Phylogeography is experiencing a revolution brought on by next-generation sequencing methods. A historical survey of the phylogeographic literature suggests that phylogeography typically incorporates new questions, expanding on its classical domain, when new technologies offer novel or increased numbers of molecular markers. A variety of methods for subsampling genomic variation, including restriction site associated DNA sequencing (Rad-seq) and other next generation approaches, are proving exceptionally useful in helping to define major phylogeographic lineages within species as well as details of historical demography. Next-generation methods are also blurring the edges of phylogeography and related fields such as association mapping of loci under selection, and the emerging paradigm is one of simultaneously inferring both population history across geography and genomic targets of selection. However, recent examples, including some from our lab on Anolis lizards and songbirds, suggest that genome subsampling methods, while extremely powerful for the classical goals of phylogeography, may fail to allow phylogeography to fully achieve the goals of this new, expanded domain. Specifically, if genome-wide linkage disequilibrium is low, as is the case in many species with large population sizes, most genome subsampling methods will not sample densely enough to detect selected variants, or variants closely linked to them. We suggest that whole-genome resequencing methods will be essential for allowing phylogeographers to robustly identify loci involved in phenotypic divergence and speciation, while at the same time allowing free choice of molecular markers and further resolution of the demographic history of species.

We present an overview of the emerging field of species-level distributional ecology, particularly as it relates to phylogeographic studies of birds in Eurasia. This field centers around distributional inferences and predictions deriving from the use of ecological niche modeling. We provide a brief historical review, and then proceed to outline a number of crucial methodological considerations, if models are to have biological meaning and reality. We then proceed to provide a worked example, as well as some thinking about directions in which the field should be moving in terms of questions and approaches.

Host-parasite cospeciation, in which parasite divergence occurs in response to host divergence, is commonly proposed as a driver of parasite diversification, yet few empirical examples of strict cospeciation exist. Host-parasite co-evolutionary histories commonly reflect complex mosaics of cospeciation, dispersal, lineage extinction and other phenomena. The episodic host-switching model of parasite diversification accounts for complexity by suggesting that diversification and faunal assembly is a consequence of fluctuation between environmental disruption and environmental stability. The phylogeographic predictions of the strict cospeciation and episodic host-switching models were tested using the North American pika/parasite assemblage, with a primary focus on the American pika, Ochotona princeps (Richardson, 1828), and a suite of its endoparasitic cestodes and nematodes. This approach integrating phylogeographic and demographic methods with inferences drawn from species distribution modelling revealed that the parasite community of pikas has been shaped by climate-driven range fluctuation of hosts and bouts of geographic and host colonization by parasites associated with transitions between glacial and interglacial phases.

The formation of ring species might provide an explanation of how speciation can occur despite ongoing gene flow. However, few species fit all of the criteria of a classic ring species that formed via isolation by distance around a barrier. Population genetic analyses and ecological niche models were used to examine a ring of song sparrow (Melospiza melodia) subspecies that surround the Sierra Nevada in North America. Eight models were compared that included both geography-based and ecology-based scenarios of ring formation. Song sparrows do fit some aspects of a classic ring species that formed via expansion around a barrier; however, admixture rather than complete reproductive isolation occurred when populations met at the terminus of the ring in southern California. Nichemodels show that variation among subspecies is likely to reflect adaptation to local conditions coupled with current limitations to gene flow across ecotones and that birds are likely to have expanded from a refugium in the southwestern United States. Given that simple isolation-based models often fail to explain many ring species patterns, alternative models that incorporate ecological factors might provide a better explanation of how most ring species formed. Isolation and subsequent partitioning of populations by ecotones can be important drivers of geographic variability in ring species.

