Pleistocene divergence of two disjunct conifers in the eastern Australian temperate zone

The eastern Australian temperate biota harbours many plants with fragmented geographic ranges distributed over 1000s of kilometres, yet the spatial genetic structure of their populations remains largely unstudied. In this study, we investigated genetic variation of the nuclear internal transcribed spacer (ITS) and chloroplast DNA sequences to disentangle the phylogeography of two widely distributed but highly fragmented eastern Australian fire-sensitive temperate conifers: Callitris oblonga (12 populations and 121 individuals) and C. rhomboidea (22 populations and 263 individuals). The three highly disjunct populations of C. oblonga all had unique chloroplast and ITS haplotypes consistent with the classification of these three populations as distinct subspecies. Molecular dating indicates that divergences of these populations occurred pre- to mid- Pleistocene (2.66 to 1.08 mya). Callitris rhomboidea showed greater diversity of chloroplast haplotypes which was strongly phylogeographically structured (Gst = 0.972), with haplotypes unique to specific geographic regions. ITS haplotype diversity was far higher than in C. oblonga with 38 haplotypes displaying high geographic structuring (Gst = 0.387) with many population-specific haplotypes. A phylogeographic break was identified between populations north and south of eastern Victoria dated at 0.43–0.47 mya. In both species, the strong genetic structuring of both chloroplast and ITS haplotypes provides evidence that their widespread ranges have resulted from long term persistence in low fire frequency refugia combined with poor dispersal. Any loss of populations due to increasing fire frequency or habitat loss is likely to result in a reduction of genetic diversity

Disease induced changes in gene flow patterns among Tasmanian devil populations

Infectious diseases of wildlife reduce population size and may erode genetic diversity, constituting an extinction threat. The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction by an infectious cancer, the devil facial tumour disease (DFTD). In less than two decades, DFTD has caused a more than 85% overall population decline. We used ten polymorphic microsatellite loci to quantify the effects of this decline on genetic diversity, population differentiation, effective population size, and gene flow. Samples from 1999 and 2006 at five locations were analysed, three of which had been affected by DFTD during this time interval. Significant increases in inbreeding coefficient (f) and non-significant reductions in effective population size were observed for both diseased and non-diseased populations, and therefore there was no consistent effect of DFTD. There was significant but stable structuring of genetic variation among locations through time, although a dynamic “source-sink” relationship was evident for gene flow associated with disease-mediated changes in population densities. These changes in gene flow may have contributed to the maintenance of genetic diversity in disease-affected areas. Simulations suggest that the estimated population declines, although severe, have been insufficient to yield significant changes in genetic variation; this may have been exacerbated by disequilibrium between population sizes and genetic diversity at the time of DFTD emergence, owing to elevated devil abundances following the extinction of the previous apex predator—the thylacine—approximately 80years ago.Anna Bruniche-Olsen, Christopher P. Burridge, Jeremy J. Austin and Menna E. Jone

Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds

The rate of mutation accumulation in germline cells can be affected by cell replication and/or DNA damage, which are further related to life history traits such as generation time and body mass. Leveraging the existing datasets of 233 neoavian bird species, here, we investigated whether generation time and body mass contribute to the interspecific variation of orthologous microsatellite length, transposable element (TE) length, and deletion length and how these genomic attributes affect genome sizes. In nonpasserines, we found that generation time is correlated to both orthologous microsatellite length and TE length, and body mass is negatively correlated to DNA deletions. These patterns are less pronounced in passerines. In all species, we found that DNA deletions relate to genome size similarly as TE length, suggesting a role of body mass dynamics in genome evolution. Our results indicate that generation time and body mass shape the evolution of genomic attributes in neoavian birds