Ecological niche models in phylogeographic studies: applications, advances and precautions

Abstract

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.

Avian SDMs: current state, challenges, and opportunities

“…when studying genera or families that frequently diversified over millions of years. Phylogenetic comparative methods (Felsenstein 1985, Webb et al 2002 are typically (although not exclusively) used for a direct integration of niche models into phylogeographic studies (Chan et al 2011, AlvaradoSerrano andKnowles 2014). In an early avian study, Rice et al (2003) used SDMs to reconstruct the niche evolution in Aphelocoma jays and found strong deviation from niche conservatism; however, these results were contradicted by McCormack et al (2009).…”

Performance metrics and variance partitioning reveal sources of uncertainty in species distribution models

“…As a result of the rapid adoption of SDMs in the last decade, several aspects of SDM use and interpretation are actively evolving, including their application in phylogenetic studies and their ability to predict population density (Alvarado-Serrano and Knowles, 2014;Oliver et al, 2012;Pagel and Schurr, 2012). Many SDM studies compare alternative methodological approaches that help reduce or more accurately characterize uncertainty in the analysis of species-environment relationships (Dormann et al, 2008;Elith et al, 2006;Gritti et al, 2013;Synes and Osborne, 2011).…”

Trapped by climate: interglacial refuge and recent population expansion in the endemic Iberian adder Vipera seoanei

“…The combination of genetic and environmental data in spatial frameworks has increased research perspectives in biogeography and evolutionary biology (Kozak et al, 2008;Alvarado-Serrano & Knowles, 2014). Such approaches have allowed characterizing species environmental preferences (Barata et al, 2012), identifying the potential location of past climatic refugia (Waltari et al, 2007), understanding the role of past climatic changes in spatial and genetic connectivity (Velo-Ant on et al, 2013), or studying the dynamics of hybrid zones (Tarroso et al, 2014).…”