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Evolution of Tibetan wild boars a Sulawesi warty pig To the Editor: (S. celebensis) The analysis presented by Li et al.1 in ~2 their report of the genome sequence of Java warty pig the Tibetan wild boar provides interesting (S. verrucosus) insights into the genetic architecture of Tibetan wild boar high-altitude adaptation in this species. (S. scrofa) However, despite the large volume of novel data, we found shortcomings in several parts 4.1 (5.3–3.5) North Chinese wild boar 2.5 (4–1.3) (S. scrofa) of the study, suggesting that some specific 14 (28–8)* findings presented by Li et al. result from Sourth Chinese wild boar overinterpretation of the data. In addition, (S. scrofa) 1.2 (2–0.8) several of their conclusions contradict those ? 2–5 6.9 (21.9–3.1) reported in previous analyses . Duroc reference genome More specifically, the authors infer that ~15 9.8 (12–7.5) ~0.8 (S. scrofa) 10.8 (14–7) Tibetan wild boar and Duroc breeds (Sus 26 (50–13)* European wild boar scrofa Ssc10.2 reference genome) diverged (S. scrofa) during the Miocene, ~6.8 million years ago. This estimated date is nearly ten times Sumatran wild boar more ancient than the recently reported split (S. scrofa) between Asian and European wild boars ~5.5 2,4 Warthog (0.8–2 million years ago) . In addition, (P. africanus) 0.004 substitutions/site previous studies2,3 estimated the divergence b time between S. scrofa and other Sus species Demographic history of Eurasian wild boars

) 4.0 from Island Southeast Asia (outgroups in 4

10 3.5 Nature America, Inc. All rights reserved. America, Inc. © 201 5 Nature Fig. 2b,e of ref. 1) to be 1.3–5.3 million years × ago. Li et al.1 do not describe the details of the 3.0 2.5 Tibet molecular clock analysis other than stating South China 2.0 North China 6 Europe npg that PAML (MCMCtree) was used with 1.5 three molecular clock–based calibrations 1.0

(as opposed to fossil-based calibrations), 0.5

and they neither specify which nodes population size ( Effective 0 were calibrated nor did they include the 104 105 106 107 uncertainties of these calibrations in their Years age priors. Moreover, we believe that the tree used for the molecular clock analysis Figure 1 Evolutionary history of Sus species. (a) Maximum-likelihood phylogenetic tree for Suinae was too sparsely sampled to be informative (Supplementary Note). All nodes besides the node for Tibetan or northern Chinese wild boars (support of 47%) are supported by 100% bootstrap replicates. Node labels represent time estimates in millions for the Duroc (S. scrofa reference genome) of years from refs. 2, 3 and 1, respectively; an asterisk indicates divergence times that were converted and Tibetan split time. Indeed, different using branch lengths estimated in this study and the times reported by Li et al.1 (Supplementary mutation rates are expected for the deep Note). Gray dots represent well-known fossils, with time in millions of years. (b) Demographic history of internal branches separating mammalian Eurasian wild boar (Supplementary Note). Generation time (g) = 5, mutation rate (+) = 2.5 × 10–8. orders and the short branches separating the two subspecies of S. scrofa2,4,7. Hence, resulting in a gross overestimation of the constructed a phylogenetic tree using data estimating a subspecies split time using rates subspecies divergence time. from a Tibetan wild boar1 together with estimated from the divergence of mammalian Furthermore, the authors do not take into seven other Sus samples (Fig. 1a) that were orders is nearly certain to bias the estimate, account the suid paleontological literature used in two previous studies2,4 and the leading to an incorrect conclusion. We that provides specific examples contradictory study of Li et al.1 (Supplementary Note). therefore believe that this analysis is likely to their conclusions (Fig. 1a) and would have We further annotated the tree with well- to have been influenced both by prior age provided useful calibrations (see Additional known fossils and our own time estimates2,3,8 misspecification and biased taxon sampling, File 6 in ref. 2). To illustrate our concerns, we (Fig. 1a). Our results demonstrate that

