Whole-genome analyses resolve early branches in the tree of life of modern birds

Abstract

To better determine the history of modern birds, we performed a genome-scale phylogenetic analysis of 48 species representing all orders of Neoaves using phylogenomic methods created to handle genome-scale data. We recovered a highly resolved tree that confirms previously controversial sister or close relationships. We identified the first divergence in Neoaves, two groups we named Passerea and Columbea, representing independent lineages of diverse and convergently evolved land and water bird species. Among Passerea, we infer the common ancestor of core landbirds to have been an apex predator and confirm independent gains of vocal learning. Among Columbea, we identify pigeons and flamingoes as belonging to sister clades. Even with whole genomes, some of the earliest branches in Neoaves proved challenging to resolve, which was best explained by massive protein-coding sequence convergence and high levels of incomplete lineage sorting that occurred during a rapid radiation after the Cretaceous-Paleogene mass extinction event about 66 million years ago.

Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

“…The total assembly length was ~1.2 Gb, similar to other bird genomes (Jarvis et al., 2014), and average k‐mer coverage was ~40× (see Table S1 for assembly statistics). ray reported peak coverage at 20×, but it was mislead by the first peak of higher coverage (two peaks are expected because of heterozygous sites; Fig.…”

Evolution of the immune system influences speciation rates in teleost fishes

“…Following Jarvis et al 29 , we mapped genomic insertions and deletions on the rooted topology and found no correlation between branch lengths and uniquely mapped indels. This lack of correlation indicates that incomplete lineage sorting did not substantially affect divergences between the teleost lineages included in our phylogeny 29 and supports concatenation as the most appropriate strategy for species phylogeny estimation with our data (Supplementary Note).…”

Combining phylogenomic and supermatrix approaches, and a time-calibrated phylogeny for squamate reptiles (lizards and snakes) based on 52 genes and 4162 species

“…For example, large-scale sequencing projects have been undertaken for many important clades, in which hundreds of loci are sequenced (e.g. Dunn et al, 2008;Regier et al, 2010;Kocot et al, 2011;Chiari et al, 2012;Struck et al, 2011;Jarvis et al, 2014;Weigert et al, 2014). Yet, at the same time, most species in many clades may still have data for no more than a few genes each (see below).…”

“…One extreme approach is to focus on resolving higher-level relationships by sampling large numbers of genes in a relatively small sample of species: this is the common approach in phylogenomic studies (e.g. Chiari et al, 2012;Jarvis et al, 2014;Weigert et al, 2014). Another extreme approach is to include hundreds or thousands of species but for a smaller number of genes: this is the typical approach in supermatrix studies (e.g.…”