Inferring population history from genealogies
Lohse, Konrad R.
This thesis investigates a range of genealogical approaches to making quantitative inferences about the spatial and demographic history of populations with application to two insect systems: A local radiation of high alpine ground beetles (Carabidae) in the genus Trechus and major refugial populations of the oak gall parasitoid Cecidostiba fungosa (Pteromalidae). i) Summary statistics, which make explicit use of genealogical information are developed. Using simulations their power to detect a history of population growth is shown to be higher than that of standard measures such as Tajima’s D for single and multilocus data. The improvement arises from the fact that in contrast to pairwise measures, the new statistics are minimally confounded with the topology. ii) A Bayesian method to reconstructing character states is used to infer the Pleistocene history of populations of high alpine Trechus sampled along a singlemountain range frommitochondrial and nuclear data. Despite evidence for some incomplete lineage sorting, a simple model of a series of extreme founder events out of two refugia during or before the last glacial maximum provides a good fit to the data. iii) A large set of exon-primed, intron-spanning (EPIC) loci is developed for Hymenoptera from EST and genomic data. Amplification success is screened on a range of Hymenopteran species associated with two insect-plant interactions: Oak galls and figs. iv) Borrowing model-based approaches developed to quantify species divergence, the new EPIC loci are used to investigate the relationships between three major European refugia in the oak gall parasitoid C. fungosa. These analyses reveal strong support for an eastern origin, effective ancestral population sizes comparable to insect model species and evidence for recent population divergence during the last interglacial. The results also suggest that there is significant information in minimal samples provided a large number of loci are available. v) Results for the probability of gene tree topologies are derived for a model of divergence with gene flow between three populations. I outline how the asymmetries in the frequency of gene tree topologies may be used to distinguish incomplete lineage sorting from migration and discuss the results in the context of next generation sequence data from D. melanogaster and humans and Neanderthals.