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Tibetan wild boar clusters together with claims, we reanalyzed the data of Li et al. by AUTHOR CONTRIBUTIONS Chinese wild boar (as also suggested by the aligning short-read sequences from a single L.A.F.F. and M.A.M.G. designed the study with input ancestry and phylogenetic analyses of Li Tibetan wild boar that was used for de novo from H.-J.M., O.M. and G.L. L.A.F.F. analyzed the data with help from H.-J.M., Y.P., M.B., R.P.M.A.C. et al.). On the basis of our molecular clock assembly (over 10× coverage; Supplementary and J.G.S. L.A.F.F. wrote the manuscript with input analyses2,3, we conclude that Tibetan and Note) to the Ssc10.2 reference genome and from all authors. European wild boars are not different species conducted a similar pairwise sequentially but instead are closely related subspecies Markovian coalescence (PSMC) analysis to COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. that diverged during the Pleistocene. In the one carried out by Li et al.1. Our results addition, we show that the evolutionary demonstrate that Tibetan and southern Laurent A F Frantz1,5, Ole Madsen1, time scale proposed by Li et al.1 for the Sus Chinese wild boars have similar demographic Hendrik-Jan Megens1, Joshua G Schraiber2,3, genus implies a significantly older speciation histories (Fig. 1b). In particular, we show that Yogesh Paudel1, Mirte Bosse1, timeframe that contradicts the fossil record Tibetan wild boar underwent fluctuations Richard P M A Crooijmans1, 4,5 1 (Fig. 1a). Furthermore, according to our in population size during the Pleistocene, Greger Larson & Martien A M Groenen branch length estimates (Supplementary contrary to the conclusions of Li et al. This 1Animal Breeding and Genomics Group, Note), a divergence time for European and analysis shows that the claim that Tibetan Wageningen University, Wageningen, the Asian wild boars of 6.8 million years ago1 wild boar experienced no demographic Netherlands. 2Department of Integrative Biology, (confidence interval of 2.4–12.9 million years fluctuations owing to the presence of refugia University of California, Berkeley, Berkeley, 3 ago) would imply that African and Eurasian in Tibet is incorrect. California, USA. Department of Genome Suinae diverged roughly 26 million years In light of the Assemblathon 2.0 (ref. 10), Sciences, University of Washington, Seattle, Washington, USA. 4Durham Evolution and ago (confidence interval of 13–50 million we believe that it is important not to Ancient DNA, Department of Archaeology, years ago), an estimate that bears no overinterpret data from de novo assemblies Durham University, Durham, UK. 5Present correspondence with the fossil timeframe of next-generation short-read sequencing address: Palaeogenomics and Bio-Archaeology 8 for Suinae . The erroneous time inference data, especially when comparing these to an Research Network, Research Laboratory for presented by Li et al. contributes to their assembly built from Sanger sequencing reads Archaeology and the History of Art, University of generally implausible results. combined with a high-resolution linkage Oxford, Oxford, UK. Another point of concern is the results map. Here we show that the overconfidence e-mail: [email protected] or of their demographic analysis9, shown in of the authors in their de novo assembly [email protected] 1 Figure 2e of Li et al. , which highlight the low and divergence time estimates misled their 1. Li, M. et al. Nat. Genet. 45, 1431–1438 (2013). coverage of the data set and the shortcomings interpretation of the evolutionary history of 2. Frantz, L.A.F. et al. Genome Biol. 14, R107 (2013). 3. Gongora, J. et al. Zool. Scr. 40, 327–335 (2011). of a next-generation sequence–based Tibetan wild boars. Furthermore, we believe 4. Groenen, M.A.M. et al. Nature 491, 393–398 (2012). genome assembly. The authors present the that some results presented in the study 5. Paudel, Y. et al. BMC Genomics 14, 449 (2013). demographic history as inferred both from by Li et al.1, in particular, large-scale gene 6. Yang, Z. Mol. Biol. Evol. 24, 1586–1591 (2007). 7. Ho, S.Y.W. & Larson, G. Trends Genet. 22, 79–83 boar genomes resequenced and aligned to family expansion and/or contraction since (2006). their assembly (green and pink lines in Fig. the European-Tibetan wild boar split, are 8. Orliac, M.J., Pierre-Olivier, A. & Ducrocq, S. Zool. Scr. 39, 315–330 (2010). 2e in ref. 1) and previously sequenced boar dubious. The interpretation of these results 9. Li, H. & Durbin, R. Nature 475, 493–496 (2011). genomes aligned to the high-quality draft as being due to a genuine biological signal 10. Bradnam, K.R. et al. Gigascience 2, 10 (2013).

