Mitochondrial Introgression and Incomplete Lineage Sorting Through Space and Time: Phylogenetics of Crotaphytid Lizards

McGuire, Jimmy A.; Linkem, Charles W.; Koo, Michelle S.; Hutchison, Delbert W.; Lappin, A. Kristopher; Orange, David; Lemos‐Espinal, Julio A.; Riddle, Brett R.; Jaeger, Jef R.

doi:10.1111/j.1558-5646.2007.00239.x

Cited by 255 publications

(232 citation statements)

References 74 publications

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“…The finding of myrtle warbler (Setophaga coronata) mtDNA throughout the majority of the range of the Audubon's warbler (S. auduboni), with considerably less nuclear introgression, also presents the potential for adaptive introgression, which authors presents may be correlated to a shift in migratory strategy (Brelsford et al 2011;Milá et al 2011). The repeated waves of introgression of common collared lizard (Crotaphytus collaris) mtDNA into populations of the Great Basin collared lizard (C. bicinctores) is a pattern that would not be expected under a neutral scenario and, as the authors suggest, is consistent with C. collaris mtDNA having a selective advantage (McGuire et al 2007). In one of the few studies to test for the selective advantage of mtDNA, Aubert & Solignac (1990) found that experimental labora-…”

Section: Box 3 Mitochondrial Structure In the Absence Of Geographicsupporting

confidence: 52%

The biogeography of mitochondrial and nuclear discordance in animals

2012

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Combining nuclear (nuDNA) and mitochondrial DNA (mtDNA) markers has improved the power of molecular data to test phylogenetic and phylogeographic hypotheses and has highlighted the limitations of studies using only mtDNA markers. In fact, in the past decade, many conflicting geographic patterns between mitochondrial and nuclear genetic markers have been identified (i.e. mito-nuclear discordance). Our goals in this synthesis are to: (i) review known cases of mito-nuclear discordance in animal systems, (ii) to summarize the biogeographic patterns in each instance and (iii) to identify common drivers of discordance in various groups. In total, we identified 126 cases in animal systems with strong evidence of discordance between the biogeographic patterns obtained from mitochondrial DNA and those observed in the nuclear genome. In most cases, these patterns are attributed to adaptive introgression of mtDNA, demographic disparities and sex-biased asymmetries, with some studies also implicating hybrid zone movement, human introductions and Wolbachia infection in insects. We also discuss situations where divergent mtDNA clades seem to have arisen in the absence of geographic isolation. For those cases where foreign mtDNA haplotypes are found deep within the range of a second taxon, data suggest that those mtDNA haplotypes are more likely to be at a high frequency and are commonly driven by sex-biased asymmetries and ⁄ or adaptive introgression. In addition, we discuss the problems with inferring the processes causing discordance from biogeographic patterns that are common in many studies. In many cases, authors presented more than one explanation for discordant patterns in a given system, which indicates that likely more data are required. Ideally, to resolve this issue, we see important future work shifting focus from documenting the prevalence of mito-nuclear discordance towards testing hypotheses regarding the drivers of discordance. Indeed, there is great potential for certain cases of mitochondrial introgression to become important natural systems within which to test the effect of different mitochondrial genotypes on whole-animal phenotypes.

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Section: Box 3 Mitochondrial Structure In the Absence Of Geographicsupporting

confidence: 52%

The biogeography of mitochondrial and nuclear discordance in animals

2012

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“…yunnanense shared a nuclear haplotype (N15, Fig. 2), which might have resulted from incomplete lineage sorting of haplotypes present in their common ancestor (McGuire et al, 2007). This scenario of ancestral polymorphism retained in LCNGs seems probable given that the populations that carry identical nuclear haplotypes (N15, Fig.…”

Section: Phylogenetic Relationships Within Cardiocrinummentioning

confidence: 99%

Molecular phylogeny, biogeography and ecological niche modelling ofCardiocrinum(Liliaceae): insights into the evolutionary history of endemic genera distributed across the Sino-Japanese floristic region

Yang

Xie

et al. 2016

Ann Bot

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Background and Aims The patterns of evolutionary assembly in the Sino-Japanese floristic region (SJFR) remain largely unknown due to a lack of integrative multidimensional studies throughout the region. To address this issue, we elucidated the evolutionary history of Cardiocrinum (Liliaceae), a genus containing four taxa distributed across the SJFR.Methods Fifty-four populations were sampled throughout the geographical range of Cardiocrinum to assess genetic structure, analyse phylogenetic relationships and reconstruct ancestral area based on six chloroplast DNA (cpDNA) fragments and three low copy nuclear genes (LCNG). Ecological niche modelling was used to examine the potential range shifts of Cardiocrinum in response to climatic change.Key Results The molecular data showed high genetic similarity in the cpDNA (98Á37 %) and LCNG (94Á53 %) sequences. The biogeographical analyses revealed that the ancestor of Cardiocrinum diversified during the late Miocene (approx. 7Á32 Mya) in Central China. The ancestor of the C. giganteum lineage dispersed westward to the Himalayas and south-west China with the split between C. giganteum and C. giganteum var. yunnanense occurring around 4Á11 Mya consistent with the period of orogeny of the Hengduan Mountains. Some populations of the C. cathayanum lineage dispersed eastward to south Japan via the land bridge approx. 4Á97 Mya, providing opportunities for allopatric speciation of C. cordatum. The predicted suitable habitats of Cardiocrinum have become smaller and more fragmented since the Last Glacial Maximum.Conclusions Our study provides evidence of a biogeographical pattern of dispersal from Central China to the Himalayas in the west and Japan in the east for genera distributed across the SJFR, and highlights that the orogeny of the Hengduan Mountains and fluctuations of the sea level of the East China Sea played important roles in promoting species divergence.

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“…the real species phylogeny (Tajima, 1983). The conflicts between gene trees and species trees could be caused by incomplete lineage sorting, hybridization, gene duplication or branch length heterogeneity (Edwards, 2009;McCracken and Sorenson, 2005;McGuire et al, 2007). Therefore, results from species-level phylogenies that have used only a single locus or a concatenated gene matrix should be interpreted cautiously (Wahlberg et al, 2009).…”

Section: Gene-tree and Species-tree Conflicts On Phylogenetic Inferencementioning

confidence: 99%

Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods

Jiang

Guo

Huang

et al. 2014

Molecular Phylogenetics and Evolution

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Mitochondrial Introgression and Incomplete Lineage Sorting Through Space and Time: Phylogenetics of Crotaphytid Lizards

Cited by 255 publications

References 74 publications

The biogeography of mitochondrial and nuclear discordance in animals

The biogeography of mitochondrial and nuclear discordance in animals

Molecular phylogeny, biogeography and ecological niche modelling ofCardiocrinum(Liliaceae): insights into the evolutionary history of endemic genera distributed across the Sino-Japanese floristic region

Assessing species boundaries and the phylogenetic position of the rare Szechwan ratsnake, Euprepiophis perlaceus (Serpentes: Colubridae), using coalescent-based methods

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