 Cherryvalley EBI 5.2 SRR6323934 Cherryvalley EBI 3.9 SRR6323936 Cherryvalley EBI 4.3 SRR6323938 Cherryvalley EBI 8 SRR6323940 Cherryvalley EBI 4.5 SRR6323941 Cherryvalley EBI 4.5 SRR6323943 Cherryvalley EBI 4.7 SRR6323945 Cherryvalley EBI 4.5 SRR6323885 Gaoyou EBI 5.2 SRR6323891 Gaoyou EBI 4.2 SRR6323915 Gaoyou EBI 9.7 SRR6323916 Gaoyou EBI 5.4 SRR6323917 Gaoyou EBI 4.3 SRR6323920 Gaoyou EBI 5.1 SRR6323937 Gaoyou EBI 4.8 SRR6323944 Gaoyou EBI 5.2 SRR7091480 Gaoyou EBI 8.8 SRR7091481 Gaoyou EBI 7.9 SRR7091482 Gaoyou EBI 11.4 SRR6323880 Jinding EBI 4.9 SRR6323881 Jinding EBI 5.5 SRR6323884 Jinding EBI 10.5 SRR6323887 Jinding EBI 5.2 SRR6323911 Jinding EBI 4.5 SRR6323912 Jinding EBI 5.1 SRR6323913 Jinding EBI 5.2 SRR6323914 Jinding EBI 5.7 SRR7091483 Jinding EBI 6.5 SRR7091484 Jinding EBI 7.9 SRR7091485 Jinding EBI 9.2 SRR6323877 Mapleleaf EBI 5.1 SRR6323886 Mapleleaf EBI 4.9 SRR6323888 Mapleleaf EBI 4.5 SRR6323889 Mapleleaf EBI 4.6 SRR6323892 Mapleleaf EBI 4.9 SRR6323893 Mapleleaf EBI 4.4 SRR6323897 Mapleleaf EBI 4.2 SRR6323898 Mapleleaf EBI 5.3 SRR6323868 Pekin EBI 4.6 SRR6323869 Pekin EBI 8.1 SRR6323872 Pekin EBI 4.3 SRR6323873 Pekin EBI 5.2 SRR6323874 Pekin EBI 5.1 SRR6323875 Pekin EBI 4.1 SRR6323878 Pekin EBI 5.3 SRR6323879 Pekin EBI 4.2 SRR7091411 Pekin EBI 10.3 SRR7091412 Pekin EBI 10.8 SRR7091413 Pekin EBI 4.8 SRR7091414 Pekin EBI 6.5 SRR7091417 Pekin EBI 6.7 SRR7091418 Pekin EBI 5.7 SRR7091419 Pekin EBI 6.4 SRR7091432 Pekin EBI 11.8 SRR7091487 Pekin EBI 7.4 SRR7091488 Pekin EBI 7.9 SRR7091500 Pekin EBI 9 SRR7091501 Pekin EBI 12 SRR7091505 Pekin EBI 10.6 SRR7091506 Pekin EBI 9.5 SRR6323882 Shanma EBI 4.9 SRR6323883 Shanma EBI 5.5 SRR6323907 Shanma EBI 5.2 SRR6323908 Shanma EBI 4.9 SRR6323909 Shanma EBI 9.7 SRR6323910 Shanma EBI 4.8 SRR6323921 Shanma EBI 5.4 SRR6323922 Shanma EBI 5 SRR6064551 Shaoxing EBI 3.3 SRR6064694 Shaoxing EBI 3.2 SRR6064695 Shaoxing EBI 3.6 SRR6064867 Shaoxing EBI 3.2 SRR6064869 Shaoxing EBI 3.4 SRR6064893 Shaoxing EBI 3.4 SRR6064902 Shaoxing EBI 3.6 SRR6064934 Shaoxing EBI 3.3 SRR6323876 Shaoxing EBI 4.8 SRR6323890 Shaoxing EBI 5.2 SRR6323894 Shaoxing EBI 5.2 SRR6323918 Shaoxing EBI 5.2 SRR6323919 Shaoxing EBI 7.9 SRR6323923 Shaoxing EBI 5.3 SRR6323935 Shaoxing EBI 4.4 SRR6323942 Shaoxing EBI 4.8 CRR056777 Chinese spot-billed GSA 27.7 CRR056784 Chinese spot-billed GSA 21.4 CRR056778 Chinese spot-billed GSA 15.3 CRR056779 Chinese spot-billed GSA 13.5 CRR056780 Chinese spot-billed GSA 13.8 CRR056782 Chinese spot-billed GSA 12.1 CRR056783 Chinese spot-billed GSA 13.7 SRR6040147 Chinese spot-billed EBI 34.5 SRR6040148 SRR6040149 