Nature America, Inc. All rights reserved. America, Inc. © 201 5 Nature reference genome4 (Ssc10.2; blue and black rather than assembly artifact might have been lines in Fig. 2e in ref. 1). Surprisingly, the misled by the gross overestimation of the Li et al. reply: results show that the alignments of Chinese evolutionary timeframe of S. scrofa. Frantz et al. reanalyzed our data1 by aligning

npg wild boar to Ssc10.2 and the de novo assembly We suggest that the experimental design a small part of our short-read sequences significantly disagree (compare South China of studies describing the resequencing of from a Tibetan wild boar that were used for with Southwest China in Fig. 2e in ref. 1). closely related species or subspecies needs de novo assembly (33.2 Gb of 319 Gb, This lack of correspondence is worrying as to be different from the analysis conducted or ~10%) to the reference genome for the these individuals have similar ancestry and on newly sequenced genomes. For example, European domesticated Duroc pig breed are very closely related (Fig. 1a; see also Fig. a more relevant analysis would have been (Sus scrofa Ssc10.2)2. As a result, they 2b in ref. 1). The authors do not address this to compare the genomes of the ‘wild’ Sus propose alternative interpretations and discrepancy but instead draw the conclusion: species and warthog2,4 to the genome of the question two of our findings. They also “to our knowledge this is the first study Tibetan wild boar rather than comparing suggest that a resequencing strategy should supporting the refuge theory on the basis of evolutionary processes that occurred during be applied for the comparison of Tibetan demographic history revealed by genome- the last million years (Asian-European pig wild boar and Duroc pig, rather than for the wide analysis.” We believe that this result split) with processes that occurred since comparison of the two de novo assemblies as does not reflect a realistic population size for the common ancestor of human and pigs, we reported. wild boar in Tibet during the Pleistocene but roughly 100 million years ago. With the First, Frantz et al. claim that our proposed instead illustrates the lack of resolution of de power of multiple complete genomes comes time of divergence between Duroc pig and novo–assembled genomes for demographic the responsibility to interpret them in Tibetan wild boar is an overestimation that estimations in combination with light of both the potential pitfalls of next- can be attributed to the lack of appropriate underestimation of true heterozygosity due to generation sequencing and the published calibration points and insufficient sampling low-coverage resequencing data (5× coverage genomic and paleontological evidence. in the Sus lineage. Using three fossil-based for individuals resequenced in Li et al.1 calibration points and resequencing data versus 10× coverage for previously published Note: Any Supplementary Information and Source Data from eight Sus samples (including our resequenced individuals). To support our files are available in the online version of the paper. Tibetan wild boar) and an outgroup species,

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they reconstruct the phylogeny and provide previous studies (8–10× average depth)2 and evaluating this claim in a hypothesis their previous estimation of divergence times is comparable to other recent population testing framework. for some nodes, which are considerably genetics studies based on genome Regarding experimental design, we more recent than our divergence time resequencing, such as silkworm (3× coverage propose that, with further reduction in estimates. We agree that more taxa should be per individual)5, chicken (3–6× coverage)6, sequencing cost, evolutionary studies included and more recent calibration points soybean (5× coverage)7 and maize (4–5× of closely related species or subspecies should have been employed. However, no coverage)8. In general, genomic sequences should be based on comparison between other pig genome assemblies are available with over 30× coverage are desirable for independently assembled genomes besides those for Duroc pig and Tibetan high accuracy, but it is currently still too rather than resequencing. Our study wild boar. In the future, high-coverage expensive for most population genomics uncovered significantly more genetic genome sequences from multiple taxa will studies to adopt this standard. How the variations between the Tibetan wild boar allow more accurate reconstruction of the demographic history inferred using a hidden and European domesticated Duroc pig phylogeny and estimation of the divergence Markov model approach as implemented genomes, and these differences would time for internal nodes in the lineage, in pairwise sequentially Markovian be missed by applying a resequencing helping to address the discrepancies pointed coalescence (PSMC)9 changes as a factor of strategy. Even among populations of out by Frantz et al. sequencing depth is a topic worthy of future modern humans, surprisingly large The two genome assemblies we used, investigation. amounts of variation have been uncovered however, harbor abundant and unbiased We maintain that it is more reasonable by de novo assemblies10. genetic information that cannot be obtained to map the closely related Chinese and from resequencing data, which by their Tibetan wild boar resequencing data onto COMPETING FINANCIAL INTERESTS The authors declare no competing financial interests. nature are limited to less differentiated the Tibetan wild boar genome assembly areas in the genome. Using resequencing than to a more distantly related genome Mingzhou Li1, Ying Li1, Carol K L Yeung2, data to reconstruct the phylogeny as such as that of European domesticated Shilin Tian2, Xuewei Li1 & Ruiqiang Li2 Frantz et al. have done may result in the Duroc pig. The low mapping rate of 82% to 1Institute of Animal Genetics and Breeding, systematic underestimation of divergence the Duroc genome, as opposed to 92% on College of Animal Science and Technology, time. Moreover, the genome assemblies average when mapping to the Tibetan wild Sichuan Agricultural University, Ya’an, China. also provided other lines of evidence, such boar assembly (see Supplementary Table 2Novogene Bioinformatics Institute, Beijing, as the extent of structural variation and 31 in ref. 1), reflects substantial differences China. synteny between the Tibetan wild boar in genome architecture between Tibetan e-mail: [email protected], and Duroc pig genomes, which suggest a wild boar and Duroc pig, which might [email protected] or [email protected] substantial divergence time. More than 187 distort the results. Although it remains 1. Li, M. et al. Nat. Genet. 45, 1431–1438 (2013). Mb of sequence is inverted between the unclear why different reference genomes 2. Groenen, M.A. et al. Nature 491, 393–398 (2012). 3. Feuk, L. et al. PLoS Genet. 1, e56 (2005). Tibetan wild boar and Duroc pig genomes lead to different PSMC results, it seems 4. Qiu, Q. et al. Nat. Genet. 44, 946–949 (2012). 5. Xia, Q. et al. Science 326, 433–436 (2009). (see Supplementary Fig. 3 in ref. 1), which arbitrary to jump to the conclusion that 6. Rubin, C.J. et al. Nature 464, 587–591 (2010). is slightly more than the 1,576 inversions the discrepancy is due to what Frantz et 7. Lam, H.M. et al. Nat. Genet. 42, 1053–1059 (2010). 8. Hufford, M.B. et al. Nat. Genet. 44, 808–811 (2012). covering more than 154 Mb of sequence al. consider the lower quality of short- 9. Li, H. & Durbin, R. Nature 475, 493–496 (2011). Nature America, Inc. All rights reserved. America, Inc. © 201 5 Nature for the human and chimpanzee genomes read de novo genome assembly without 10. Li, R. et al. Nat. Biotechnol. 28, 57–63 (2010). (with a divergence time of ~6 million years ago)3. The degree of synteny between

