Does habitat stability structure intraspecific genetic diversity? It’s complicated...

Regional phylogeographic studies have long been conducted in the southeastern United States for a variety of species. With some exceptions, many of these studies focus on single species or single clades of organisms, and those considering multiple species tend to focus on deep historical breaks causing differentiation. However, in many species more recent factors may be influencing genetic diversity. To understand the roles of historic and contemporary processes in structuring genetic diversity, we reanalyzed existing genetic data from Southeast of North America using approaches gleaned from phylogeographic and landscape genetic literature that were implemented across species including AMOVAs, PCoAs, Species Distribution Modelling, and tests of isolation by distance, environment, and habitat instability. Genetic variance was significantly partitioned by ecoregions, watersheds, and across phylogeographic breaks in the majority of species. Similarly, genetic variation was significantly associated with some combination of geographic or environmental distance or habitat instability in most species. Patterns of genetic variation were largely idiosyncratic across species. While habitat instability over time is significantly correlated with genetic diversity in some species, it appears generally less important than isolation by geographic or environmental distance. Our results suggest that many factors, both historical and contemporary, impact genetic diversity within a species, and more so, that these patterns aren’t always similar in closely related species. This supports the importance of species- specific factors and cautions against assumptions that closely related species will respond to historical and contemporary forces in similar ways

On the Use of Median-joining Networks: A Philosophical and Empirical Evaluation of Its Suitability in Evolutionary Biology

A phylogenetic tree is a branching diagram illustrating the inferred evolutionary history of taxa. It only represents the vertical transmission of DNA due to its structure. Phylogenetic networks have been proposed to overcome this limitation and to show complex scenarios such as hybridization in a cyclic structure known as reticulation. Median-Joining Networks (MJNs) are one of the most popular approaches to discovering reticulations, but it has been used hastily in evolutionary studies without critical examination of its assumptions, performance and suitability. The MJ algorithm is based on phenetics, and the networks lack evolutionary direction. I evaluate the extent of congruence between MJNs and Bayesian inference phylogenies through likelihood-based tests and detect a significant difference in branching order between the two methods in more than one-third of unambiguous cases. Analyses document that MJNs are inappropriate for evolutionary inference, and I encourage the biologists to take a pause and reassess its usage.M.Sc

Additional threat to Hynobius salamander eggs: Predation by loaches (Misgurnus sp.) in agricultural wetlands

Anthropogenic modifications of the environment have clear negative impacts on species. These effects may reach a higher magnitude in highly altered habitats, for example in wetlands transformed into rice paddies. This is the case for the amphibian species of the genus Hynobius in the Republic of Korea, which originally breed in slow streams and valleys. However, a comparatively high proportion of the natural breeding sites used by the species in the lowlands has been transformed into rice paddies. Here, we assessed whether anthropogenic modification of wetlands leads to an additional threat to breeding Hynobius spp. in the form of increased vulnerability of their egg clutches to loach predators (Misgurnus species) in such modified habitats. We conducted weekly occurrence surveys at 27 randomly selected sites in the Republic of Korea and recorded the following information: type of site (natural versus agricultural), air temperature, water conductivity, moon phase and predation by Misgurnus sp. Our results reveal, for the first time, cases of predation of Hynobius spp. eggs by Misgurnus loaches. We also show that the risk of predation was higher in agricultural sites in comparison to natural sites. In conclusion, we demonstrate the increased predation risk of Hynobius spp. eggs by Misgurnus sp. at anthropogenically disturbed sites, and thus a new type of threat to Hynobius populations. This new type of threat may, however, be due to expansion of the breeding habitats following human disruptions to landscapes. We therefore call for the development of mitigating measures to wetland modifications