SRR6040150 SRR6040151 SRR6040167 Mallard EBI 33.9 SRR6040168 SRR6040169 SRR6040170 SRR6040171 SRR6323870 Mallard EBI 9.7 SRR6323871 Mallard EBI 9.9 SRR6323899 Mallard EBI 4.8 SRR6323900 Mallard EBI 9 SRR6323901 Mallard EBI 4.7 SRR6323902 Mallard EBI 10.6 SRR6323904 Mallard EBI 9.1 SRR6323905 Mallard EBI 10.4 SRR6323906 Mallard EBI 9.3 SRR6323924 Mallard EBI 8.3 SRR6323926 Mallard EBI 5.3 SRR6323928 Mallard EBI 17.5 SRR6323929 Mallard EBI 5.2 SRR6323930 Mallard EBI 5.2 SRR6323931 Mallard EBI 4.8 SRR6323932 Mallard EBI 5.2 SRR6323933 Mallard EBI 5.4 SRR6323939 Mallard EBI 8.5 SRR7091437 Mallard EBI 7.9 SRR7091438 Mallard EBI 7.9 SRR7091439 Mallard EBI 8 SRR7091440 Mallard EBI 9.3 SRR7091445 Mallard EBI 12 SRR7091473 Mallard EBI 8.6 SRR6364413 Muscovy duck(Out group) EBI 49.2 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 
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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.
Muscovyduck mallard or spot-billed P1 P2 Z value Muscovyduck mallard cherryvalley pekin 7.857371 Muscovyduck mallard cherryvalley mapleleaf 6.914372 Muscovyduck mallard cherryvalley jinding 6.541389 Muscovyduck mallard cherryvalley shanma -7.55236 Muscovyduck mallard cherryvalley shaoxing -12.8254 Muscovyduck mallard cherryvalley gaoyou -0.18837 Muscovyduck mallard pekin cherryvalley -7.85736 Muscovyduck mallard pekin mapleleaf 3.147368 Muscovyduck mallard pekin cherryvalley -7.85736 Muscovyduck mallard pekin shanma -12.2904 Muscovyduck mallard pekin shaoxing -19.2684 Muscovyduck mallard pekin gaoyou -8.26936 Muscovyduck mallard mapleleaf cherryvalley -6.91435 Muscovyduck mallard mapleleaf pekin -3.14736 Muscovyduck mallard mapleleaf jinding -0.76638 Muscovyduck mallard mapleleaf shanma -12.0633 Muscovyduck mallard mapleleaf shaoxing -16.3974 Muscovyduck mallard mapleleaf gaoyou -8.28535 Muscovyduck mallard jinding cherryvalley -6.54137 Muscovyduck mallard jinding pekin -2.22636 Muscovyduck mallard jinding mapleleaf 0.76638 Muscovyduck mallard jinding shanma -13.6674 Muscovyduck mallard jinding shaoxing -20.1153 Muscovyduck mallard jinding gaoyou -7.88537 Muscovyduck mallard shanma cherryvalley 7.552381 Muscovyduck mallard shanma pekin 12.29039 Muscovyduck mallard shanma mapleleaf 12.06339 Muscovyduck mallard shanma jinding 13.66739 Muscovyduck mallard shanma shaoxing -4.65336 Muscovyduck mallard shanma gaoyou 8.018384 Muscovyduck mallard shaoxing cherryvalley 12.8254 Muscovyduck mallard shaoxing pekin 19.26841 Muscovyduck mallard shaoxing mapleleaf 16.39741 Muscovyduck mallard shaoxing jinding 20.1154 Muscovyduck mallard