npg Tibetan wild boar and Duroc pig (2.34 Gb; 93.41% of the Tibetan wild boar genome; see On genetic differentiation between Supplementary Fig. 3 in ref. 1) is comparable to that between yak and cattle (2.51 Gb; 94% domestic pigs and Tibetan wild boars of the yak genome; divergence time of ~4.9 million years ago)4. To the Editor: Chinese domestic pigs are genetically indis- The second criticism concerns the In their report of the genome sequence and tinguishable at an overall genomic level” (on accuracy of the reconstruction of assembly of Tibetan wild boar, Li et al.1 the basis of the principal-component analysis demographic histories. Through mapping dated the divergence between Tibetan wild in Fig. 2d of ref. 1). It is difficult to reconcile our data to the Duroc pig genome, Frantz et boar and Duroc pig to 6.9 million years a divergence time of 6.9 million years ago al. obtain a different historical population ago (bounds of 3.4–12.9 million years ago) between European domestics and Tibetan size for Tibetan wild boar and believe that using a list of 1,141 orthologous genes for wild boar and, simultaneously, a clustering our result is due to the lack of resolution of pig, cattle, dog and human. This divergence of Tibetan wild boar with Asian domestics, as de novo assembly and underestimation of time is unlikely and even predates the cur- the divergence between Asian and European heterozygosity. It goes without saying that rently accepted time for suid speciation2. If wild boars has repeatedly been estimated to resequencing data with higher coverage the divergence times estimated by Li et al. date to around ~700,000 years ago3 and to would be more powerful in carrying out were correct, it would mean that Tibetan 1.2 million years ago4 using mitochondrial such analysis and would provide more wild boars would have constituted a separate and genomic data, respectively. The results of accurate calculations. Our resequencing clade that colonized Tibet far earlier than Sus an extensive mitochondrial DNA (mtDNA) coverage depths were around 5× per scrofa migrated through Eurasia around 1.2 analysis of Tibetan and Asian pigs by Yang individual (n = 30), which is not significantly million years ago. However, the same authors et al.5 are also difficult to reconcile with the lower than the depth achieved in their also report that “Tibetan wild boars and large divergence obtained by Li et al.1 from

