This is a time of unprecedented transition in DNA sequencing technologies. Next-generation sequencing (NGS) clearly holds promise for fast and cost-effective generation of multilocus sequence data for phylogeography and phylogenetics. However, the focus on non-model organisms, in addition to uncertainty about which sample preparation methods and analyses are appropriate for different research q...

Lizards have been model organisms for ecological and evolutionary studies from individual to community levels at multiple spatial and temporal scales. Here we highlight lizards as models for phylogeographic studies, review the published population genetics/phylogeography literature to summarize general patterns and trends and describe some studies that have contributed to conceptual advances. O...

In the newly emerging field of statistical phylogeography, consideration of the stochastic nature of genetic processes and explicit reference to theoretical expectations under various models has dramatically transformed how historical processes are studied. Rather than being restricted to ad hoc explanations for observed patterns of genetic variation, assessments about the underlying evolutiona...

the identification of the efficiency of some mtdna genes of mus musculus species complex (house mouse) for biosystematics research was studied in this approach. recent studies have made use of different mitochondrial genes including nadh dehydrogenase genes, cytochrome b gene, cytochrome oxidase genes, d-loop region and whole mtdna genome to study the house mouse species. usage of each of these...

the japanese threadfin bream, nemipterus japonicus, the most abundant and crucially economic nemipterus species is widespread throughout the indo-west pacific. the species has been studied widely for various aspects but genetic studies are scanty. this preliminary study contributes to the species phylogeography through the study of the genetic diversity and historical demography of n. japonicus...

Figs 2–5 have been corrected for improved readability. Please see the corrected Fig 2 here. access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

For three decades, comparative phylogeography has conceptually and methodologically relied on the concordance criterion for providing insights into the historical/biogeographic processes driving population genetic structure and divergence. Here we discuss how this emphasis, and the corresponding lack of methods for extracting information about biotic/intrinsic contributions to patterns of genet...

The geographic diffusion of highly pathogenic influenza A H5N1 has largely been traced from the perspective of the virus's victims. Birds of a variety of avian orders have been sampled across localities, and their infection has been identified by a general genetic test. Another approach tracks the migration from the perspective of the virus alone, by way of a phylogeography of H5N1 genetic sequ...

An area of endemism (AOE) is a complex expression of the ecological and evolutionary history of a species. Here we aim to address the principal drivers of avian diversification in shaping patterns of endemism in China by integrating genetic, ecological, and distributional data on the Red-headed Tree Babbler (Stachyridopsis ruficeps), which is distributed across the eastern Himalayas and south C...

The genetic landscape of the European flora and fauna was shaped by the ebb and flow of populations with the shifting ice during Quaternary climate cycles. While this has been well demonstrated for lowland species, less is known about high altitude taxa. Here we analyze the phylogeography of the leaf beetle Oreina elongata from 20 populations across the Alps and Apennines. Three mitochondrial a...