shaoxing gaoyou 15.0484 Muscovyduck mallard shaoxing shanma 4.653375 Muscovyduck mallard gaoyou shaoxing -15.0484 Muscovyduck mallard gaoyou cherryvalley 0.188367 Muscovyduck mallard gaoyou pekin 8.269376 Muscovyduck mallard gaoyou mapleleaf 8.285376 Muscovyduck mallard gaoyou jinding 7.885386 Muscovyduck mallard gaoyou shanma -8.01836 Muscovyduck spot-billed cherryvalley mallard 1.220391 Muscovyduck spot-billed cherryvalley pekin 28.13342 Muscovyduck spot-billed cherryvalley mapleleaf 9.066393 Muscovyduck spot-billed cherryvalley jinding 40.2225 Muscovyduck spot-billed cherryvalley shanma -3.34938 Muscovyduck spot-billed cherryvalley shaoxing 0.670404 Muscovyduck spot-billed cherryvalley gaoyou 9.4924 Muscovyduck spot-billed pekin mallard -27.0174 Muscovyduck spot-billed pekin cherryvalley -28.1334 Muscovyduck spot-billed pekin mapleleaf -11.6024 Muscovyduck spot-billed pekin cherryvalley -28.1334 Muscovyduck spot-billed pekin shanma -20.3224 Muscovyduck spot-billed pekin shaoxing -18.9394 Muscovyduck spot-billed pekin gaoyou -17.6114 Muscovyduck spot-billed mapleleaf mallard -9.28538 Muscovyduck spot-billed mapleleaf cherryvalley -9.06636 Muscovyduck spot-billed mapleleaf pekin 11.6024 Muscovyduck spot-billed mapleleaf jinding 29.82049 Muscovyduck spot-billed mapleleaf shanma -9.54237 Muscovyduck spot-billed mapleleaf shaoxing -6.76139 Muscovyduck spot-billed mapleleaf gaoyou -1.99738 Muscovyduck spot-billed jinding cherryvalley -40.2223 Muscovyduck spot-billed jinding pekin -31.2744 Muscovyduck spot-billed jinding mapleleaf -29.8204 Muscovyduck spot-billed jinding shanma -44.7563 Muscovyduck spot-billed jinding shaoxing -48.0563 Muscovyduck spot-billed jinding gaoyou -37.9684 Muscovyduck spot-billed shanma cherryvalley 3.349393 Muscovyduck spot-billed shanma pekin 20.32244 Muscovyduck spot-billed shanma mapleleaf 9.54241 Muscovyduck spot-billed shanma jinding 44.75651 Muscovyduck spot-billed shanma shaoxing 4.666403 Muscovyduck spot-billed shanma gaoyou 10.66641 Muscovyduck spot-billed shaoxing cherryvalley -0.6704 Muscovyduck spot-billed shaoxing pekin 18.93944 Muscovyduck spot-billed shaoxing mapleleaf 6.761423 Muscovyduck spot-billed shaoxing jinding 48.0565 Muscovyduck spot-billed shaoxing gaoyou 7.474418 Muscovyduck spot-billed shaoxing shanma -4.66639 Muscovyduck spot-billed gaoyou cherryvalley -9.49238 Muscovyduck spot-billed gaoyou pekin 17.61142 Muscovyduck spot-billed gaoyou mapleleaf 1.997389 Muscovyduck spot-billed gaoyou jinding 37.96849 Muscovyduck spot-billed gaoyou shanma -10.6664
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