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a boars (mean FST = 0.15, s.d. = 0.08). The FST between Tibetan and Duroc pigs was 0.31 (s.d. = 0.11), somewhat lower than that observed between Meishan and Duroc pigs with FST = 0.38 (s.d. = 0.15). An interesting feature of Duroc pig FST values in comparison to other populations, whether Tibetan or Meishan, is their wide, flat distribution across genomic windows relative to FST values for the other breeds (Fig. 1c). This feature is likely due to the admixed nature of international pig breeds, including Duroc, which were F F 6 b ST (Tibetan vs. rest) c ST (Duroc vs. rest) introgressed with Chinese germplasm . A 10 10 Duroc Tibetan simulation model for pig demographic history Domestic Domestic Meishan Meishan actually predicts large variability in FST values 8 Wild boar 8 Wild boar S. verrucosus S. verrucosus across windows due to Chinese introgression 7 6 6 into European germplasm . Also of note is the absence of a clear 4 4 genetic divide between wild boar and Density Density Chinese domestic pigs, in agreement with 2 2 putative multiple domestication events across China8. Further, the complete mitochondrial 0 0 phylogeny (Fig. 1e) also suggests a 0 0.2 0.4 0.6 0.8 1.0 0 0.2 0.4 0.6 0.8 1.0 F F polyphyletic origin within Tibetan pigs, as ST ST found in previous studies that used only the de hypervariable mitochondrial region5. F (Meishan vs. rest) To conclude, Tibetan wild boars are ST Domestic 10 Tibetan closer to S. scrofa, including Duroc pigs, Duroc Meishan Domestic than to other suids. Genetic differentiation Wild boar 8 S. verrucosus Wild boar between Tibetan wild boar and Chinese Tibetan wild boar pigs is comparable to that among other 6 S. verrucosus Chinese pig breeds or with wild boar. The differentiation between Tibetan and 4 Density Duroc pigs is also similar to that between

2 other Chinese domestics (for example, Meishan) and the Duroc breed. The early

Nature America, Inc. All rights reserved. America, Inc. © 201 5 Nature 0 divergence time inferred by Li et al. is likely 0 0.2 0.4 0.6 0.8 1.0 an artifact that may have been caused by the F ST misspecification of evolution rates, possibly

npg as a consequence of using the root of the human-pig tree (89–99 million years ago) Figure 1 Tibetan pig photographs and genetic relatedness to other pigs. (a) Pigs in Shangri-La (Yunnan for calibration; this distant root is not precise Province, near Tibet), altitude ~3,800 m (photographs by M.P.-E.). (b) Distribution of FST values across enough for dating relatively short divergence 500-kb autosomal windows of Tibetan wild boar versus other pig populations. (c) FST distribution of times such as those between Tibetan Duroc pig versus other populations. (d) FST distribution of Meishan pig versus other populations. In b–d, wild boar and other pigs. Furthermore, Chinese domestics included Xian, Penzhou, Wujin, Yanan and Neijan; the three wild boar populations phylogenetic methods for dating divergence included one group from northern China and two groups from southern China. (e) Neighbor-joining tree of complete mitochondrial sequence using Tibetan samples, Meishan, the rest of the Chinese between populations of the same species domestics and wild boars; S. verrucosus is shown as an outgroup. For clarity, only a subsample of all should be used with care because critical individuals are shown in the tree. The scale bar represents the nucleotide substitution rate per site. parameters such as migration or population size may distort the divergence estimate if not properly considered. orthologous gene analysis. Our own obser- populations show that porcine populations Note: Any Supplementary Information and Source Data vation of Tibetan pigs suggests that they are are heavily structured and that there is a large files are available in the online version of the paper. indeed S. scrofa (Fig. 1a). degree of heterogeneity among F values ST ACKNOWLEDGMENTS To further investigate the genomic (Fig. 1b–d). Clearly, Tibetan pigs are more W.B.-P. is funded by COLCIENCIAS (Francisco José relationships of Tibetan wild boar with closely related to the Duroc pigs and other de Caldas fellowship 497/2009, Colombia). Work was the rest of the Asian pigs, Duroc pigs and S. scrofa populations than they are to the funded by grant AGL2010-14822 (Spain) to M.P.-E. suids, we downloaded and reanalyzed outgroup (Sus verrucosus), as were the rest of AUTHOR CONTRIBUTIONS complete sequence data from 65 individuals the domestics analyzed, Duroc and Meishan. M.P.-E. conceived and wrote the manuscript with (Supplementary Note). Autosomal In terms of FST, the closest population to help from W.B.-P. and S.E.R.-O. M.P.-E. and W.B.-P. differentiation metrics (FST values) among pig Tibetan pigs was southern Chinese wild analyzed data. S.E.R.-O. provided analytical tools.

