Abstract
Understanding the nature, timing and geographic context of historical events and population processes that shaped the spatial distribution of genetic diversity is critical for addressing questions relating to speciation, selection, and applied conservation management. Cladistic analysis of gene trees has been central to phylogeography, but when coupled with approaches that make use of different components of the information carried by DNA sequences and their frequencies, the strength and resolution of these inferences can be improved. However, assessing concordance of inferences drawn using different analytical methods or genetic datasets, and integrating their outcomes, can be challenging. Here we overview the strengths and limitations of different types of genetic data, analysis methods, and approaches to historical inference. We then turn our attention to the potentially synergistic interactions among widely-used and emerging phylogeographic analyses, and discuss some of the ways that spatial and temporal concordance among inferences can be assessed. We close this review with a brief summary and outlook on future research directions.
Highlights
Phylogeography focuses on understanding how population processes and historical events influence the spatial distribution of biodiversity in extant species [1,2]
It is common practice to start by assessing ancient subdivisions via phylogenetic analysis of DNA sequences, and if geographically localized clades are identified from the estimated gene tree, these are subsequently used as population units in analyses that focus on demography over intermediate timescales
American taxa, pointing towards a scenario of rapid northward range expansions following the retreat of Quaternary ice sheets in that region. This time centered in the Wet Tropics of north-eastern Australia, Hugall et al [53] used FLUCTUATE analysis of mitochondrial DNA (mtDNA) from a low-mobility forest-restricted land snail to assess whether genetic data were consistent with predictions from paleoclimatic modeling of the species’ Quaternary habitat distributions
Summary
Phylogeography focuses on understanding how population processes (e.g., gene flow) and historical events (e.g., vicariance or range expansion) influence the spatial distribution of biodiversity in extant species [1,2]. Statistical phylogeographic analyses have advanced over recent years [29,30,31,32], and researchers are well-equipped to address questions that were previously intractable This is due to the emergence of sophisticated model-driven approaches to estimating population genetic parameters and their confidence intervals, and this information can be used to generate more robust inferences [33,34,35,36,37,38,39,40]. Complex population divergence scenarios can be assessed by framing questions in a spatially- and temporally-explicit manner (e.g., are the empirical DNA sequence data consistent with a scenario of differentiation in separate refugia isolated during Last Glacial Maximum, followed by Holocene range expansion?) These developments have facilitated hypothesis-driven approaches to phylogeography. We examine some of the challenges relating to assessing concordance among inferences drawn using different methods or datasets and integrating their outcomes, and suggest practical solutions
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
