Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci

Liu, Jiang; Yu, Li; Arnold, Michael L.; Wu, Chunhua; Wu, Shi-Fang; Lü, Xin; Zhang, Yaping

doi:10.1186/1471-2148-11-223

Cited by 39 publications

(62 citation statements)

References 83 publications

(103 reference statements)

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“…As with the Iberian species, Asian Lepus species also reflect the important role of ancient and contemporaneous hybridization and introgression. Significantly, and as predicted by Alves et al (2008), the genetic legacy of L. timidus was also detected in Asian species as well (Liu et al 2011). For example, the mtDNA haplotypes present in Lepus mandshuricus and L. capensis consisted of those from L. timidus and a second species, L. sinensis.…”

Section: European and Asian Haresmentioning

confidence: 86%

“…For example, the mtDNA haplotypes present in Lepus mandshuricus and L. capensis consisted of those from L. timidus and a second species, L. sinensis. Recent hybridization among a number of Asian Lepus species was also indicated by the presence of a number of individuals that were heterozygous for species-specific alleles at nuclear loci (Liu et al 2011). Similarly, a population genetic/phylogenetic analysis of the Asian species, L. capensis and L. yarkandensis, revealed bidirectional introgression of Y chromosome and mtDNA between these ecologically and morphologically distinct species .…”

Section: European and Asian Haresmentioning

confidence: 95%

See 1 more Smart Citation

Divergence-with-Gene-Flow—What Humans and Other Mammals Got up to

Arnold¹,

Hamlin²,

Taylor³

et al. 2015

Interdisciplinary Evolution Research

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In this review, we posit the hypothesis that divergence-with-gene-flow or, using the terminology that has historical precedence, evolution-with-hybridization is not the exception as argued by the neo-Darwinian architects, but rather the rule. In particular, we will discuss briefly how the definition of species and the process of speciation that emerged from the Modern Synthesis limited greatly how evolutionary diversification was perceived to occur. This, in turn, resulted in only certain hypotheses and research directions being deemed legitimate for evolutionary biologists. Yet, we will also argue that in general, the assumptions that resulted in the definitions and concepts surrounding speciation were made much stronger by a dearth, rather than a wealth, of the data needed to test hypotheses. Specifically, these alternative hypotheses were divergence in allopatry versus divergence with at least some genetic exchange. We will point to the observation made by Anderson-the architect of studies of introgressive hybridization-that to test for contemporaneous or ancient gene flow between diverging/divergent lineages requires discrete markers. Thus, not until the advent of methods for analyzing the genetic constitution of individual organisms was it possible to test rigorously the alternate modes of divergence. To illustrate our hypotheses and conclusions, we will focus on mammalian lineages, including our own species. This focus reflects our desire to emphasize that not only prokaryotes and plants, but animals as well, reflect the process of reticulate evolution.

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Section: European and Asian Haresmentioning

confidence: 86%

Section: European and Asian Haresmentioning

confidence: 95%

Divergence-with-Gene-Flow—What Humans and Other Mammals Got up to

Arnold¹,

Hamlin²,

Taylor³

et al. 2015

Interdisciplinary Evolution Research

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show abstract

“…10 ). This conclusion means that several introgression events might have occurred leading to a reticulated evolution during the emergence of various genera [Nosil, 2008;Liu et al, 2011]. The long persistence of heterozygosity implies that these chromosome rearrangements were probably permissive, i.e.…”

Section: Chromosome Evolution In Ochotonidae Leporidae and Sciuridaementioning

confidence: 95%

“…This is the interpretation chosen in figure 8 . The presence of heterozygosity for some inversions and Robertsonian translocations is proposed during the basal steps of the Glires diversification, which could result from hybridization events between homozygous populations (introgression) or conservation of heterozygous individuals, leading to a reticulated evolution [Chang et al, 2011;Liu et al, 2011]. …”

Section: Chromosome Evolution Since the Eutherian Ancestormentioning

confidence: 99%

Low, Complex and Probably Reticulated Chromosome Evolution of Sciuromorpha (Rodentia) and Lagomorpha

