Phylogeography and lineage-specific patterns of genetic diversity and molecular evolution in a group of North American skinks
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Geography influences the evolutionary trajectory of species by mediating opportunities for hybridization, gene flow, demographic shifts and adaptation. We sought to understand how geography and introgression can generate species-specific patterns of genetic diversity by examining phylogeographical relationships in the North American skink species Plestiodon multivirgatus and P. tetragrammus (Squamata: Scincidae). Using a multilocus dataset (three mitochondrial genes, four nuclear genes; a total of 3455 bp) we discovered mito-nuclear discordance, consistent with mtDNA introgression. We further tested for evidence of species-wide mtDNA introgression by using comparisons of genetic diversity, selection tests and extended Bayesian skyline analyses. Our findings suggest that P. multivirgatus acquired its mitochondrial genome from P. tetragrammus after their initial divergence. This putative species-wide mitochondrial capture was further evidenced by statistically indistinguishable substitution rates between mtDNA and nDNA in P. multivirgatus. This rate discrepancy was observed in P. multivirgatus but not P. tetragrammus, which has important implications for studies that combine mtDNA and nDNA sequences when inferring time since divergence between taxa. Our findings suggest that by facilitating opportunities for interspecific introgression, geography can alter the course of molecular evolution between recently diverged lineages.Keywords:
Lineage (genetic)
Phylogeography: The History and Formation of Species. John C. Avise. Harvard University Press, Cambridge, Massachusetts, 2000, viii + 447 pp., $49.95, (ISBN 0-674-66638-0).
Breakthroughs in DNA sequencing technology in the 1980's revolutionized evolutionary biology, and out of this revolution emerged what has become a highly influential discipline known as phylogeography. Formally introduced a little more than a decade ago by John Avise and his colleagues (Avise et al., 1987), phylogeography is a highly integrative approach used to investigate the relationship between earth history, ecology, and biotic diversification. Phylogeography combines information from population genetics, phylogenetics, geoclimatic history, paleontology, population biology, molecular evolution, and historical biogeography in order to characterize the geographic distributions of genealogical lineages across the geographic landscape (referred to as phylogeographic patterns), and to infer the evolutionary, demographic and biogeographic processes that have shaped these patterns.
In this book, Avise provides an overview of the historical development of phylogeography, from its early stages when animal mitochondrial DNA (mtDNA) was used (almost exclusively) to examine phylogeographic patterns within single species, to today, when an increasingly wider range of additional molecular markers are being used to compare phylogeographic patterns among co-distributed taxa (comparative phylogeography). As the principle founder of the field, no one is better qualified to write a book recounting the history of phylogeography, and Avise excels at providing …
Population Genetics
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The phylogeographic analysis of Stylodipus telum was performed based on cytochrome b mitochondrial gene. Two westernmost subspecies, S.t. falzfeini and S.t. turovi, both formed independent monophyletic clades, but the genetic distance between them clearly indicates that neither should be treated as a separate species. Individuals from remote populations of S.t. falzfeini mix together and do not have a clear phylogeographic structure, which could indicate a recent panmixia within the subspecies. Populations in Kherson Region are under threat due to the ongoing Russian invasion.
Subspecies
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That lineage system was well-developed in Huizhou area was a result of local intellectual’s endeavour to make this system cater to the common people. This result was not only relevant to the practice of patriarchal system, but also a new explanation of the patriarchal-lineage theory to local lineage’s construction. Wang Dao- kun’s claim of constructing the genealogy and his actions were just based on the forefather culture of common people. His emphasis on the idea that all the relatives should be included in the lineage was a new explanation to local lineage’s activities. The practice of lineage’s construction promoted the development of patriarchal system catering to the common people.
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This chapter contains sections titled: What is phylogeography? Molecular markers in phylogeography Molecular clocks Bifurcating trees The coalescent Networks Nested Clade Phylogeographic analysis and statistical phylogeography The distributions of genetic lineages Comparative phylogeography Allele sharing between species Overview Chapter summary Useful websites and software Further reading Online activities Review questions
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Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes, contributing to the inference of vicariance, dispersal, speciation, and other population-level processes. Phylogeographic surveys usually require considerable effort and time to obtain numerous samples from many geographical sites covering the distribution range of target species; this associated high cost limits their application. Recently, environmental DNA (eDNA) analysis has been useful not only for detecting species but also for assessing genetic diversity; hence, there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results obtained from eDNA analysis accurately reflect known phylogeographic patterns. For these purposes, we performed quantitative eDNA metabarcoding using group-specific primer sets in five freshwater fish species belonging to two taxonomic groups from a total of 94 water samples collected from western Japan. As a result, three-step data screening based on the DNA copy number of each haplotype detected successfully eliminated suspected false positive haplotypes. Furthermore, eDNA analysis could almost perfectly reconstruct the phylogenetic and phylogeographic patterns obtained for all target species with the conventional method. Despite existing limitations and future challenges, eDNA-based phylogeography can significantly reduce survey time and effort and is applicable for simultaneous analysis of multiple species in single water samples. eDNA-based phylogeography has the potential to revolutionize phylogeography.
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Central America is an ideal region for comparative phylogeographic studies because of its intricate geologic and biogeographic history, diversity of habitats and dynamic climatic and tectonic history. The aim of this work was to assess the phylogeography of two rodents codistributed throughout Central America, in order to identify if they show concordant genetic and phylogeographic patterns. The synopsis includes four parts: (1) an overview of the field of comparative phylogeography; (2) a detailed review that describes how genetic and geologic studies can be combined to elucidate general patterns of the biogeographic and evolutionary history of Central America; and a phylogeographic analysis of two species at both the (3) intraspecific and (4) comparative phylogeographic levels. The last incorporates specific ecological features and evaluates their influence on the species’ genetic patterns. Results showed a concordant genetic structure influenced by geographic distance for both rodents, but dissimilar dispersal patterns due to ecological features and life history.
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Vicariance
Coalescent theory
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In this chapter, lineage organization and lineage ideology are discussed in detail. In particular I am concerned with the relationship between an ideology that emphasizes lineage solidarity and a socioeconomic system that is based on clear economic inequalities. In Chapter 2 I discussed the early history of the Teng lineage; the present chapter is concerned with the lineage during the twentieth century, although the patterns described are very likely representative of earlier periods as well. The data presented in the following pages are based upon conversations with lineage elders, personal observations, and analyses of the many lineage rituals I attended. Lineage genealogies also provide an important source of information.
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