The increased availability of spatial data and methodological developments in species distribution modelling has lead to concurrent advances in phylogeography, broadening the scope of questions studied, as well as providing unprecedented insights. Given the species-specific nature of the information provided by ecological niche models (ENMs), whether it is on the environmental tolerances of species or their estimated distribution, today or in the past, it is perhaps not surprising that ENMs have rapidly become a common tool in phylogeographic analysis. Such information is essential to phylogeographic tests that provide important biological insights. Here, we provide an overview of the different applications of ENMs in phylogeographic studies, detailing specific studies and highlighting general limitations and challenges with each application. Given that the full potential of integrating ENMs into phylogeographic cannot be realized unless the ENMs themselves are carefully applied, we provide a summary of best practices with using ENMs. Lastly, we describe some recent advances in how quantitative information from ENMs can be integrated into genetic analyses, illustrating their potential use (and key concerns with such implementations), as well as promising areas for future development.

Understanding the genetic consequences of shifting species distributions is critical for evaluating the impact of climate-induced distributional changes. However, the demographic expansion associated with the colonization process typically takes place across a heterogeneous environment, with population sizes and migration rates varying across the landscape. Here we describe an approach for coupling ecological-niche models (ENMs) with demographic and genetic models to explore the genetic consequences of distributional shifts across a heterogeneous landscape. Analyses of a flightless grasshopper from the sky islands of the Rocky Mountains of North America are used to show how biologically informed predictions can be generated about the genetic consequences of a colonization process across a spatially and temporally heterogeneous landscape (i.e. the suitability of habitats for the montane species differs across the landscape and is itself not static, with the displacement of contemporary populations into glacial refugia). By using (i) ENMs for current climatic conditions and the last glacial maximum to (ii) parameterize a demographic model of the colonization process, which then (iii) informs coalescent simulations, a set of models can be generated that capture different processes associated with distributional shifts. We discuss how the proposed approach for model generation can be integrated into a statistical framework for estimating key demographic parameters and testing hypotheses about the conditions for which distributional shifts may (or may not) enhance species divergence, including the importance of habitat stability, past gene-flow among currently isolated populations, and maintenance of refugial populations in multiple geographic regions.

We apply a comparative framework to test for concerted demographic changes in response to climate shifts in the neotropical lowland forests, learning from the past to inform projections of the future. Using reduced genomic (SNP) data from three lizard species codistributed in Amazonia and the Atlantic Forest (Anolis punctatus, Anolis ortonii, and Polychrus marmoratus), we first reconstruct former population history and test for assemblage-level responses to cycles of moisture transport recently implicated in changes of forest distribution during the Late Quaternary. We find support for population shifts within the time frame of inferred precipitation fluctuations (the last 250,000 y) but detect idiosyncratic responses across species and uniformity of within-species responses across forest regions. These results are incongruent with expectations of concerted population expansion in response to increased rainfall and fail to detect out-of-phase demographic syndromes (expansions vs. contractions) across forest regions. Using reduced genomic data to infer species-specific demographical parameters, we then model the plausible spatial distribution of genetic diversity in the Atlantic Forest into future climates (2080) under a medium carbon emission trajectory. The models forecast very distinct trajectories for the lizard species, reflecting unique estimated population densities and dispersal abilities. Ecological and demographic constraints seemingly lead to distinct and asynchronous responses to climatic regimes in the tropics, even among similarly distributed taxa. Incorporating such constraints is key to improve modeling of the distribution of biodiversity in the past and future.phylogeography | population genomics | Amazon Forest | Atlantic Forest | climate change

To our knowledge, this is the first study to provide spatially explicit predictions of within-species genetic diversity using climatic, demographic, and genetic data. Our approach accounts for climatic, geographic, and biological complexity. This framework is promising for understanding evolutionary consequences of climate change, and guiding conservation planning.