Richard

Dutrillaux

2012

Cytogenet Genome Res

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Lagomorpha (rabbits and pikas) and Sciuromorpha (squirrels) are grouped in the Glires superorder. Their chromosome diversification, since their separation from the eutherian mammalian common ancestor, was characterized by a low rate of chromosome rearrangements. Consequently, the structure of some chromosomes was either conserved or only slightly modified, making their comparison easy at the genus, family and even order level. Interspecific in situ hybridization (Zoo-FISH) largely corroborates classical cytogenetic data but provides much more reliability in comparisons, especially for distant species. We reconstructed common ancestral karyotypes for Glires, Lagomorpha, Sciuromorpha, and Sciuridae species, and then, determined the chromosome changes separating these ancestors from their common eutherian ancestor. We propose that reticulated evolution occurred during the diversification of Glires, which implies that several pericentric inversions and Robertsonian translocations were conserved in the heterozygous status for an extensive period. Finally, among Lagomorpha and Sciuromorpha, we focused on Leporidae and Sciuridae chromosome evolution. In the various attempts to establish dichotomic evolutionary schemes, it was necessary to admit that multiple homoplasies (convergent and reverse rearrangements) occurred in Sciuridae and in a lesser degree, in Leporidae. In Leporidae, additional rearrangements were sufficient to propose a resolved phylogeny. However, a resolved phylogeny was not possible for Sciuridae because most of the rearrangements occurred in terminal branches. We conclude that a reticulated evolution took place early during the evolution of both families and lasted longer in Sciuridae than in Leporidae. In Sciuridae, most chromosome rearrangements were pericentric inversions involving short fragments. Such rearrangements have only mild meiotic consequences, which may explain the long persistence of the heterozygous status characterizing reticulated evolution.

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“…Many phylogenetic reconstmctions regarding these small mammals were generated and consisted of the Leporidae (Matthee et al, 2004;Liu et al, 2011), Ochotona (Niu et al, 2004), Dipodidae (Zhang et al, 2012), Alticola (Lebedev et al, 2007), Phodopus (Meshchersky & Feoktistova, 2009), Microtus (Jaarola et al, 2004), Sciuridae (Oshida et al, 2000;Harrison et al, 2003), Castoridae (Hom et al, 2011) and Gerbillinae (Chevret & Dobigny, 2005;Ito et al, 2010) with cosmopolitan distributions. Importantly, changes in the palaeoenvironment and paleoclimate expedite the process of evolutionary divergence in mammals.…”

Section: Introductionmentioning

confidence: 99%

The divergence of small mammals in Xinjiang, China, as revealed by phylogentic analyses of COI and Cytb

et al. 2014

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Cbanges in tbe palaeoenvironment and paleoclimate expedite tbe process of evolutionary divergence in animals. Tbe evolutionary events of some small mammals distributed in Xinjiang Arid Region remain ambiguous. Tbus, it is necessary to predict tbeir evolutionary bistories based on divergence estimates. Some museum specimens were involved in tbis analysis because of sampling bmitation for tbreatened species in tbe arid region. A related problem is tbat some mutilated specimens witbout complete taxonomic data made it difficult to directly analyze species divergence. Here, sequences of cytocbrome c oxydase I were used to identify museum specimens and combined witb cytocbrome b to estimate tbe recent divergence of extant small mammals constrained witb eigbt fossil calibrations. Tbe results sbowed tbat tbe massive species differentiation emerged during tbe Middle and Late Miocene periods. We inferred tbat differentiation of tbese small mammals migbt be associated witb tbe retreat of tbe Tetbys Sea from tbe Tarim Basin around tbe Eocene-Oligocene boundary and tbe global climate fluctuations during tbe Miocene period. Furtbermore, tbe aridification and cbanges in tbe Taklimakan and Gurbantunggut Deserts migbt bave driven tbe diversification of intraspecies and tbe emergence of cryptic species since tbe Late Pleistocene.

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Reticulate evolution: frequent introgressive hybridization among chinese hares (genus lepus) revealed by analyses of multiple mitochondrial and nuclear DNA loci

Cited by 39 publications

References 83 publications

Divergence-with-Gene-Flow—What Humans and Other Mammals Got up to

Divergence-with-Gene-Flow—What Humans and Other Mammals Got up to

Low, Complex and Probably Reticulated Chromosome Evolution of Sciuromorpha (Rodentia) and Lagomorpha

The divergence of small mammals in Xinjiang, China, as revealed by phylogentic analyses of COI and Cytb

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