A Molecular Supermatrix of the Rabbits and Hares (Leporidae) Allows for the Identification of Five Intercontinental Exchanges During the Miocene

Matthee, Conrad A.; Vuuren, Bettine Jansen van; Bell, Diana; Robinson, Terence J.

doi:10.1080/10635150490445715

Cited by 201 publications

(278 citation statements)

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“…Assuming a divergence time of 11.8 MY (Matthee et al 2004) between O. cuniculus and L. granatensis, divergence time between O. c. cuniculus and O. c. algirus was estimated to be on the order of 2-5 MYA (Table 7). …”

Section: Resultsmentioning

confidence: 99%

“…Finally, to estimate the divergence time of the two subspecies of O. cuniculus, maximum-likelihood net nucleotide distances between L. granatensis and O. cuniculus, and between the two main lineages found in O. cuniculus (see results), were calculated using PAUP v 4.0 (Swofford 2002). Divergence time between subspecies of O. cuniculus was calculated assuming a divergence time between L. granatensis and O. cuniculus of 11.8 million years (MY) (Matthee et al 2004).…”

Section: Methodsmentioning

confidence: 99%

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Contrasting Patterns of Introgression at X-Linked Loci Across the Hybrid Zone Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

2006

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Hybrid zones provide an excellent opportunity for studying the consequences of genetic changes between closely related taxa. Here we investigate patterns of genetic variability and gene flow at four X-linked loci within and between the two subspecies of European rabbit (Oryctolagus cuniculus cuniculus and O. c. algirus). Two of these genes are located near the centromere and two are located near the telomeres. We observed a deep split in the genealogy of each gene with the root located along the deepest branch in each case, consistent with the evolution of these subspecies in allopatry. The two centromeric loci showed low levels of variability, high levels of linkage disequilibrium, and little introgression between subspecies. In contrast, the two telomeric loci showed high levels of variability, low levels of linkage disequilibrium, and considerable introgression between subspecies. These data are consistent with suppression of recombination near the centromere of the rabbit X chromosome. These observations support a view of speciation where genomic incompatibilities at different loci in the genome create localized differences in levels of gene flow between nascent species.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Contrasting Patterns of Introgression at X-Linked Loci Across the Hybrid Zone Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

2006

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“…Genetic differentiation between the two subspecies was estimated using the F ST estimator of Hudson et al (1992) as implemented in the program SITES (Hey and Wakeley 1997). The mutation rate per locus per generation was estimated for each locus based on the net nucleotide differences D A (Nei 1987) of Oryctolagus and Lepus, assuming a divergence time of T = 11.8 MYA (Matthee et al 2004), as in Carneiro et al (2010).…”

Section: Application To European Rabbit Datamentioning

confidence: 99%

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

et al. 2013

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When divergence occurs in the presence of gene flow, there can arise an interesting dynamic in which selection against gene flow, at sites associated with population-specific adaptations or genetic incompatibilities, can cause net gene flow to vary across the genome. Loci linked to sites under selection may experience reduced gene flow and may experience genetic bottlenecks by the action of nearby selective sweeps. Data from histories such as these may be poorly fitted by conventional neutral model approaches to demographic inference, which treat all loci as equally subject to forces of genetic drift and gene flow. To allow for demographic inference in the face of such histories, as well as the identification of loci affected by selection, we developed an isolation-withmigration model that explicitly provides for variation among genomic regions in migration rates and/or rates of genetic drift. The method allows for loci to fall into any of multiple groups, each characterized by a different set of parameters, thus relaxing the assumption that all loci share the same demography. By grouping loci, the method can be applied to data with multiple loci and still have tractable dimensionality and statistical power. We studied the performance of the method using simulated data, and we applied the method to study the divergence of two subspecies of European rabbits (Oryctolagus cuniculus).U NDERSTANDING speciation requires that we determine the role played by natural selection, as well as the roles of gene exchange and other demographic factors (Dobzhansky 1951;Maynard Smith 1966;Bush 1975;Endler 1977;Templeton 1981;Arnold 1997;Barton 2001). The genetic patterns of present-day populations potentially harbor much information about these processes, and in recent years investigators have developed sophisticated methods for quantifying different kinds of factors, including levels of gene flow between populations (Beerli and Felsenstein 1999;Nielsen and Wakeley 2001), admixture proportions (Chikhi et al. 2001), times of population separation (Nielsen and Wakeley 2001), and rates of population size change (Beaumont 1999;Hey 2005). This progress has been possible mainly through the development of full-likelihood model-based statistical methods that draw upon the coalescent theory of gene genealogies. However, quantifying the effects of selection in the divergence of populations has remained a challenging problem. Diffusion-theory-based methods can incorporate selection (Gutenkunst et al. 2009); however coalescent-based approaches to modeling selection do not readily admit to the kinds of flexibility required of divergence modeling (Hudson and Kaplan 1988;Neuhauser and Krone 1997;Wakeley 2008). As a result most of the model-based methods developed in recent years for studying divergence ignore the effects of selection and rely upon an assumption that neutral mutations and demography have been the sole determinants of patterns in the data (e.g., Kuhner et al. 1998;Beerli and Felsenstein 2001;Hey and Nielsen 2007 genome, ...