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COMPETING FINANCIAL INTERESTS to that among other Chinese pig breeds or see Supplementary Fig. 3 in ref. 1) is The authors declare no competing financial interests. with wild boars, findings that are consistent comparable to that between yak and 1–3 1,2 with our report (see Fig. 2d in ref. 1). cattle (2.51 Gb; 94% of the yak genome; Miguel Pérez-Enciso , William Burgos-Paz & 4 Sebastián E Ramos-Onsins1 They suggest that our proposed time of divergence time of ~4.9 million years ago) . divergence for Duroc pig and Tibetan wild In summary, high-coverage genome 1 Centre for Research in Agricultural Genomics boar is an overestimation that is mainly sequences from multiple taxa and (CRAG), Consejo Superior de Investigaciones attributable to the usage of inappropriate appropriate fossil records in the future will Científicas (CSIC)–Institut de Recerca i Tecnologia Agroalimentàries (IRTA)–Universitat calibration points. allow more accurate reconstruction of the Autònoma de Barcelona–Universitat de Barcelona We agree that more recent calibration phylogeny and estimation of the divergence Consortium, Bellaterra, Spain. 2Department points should have been employed. time for internal nodes in the Sus lineage, of Animal Science, Universitat Autònoma de However, estimation of divergence time helping to address the discrepancies pointed Barcelona, Bellaterra, Spain. 3Institut Català using mitochondrial or resequencing out by Pérez-Enciso et al. It is likely that a de Recerca i Estudis Avançats (ICREA), data may result in the systematic systematic reevaluation of molecular clocks Barcelona, Spain. underestimation of divergence time on the basis of emerging genome data for e-mail: [email protected] caused by the conservative nature of species with fossil records will redefine many these data types, whereas de novo genome of the divergence time estimates based on 1. Li, M. et al. Nat. Genet. 45, 1431–1438 (2013). 2. Frantz, L.A. et al. Genome Biol. 14, R107 (2013). sequences harbor abundant and unbiased evidence from single genes. 3. Fernández, A.I., Alves, E., Ovilo, C., Rodríguez, M.C. & genetic information. In our report, the Silió, L. Anim. Genet. 42, 86–88 (2011). use of genome assemblies also allowed an COMPETING FINANCIAL INTERESTS 4. Groenen, M.A. et al. Nature 491, 393–398 (2012). The authors declare no competing financial interests. 5. Yang, S. et al. PLoS ONE 6, e28215 (2011). analysis of the extent of structural variation 6. Giuffra, E. et al. Genetics 154, 1785–1791 (2000). between the Tibetan wild boar and Duroc 1 2 1 7. Pérez-Enciso, M. J. Anim. Breed. Genet. 131, 85–96 pig genomes, which is comparable to that Mingzhou Li , Carol K L Yeung , Ying Li , (2014). Shilin Tian2, Xuewei Li1 & Ruiqiang Li2 8. Wu, G.S. et al. Genome Biol. 8, R245 (2007). found at or above the species level and suggestive of a substantial divergence time. 1 First, more than 187 Mb of sequence is Institute of Animal Genetics and Breeding, Li et al. reply: inverted between the Tibetan wild boar and College of Animal Science and Technology, Sichuan Agricultural University, Ya’an, China. Pérez-Enciso et al. reanalyzed our data1 Duroc pig genomes (see Supplementary 2Novogene Bioinformatics Institute, Beijing, by calculating genetic differentiation Fig. 3 in ref. 1), an amount slightly larger China. (FST) values among pig populations and than with the 1,576 inversions covering e-mail: [email protected], further constructed a neighbor-joining more than 154 Mb of sequence for the [email protected] or [email protected] phylogenetic tree on the basis of the human and chimpanzee genomes (with a mitochondrial sequences from a previous divergence time of ~6 million years ago)3. report2. As a result, they show that the Second, the degree of synteny between 1. Li, M. et al. Nat. Genet. 45, 1431–1438 (2013). 2. Yang, S. et al. PLoS ONE 6, e28215 (2011). genetic differentiation between Tibetan Tibetan wild boar and Duroc pig (2.34 Gb; 3. Feuk, L. et al. PLoS Genet. 1, e56 (2005). wild boar and Chinese pigs is comparable 93.41% of the Tibetan wild boar genome; 4. Qiu, Q. et al. Nat. Genet. 44, 946–949 (2012). Nature America, Inc. All rights reserved. America, Inc. © 201 5 Nature npg

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