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  1. ; ; ( , Journal of Biogeography)
    Abstract Aim

    Lineage fusion (merging of two or more populations of a species resulting in a single panmictic group) is a special case of secondary contact. It has the potential to counteract diversification and speciation, or to facilitate it through creation of novel genotypes. Understanding the prevalence of lineage fusion in nature requires reliable detection of it, such that efficient summary statistics are needed. Here, we report on simulations that characterized the initial intensity and subsequent decay of signatures of past fusion for 17 summary statistics applicable to DNA sequence haplotype data.

     Location

    Global.

     Taxa

    Diploid out‐crossing species.

     Methods

    We considered a range of scenarios that could reveal the impacts of different combinations of read length versus number of loci (arrangement of DNA sequence data), and whether or not pre‐fusion populations experienced bottlenecks coinciding with their divergence (historical context of fusion). Post‐fusion gene pools were sampled along 10 successive time points representing increasing lag times following merging of sister populations, and summary statistic values were recalculated at each.

     Results

    Many summary statistics were able to detect signatures of complete merging of populations after a sampling lag time of 1.5Negenerations, but the most informative ones included two neutrality tests and four diversity metrics, withZnS(a linkage disequilibrium‐based neutrality test) being particularly powerful. Correlation was relatively low among the two neutrality tests and two of the diversity metrics. There were clear benefits of many short (200‐bp × 200) loci over a handful of long (4‐kb × 10) loci. Also, only the latter genetic dataset type showed impacts of bottlenecks during divergence upon the number of informative summary statistics.

     Main conclusions

    This work contributes to identifying cases of lineage fusion, and advances phylogeography by enabling more nuanced reconstructions of how individual species, or multiple members of an ecological community, responded to past environmental change.

     
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  2. ; ; ; ; ; ( , Insect systematics and diversity)
    Lozier, J (Ed.)
    Comparative phylogeographic studies can distinguish between idiosyncratic and community-wide responses to past environmental change. However, to date, the impacts of species interactions have been largely overlooked. Here we used non-genetic data to characterize two competing scenarios about expected levels of congruence among five deadwood-associated (saproxylic) invertebrate species (i.e., a wood-feeding cockroach, termite, and beetle; a predatory centipede, and a detritivorous millipede) from the southern Appalachian Mountains—a globally recognized center of endemism. Under one scenario, abiotic factors primarily drove species’ responses, with predicted congruence based on the spatial overlap of climatically stable habitat areas estimated for each species via ecological niche modeling. The second scenario considered biotic factors to be most influential, with proxies for species interactions used to predict congruence. Analyses of mitochondrial and nuclear DNA sequences focused on four axes of comparison: the number and geographic distribution of distinct spatial-genetic clusters, phylogeographic structure, changes in effective population size, and historical gene flow dynamics. Overall, we found stronger support for the ecological co-associations scenario, suggesting an important influence of biotic factors in constraining or facilitating species’ responses to Pleistocene climatic cycles. However, there was an imperfect fit between predictions and outcomes of genetic data analyses. Thus, while thought-provoking, conclusions remain tentative until additional data on species interactions becomes available. Ultimately, the approaches presented here advance comparative phylogeography by expanding the scope of inferences beyond solely considering abiotic drivers, which we believe is too simplistic. This work also provides conservation-relevant insights into the evolutionary history of a functionally important ecological community. 
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  3. ; ; ; ( , Insect systematics and diversity)
    Mardulyn, P. (Ed.)
    In the 21st century, phylogeography has experienced dramatic growth in the data and methods used by the field. Insect (more generally, hexapod) phylogeography has contributed to major advances and many of the influential papers included hexapods as model systems. In this literature review, we: (i) highlight recent phylogeographic work in hexapod systems, and (ii) identify broader trends and critical future steps in the field. We include a summary of useful methodological approaches and identify the methods used to approach different questions asked in phylogeographic studies. An updated summary of the applications that phylogeography has contributed to the field of entomology, including spatial studies, conservation, systematics, pest control, and invasive species, is included to highlight vital work in the field. Special attention is devoted to investigations which seek to use multi-species data to understand community ecological and evolutionary processes. Finally, we overview the main challenges, opportunities, and emerging areas, highlighting the “phylogeographic shortfall” that exists between the number of described hexapod species vs. the number of species that have been the focus of phylogeographic investigation. 
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  4. ; ; ; ; ( , Journal of Biogeography)
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