Site pattern probabilities under the multispecies coalescent and a relaxed molecular clock: Theory and applications.

The first step in statistical inference of the evolutionary histories of species is developing a probability model that describes the mutation process as accurately and realistically as possible. A major complication of this inference is that different loci on the genome can have histories that diverge from the common species history and each other. The multispecies coalescent process is commonly used to model one source of this divergence, incomplete lineage sorting, or ILS. In Chifman and Kubatko (2015), the authors computed the site pattern probabilities for four taxa under a full probability model based on the Jukes-Cantor substitution model when the molecular clock holds. This paper generalizes that work to a relaxed clock model, allowing for mutation rates to differ among species. This will enable better phylogentic inference in cases where the molecular clock does not hold.

Global phylogenetic relationships, population structure and gene flow estimation of Trialeurodes vaporariorum (Greenhouse whitefly).

Trialeurodes vaporariorum (Westwood, 1856) (Greenhouse whitefly) is an agricultural pest of global importance. It is associated with damage to plants during feeding and subsequent virus transmission. Yet, global phylogenetic relationships, population structure, and estimation of the rates of gene flow within this whitefly species remain largely unexplored. In this study, we obtained and filtered 227 GenBank records of mitochondrial cytochrome c oxidase I (mtCOI) sequences of T. vaporariorum, across various global locations to obtain a final set of 217 GenBank records. We further amplified and sequenced a ~750 bp fragment of mtCOI from an additional 31 samples collected from Kenya in 2014. Based on a total of 248 mtCOI sequences, we identified 16 haplotypes, with extensive overlap across all countries. Population structure analysis did not suggest population differentiation. Phylogenetic analysis indicated the 2014 Kenyan collection of samples clustered with a single sequence from the Netherlands to form a well-supported clade (denoted clade 1a) nested within the total set of sequences (denoted clade 1). Pairwise distances between sequences show greater sequence divergence between clades than within clades. In addition, analysis using migrate-n gave evidence for recent gene flow between the two groups. Overall, we find that T. vaporariorum forms a single large group, with evidence of further diversification consisting primarily of Kenyan sequences and one sequence from the Netherlands forming a well-supported clade.