Inferring Phylogeny Despite Incomplete Lineage Sorting

Abstract

It is now well known that incomplete lineage sorting can cause serious difficulties for phylogenetic inference, but little attention has been paid to methods that attempt to overcome these difficulties by explicitly considering the processes that produce them. Here we explore approaches to phylogenetic inference designed to consider retention and sorting of ancestral polymorphism. We examine how the reconstructability of a species (or population) phylogeny is affected by (a) the number of loci used to estimate the phylogeny and (b) the number of individuals sampled per species. Even in difficult cases with considerable incomplete lineage sorting (times between divergences less than 1 N(e) generations), we found the reconstructed species trees matched the "true" species trees in at least three out of five partitions, as long as a reasonable number of individuals per species were sampled. We also studied the tradeoff between sampling more loci versus more individuals. Although increasing the number of loci gives more accurate trees for a given sampling effort with deeper species trees (e.g., total depth of 10 N(e) generations), sampling more individuals often gives better results than sampling more loci with shallower species trees (e.g., depth = 1 N(e)). Taken together, these results demonstrate that gene sequences retain enough signal to achieve an accurate estimate of phylogeny despite widespread incomplete lineage sorting. Continued improvement in our methods to reconstruct phylogeny near the species level will require a shift to a compound model that considers not only nucleotide or character state substitutions, but also the population genetics processes of lineage sorting. [Coalescence; divergence; population; speciation.].

Phylogeny of the families Pyuridae and Styelidae (Stolidobranchiata, Ascidiacea) inferred from mitochondrial and nuclear DNA sequences

“…Therefore, incongruence between 18S rDNA and COI phylogenies is not likely to be an artifact from saturation or pseudogene presence. Different gene trees can be affected by different histories of lineage sorting when there are deep coalescences (Maddison and Knowles, 2006;Kubatko and Degnan, 2007), which can hinder the inference of the true species tree. In addition, the different taxon sampling in both datasets can contribute to the lack of coherence found.…”

Evolutionary events in Lilium (including Nomocharis, Liliaceae) are temporally correlated with orogenies of the Q–T plateau and the Hengduan Mountains

“…Such discordances between phylogenies based on nuclear and chloroplast markers are generally caused by convergent evolution, lineage sorting, or ancient hybridization and introgression (Rieseberg and Soltis, 1991;Mason-Gamer et al, 1995;Rieseberg et al, 1996;Wendel and Doyle, 1998;Sang and Zhong, 2000;Comes and Abbott, 2001;Linder and Rieseberg, 2004). Among these, hybridization and incomplete lineage sorting have gained considerable attention and are known to confound phylogenetic analyses (Sang and Zhong, 2000;Maddison and Knowles, 2006;Joly et al, 2009).…”

Phylogeny of Rosa sections Chinenses and Synstylae (Rosaceae) based on chloroplast and nuclear markers

“…3 (continued) and horizontal gene transfer) can cause these phylogenetic inconsistencies (Cronn and Wendel, 2004;Linder and Rieseberg, 2004;Maddison, 1997;Rieseberg and Soltis, 1991;Wendel and Doyle, 1998;Zou and Ge, 2008). Among these causes, introgression and incomplete lineage sorting have been frequently discussed as the prominent factors of phylogenetic incongruence at lower taxonomic levels (Cronn and Wendel, 2004;Joly et al, 2009;Maddison and Knowles, 2006). Hybridization/introgression plays a significant role in the evolutionary history of most plant taxa (Abbott, 1992;Barton, 2001;Hewitt, 1988;Whitney et al, 2010).…”