A novel approach for choosing summary statistics in approximate Bayesian computation

Inferring the geographic mode of speciation by contrasting autosomal and sex-linked genetic diversity

When geographic isolation drives speciation, concurrent termination of gene flow among genomic regions will occur immediately after the formation of the barrier between diverging populations. Alternatively, if speciation is driven by ecologically divergent selection, gene flow of selectively neutral genomic regions may go on between diverging populations until the completion of reproductive isolation. It may also lead to an unsynchronized termination of gene flow between genomic regions with different roles in the speciation process. Here, we developed a novel Approximate Bayesian Computation pipeline to infer the geographic mode of speciation by testing for a lack of postdivergence gene flow and a concurrent termination of gene flow in autosomal and sex-linked markers jointly. We applied this approach to infer the geographic mode of speciation for two allopatric highland rosefinches, the vinaceous rosefinch Carpodacus vinaceus and the Taiwan rosefinch C. formosanus from DNA polymorphisms of both autosomal and Z-linked loci. Our results suggest that the two rosefinch species diverged allopatrically approximately 0.5 Ma. Our approach allowed us further to infer that female effective population sizes are about five times larger than those of males, an estimate potentially useful when comparing the intensity of sexual selection across species.

Viral phylodynamics

Viral phylodynamics is defined as the study of how epidemiological, immunological, and evolutionary processes act and potentially interact to shape viralphylogenies. Since the coining of the term in 2004, research on viral phylodynamics has focused on transmission dynamics in an effort to shed light on how these dynamics impact viral genetic variation. Transmission dynamics can be considered at the level of cells within an infected host, individual hosts within a population, or entire populations of hosts. Many viruses, especially RNA viruses, rapidly accumulate genetic variation because of short generation times and high mutation rates. Patterns of viral genetic variation are therefore heavily influenced by how quickly transmission occurs and by which entities transmit to one another. Patterns of viral genetic variation will also be affected by selection acting on viral phenotypes. Although viruses can differ with respect to many phenotypes, phylodynamic studies have to date tended to focus on a limited number of viral phenotypes. These include virulence phenotypes, phenotypes associated with viral transmissibility, cell or tissue tropism phenotypes, and antigenic phenotypes that can facilitate escape from host immunity. Due to the impact that transmission dynamics and selection can have on viral genetic variation, viral phylogenies can therefore be used to investigate important epidemiological, immunological, and evolutionary processes, such as epidemic spread[2], spatio-temporal dynamics including metapopulation dynamics[3], zoonotic transmission, tissue tropism[4], and antigenic drift[5]. The quantitative investigation of these processes through the consideration of viral phylogenies is the central aim of viral phylodynamics.