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“…Lepus hainanus from [37] and Oryctolagus cuniculus from [38] were used as the outgroup. The program MODELTEST 3.7 [53] was used to find the optimal model of DNA substitution based on the Akaike information criterion [54].…”

Section: Data Analysesmentioning

confidence: 99%

“…It speciated around 0.64 ± 0.26 million years ago (MYA) [36] and successfully survived the Quaternary. Although several species of Lepus were greatly affected by Pleistocene climatic fluctuations [11,[36][37][38][39][40], the impact of climatic oscillations on the demographic history and genetic diversity of the Yarkand hare is poorly understood [41,42]. Consequently, we analyzed mitochondrial DNA diversity from the species.…”

mentioning

confidence: 99%

Genetic consequences of postglacial colonization by the endemic Yarkand hare (Lepus yarkandensis) of the arid Tarim Basin

Shan

Liu

et al. 2011

Chin. Sci. Bull.

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Orogenesis of the Qinghai-Tibetan Plateau, which occurred in a stepwise manner, contributed to the extreme aridity of the Tarim Basin, resulting in vulnerable and unstable ecosystems. Quaternary climatic oscillations may have affected the ecosystems and, consequently, the distributions and genetic structuring of the Tarim Basin's biota. We used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated with the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis). Range-wide sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining network. Populations from the northern and eastern Tarim Basin shared a similar history, as did those from the western and southern regions. Demographical analysis and genetic diversity estimations suggested that the western and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic oscillations. The distribution of the Yarkand hare, especially in the northern and eastern parts, probably represented 3 postglacial colonization events, dated to 0.21, 0.090 and 0.054 MYA, which corresponded to known interglacial periods. Given the relatively complete geographic isolation between the eastern and southern populations, the Yarkand hare likely dispersed during postglacial periods from the southwest to the north, and then onward to the east. The absence of water likely forced the species into refugia, and this differed from other Pleistocene biogeographical drivers. The demographical and historical patterns have important implications for conservation. Chinese Sci Bull, 2011, 56: 1370−1382, doi: 10.1007 Pleistocene climatic changes imposed significant range shifts on many Palearctic biota, and contributed to their demographic history and genetic diversity [1]. Many temperate species existed only in refugia at times of glacial maxima, and recolonized or expanded into newly available habitats during interglacial periods [2,3]. Quaternary evolutionary histories of European and North American biota *These authors contributed equally to this work †Corresponding authors

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A Molecular Supermatrix of the Rabbits and Hares (Leporidae) Allows for the Identification of Five Intercontinental Exchanges During the Miocene

Cited by 201 publications

References 56 publications

Contrasting Patterns of Introgression at X-Linked Loci Across the Hybrid Zone Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

Contrasting Patterns of Introgression at X-Linked Loci Across the Hybrid Zone Between Subspecies of the European Rabbit (Oryctolagus cuniculus)

Identifying Loci Under Selection Against Gene Flow in Isolation-with-Migration Models

Genetic consequences of postglacial colonization by the endemic Yarkand hare (Lepus yarkandensis) of the arid Tarim Basin

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