Large-scale phylogeographical patterns and the underlying factors driving species divergence in Mesoamerica are poorly understood, but it is widely documented that tectonic events and Pleistocene climate changes play an important role in determining species diversification. As glaciations in Mesoamerica developed only around high mountains, one hypothesis is that the known effects of the Last Glacial Maximum on the geographical distribution and genetic diversity of bird populations, producing the contraction/ expansion latitudinal pattern observed in temperate bird species, should be largely undetected in resident bird populations inhabiting environmentally more stable habitats. To gain insight into the effects of Quaternary habitat and climate stability on the genetic diversity, we use ecological niche modelling and generalised linear modelling to determine the role of changes in habitat stability on the genetic diversity in eight widespread or range restricted hummingbird species. We found lesser changes in suitable habitat from past to present in most of the species than those predicted by palaeodistribution models at northern temperate regions. Contemporary seasonal precipitation, Quaternary habitat and climate stability had superior explanatory power, but the magnitude and directionality of their effects on genetic diversity varied between range-restricted and widely distributed species. We observed that the species studied have not responded equally to changes in climate stability in this complex region, suggesting that habitat differences and/or the altitudinal range of the hummingbird species influenced genetic diversity, and that the species-specific responses are not only linked to habitat stability in the region but also to contemporary seasonality associated with the availability of floral resources.

Molecular markers can be used to infer the demographic history of a given species, but many historic processes simultaneously impact multiple species. Thus, comparative historical demography has the potential to provide insight into drivers of evolution. In this study, we used nuclear DNA (nDNA) sequences to corroborate (or refute) demographic inferences based on earlier mitochondrial DNA (mtDNA) data from 16 species of Hispaniola birds. Our previously published analysis suggested population expansion in five of six migratory species (following glacial retreat in North America), with less evidence of expansion in non-migratory species. Additional molecular markers should reduce locus-specific bias, and so we generated sequence data for several nuclear loci. Test statistics associated with the nDNA provided only equivocal evidence for population expansion in 10 of the 16 species. Discordance between mtDNA and nDNA is not uncommon because the two genomes are exposed to different selective pressures and have different effective population sizes and modes of inheritance. The nDNA analyses reported here cast some doubt on our earlier mtDNA inferences. They also suggest that the signal to noise ratio of demographic statistics is typically low because of the inherent variability in selective regimes and coalescence across loci.

The effects of climate fluctuations on seasonally dry forests and their fauna are important to a holistic understanding of diversification in the South American lowlands. We document the intraspecific genetic structure of the burnished-buff tanager (Tangara cayana), a species common in seasonally dry tropical forests throughout South America. Using both mitochondrial sequence and nuclear microsatellite markers, we present an intraspecific phylogeny, haplotype network, and a STRUCTURE analysis. We also develop environmental niche models and project them onto two alternate paleoclimate models of the Last Glacial Maximum and mid-Holocene. Paleoclimate projections indicate a much greater extent and connectivity of suitable T. cayana habitat during the Last Glacial Maximum (LGM), decreasing through the mid-Holocene toward the present. Both microsatellite and mtDNA sequence data are consistent with a clockwise route of colonization for the current circum-Amazonian distribution of T. cayana. The species likely originated in the Cerrado of Brazil and expanded westward through Bolivia, across the seasonally dry forests at the base of the Andes, and into Guyana and northern Brazil. Northeastern populations then expanded south into coastal Pernambuco, Brazil completing the current ring-like distribution of this species.

In this study, we re-evaluated historical demography of the Eurasian green woodpecker (Picus viridis) on the basis of previously published multi-locus mitochondrial DNA (mtDNA) data and ecological niche modelling. We particularly aimed to test glacial refugia hypothesis during climatic oscillations of the late Quaternary for the Eurasian green woodpecker. Our results indicate that the Eurasian green woodpecker was sensitive to the effects of climate change. Prior to the Last Glacial Maximum (22000 years ago), the population contraction started and the Eurasian green woodpecker restricted its range to southern Europe (including France), Anatolia, and the Caucasus/Caspian region, and, afterwards, substantially expanded its range from this restricted area to its present range around 14500 years before present. Therefore, during the Last Glacial Maximum, we recognize a single large refugium for this species, located in southern Europe (including France), Anatolia, and the Caucasus/Caspian region.