Browsing by Author "Lavery SD"

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    Comparative phylogeography in the genomic age: Opportunities and challenges
    (John Wiley and Sons Ltd, 2022-12) McGaughran A; Liggins L; Marske KA; Dawson MN; Schiebelhut LM; Lavery SD; Knowles LL; Moritz C; Riginos C; Byrne M
    Aim: We consider the opportunities and challenges comparative phylogeography (CP) faces in the genomic age to determine: (1) how we can maximise the potential of big CP analyses to advance biogeographic and macroevolutionary theory; and (2) what we can, and will struggle, to achieve using CP approaches in this era of genomics. Location: World-wide. Taxon: All. Methods: We review the literature to discuss the future of CP - particularly examining CP insights enabled by genomics that may not be possible for single species and/or few molecular markers. We focus on how geography and species' natural histories interact to yield congruent and incongruent patterns of neutral and adaptive processes in the context of both historical and recent rapid evolution. We also consider how CP genomic data are being stored, accessed, and shared. Results: With the widespread availability of genomic data, the shift from a single- to a multi-locus perspective is resulting in detailed historical inferences and an improved statistical rigour in phylogeography. However, the time and effort required for collecting co-distributed species and accruing species-specific ecological knowledge continue to be limiting factors. Bioinformatic skills and user-friendly analytical tools, alongside the computational infrastructure required for big data, can also be limiting. Main conclusions: Over the last ~35 years, there has been much progress in understanding how intraspecific genetic variation is geographically distributed. The next major steps in CP will be to incorporate evolutionary processes and community perspectives to account for patterns and responses among co-distributed species and across temporal scales, including those related to anthropogenic change. However, the full potential of CP will only be realised if we employ robust study designs within a sound comparative framework. We advocate that phylogeographers adopt such consistent approaches to enhance future comparisons to present-day findings.
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    Genogeographic clustering to identify cross-species concordance of spatial genetic patterns
    (John Wiley and Sons, Ltd, 2022-04) Arranz V; Fewster RM; Lavery SD; Burridge C
    Aim: While in recent years, there have been considerable advances in discerning spatial genetic patterns within species, the task of identifying common patterns across species is still challenging. Approaches using new data from co-sampled species permit rigorous statistical analysis but are often limited to a small number of species. Meta-analyses of published data can encompass a much broader range of species, but are usually restricted by uneven data properties. There is a need for new approaches that bring greater statistical rigour to meta-analyses and are also able to discern more than a single spatial pattern among species. We propose a new approach for comparative multi-species meta-analyses of published population genetic data that address many existing limitations. Innovation: The proposed “genogeographic clustering” technique takes a three-stage approach: (i) use common genetic metrics to gain location-specific measures across the sampled range of each species; (ii) for each species, determine the spatial genetic pattern by fitting a smooth “genogeographic” trend curve to the genetic data; and (iii) quantitatively cluster species according to their similarity in spatial pattern. We apply this technique to 21 species of intertidal invertebrates from the New Zealand coastline, to resolve common spatial patterns from disparate profiles of genetic diversity. Main conclusions: The genogeographic curves are shown to successfully capture the known spatial patterns within each intertidal species and readily permit statistical comparison of those patterns, regardless of sampling and marker inconsistencies. The species clustering technique is shown to discern groups of species that clearly share spatial patterns within groups but differ significantly among groups. Genogeographic species clustering provides a novel approach to discerning multiple common spatial patterns of diversity among a large number of species. It will permit more rigorous comparative studies from diverse published data and can be easily extended to a wide variety of alternative measures of genetic diversity or divergence.