A Phylogenomic Supertree of Birds

Abstract

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution

“…The rails are frequently undersampled in phylogenomic studies (e.g., [22,62]), and our results provide a robust framework for building the phylogenomic supertree of birds. This is important for the study of avian macroevolution and biogeography [63] and for resolving discrepancies in the phylogenetic signals retrieved from geo-temporal fossils and molecular data.…”

Phylogeny, transposable element and sex chromosome evolution of the basal lineage of birds

“…It is known that the topology of phylogenetic tree is sensitive to the amount and the type of data, the number of sampled species, as well as the method of phylogenetic inference 9,31,32 .…”

Tanopicobia gen. nov., a new genus of quill mites, its phylogenetic placement in the subfamily Picobiinae (Acariformes: Syringophilidae) and picobiine relationships with avian hosts

“…The genus Pipicobia (4 species) is associated with birds of orders Passeriformes and Psittaciformes. Nowadays, there seems to be a general agreement that these two terminal clades are close, sister to each other [33][34][35][36][37][38][39][40]. On the other hand, Neopicobia (12 species) is associated with birds of the orders Passeriformes and Piciformes.…”

“…Despite Piciformes were in pre-cladistic taxonomy considered to be a near-passerine taxon [41,42] and some early cladistic analyses also put them close to each other [43], today it is believed that they represent a different, rather distant lineage of Telluraves, core land birds [44]. This taxon comprises of two main clades: Afroaves, including the Piciformes, and Australaves, including Passeriformes and Psittaciformes [38][39][40]45,46].…”

“…To summarize, the host spectrum for Neopicobia-generic group cover advanced bird clades of telluriform birds plus neoavian Charadriiformes and Gruiformes (Table 1 and Fig 5). Despite these two bird taxa comprise well supported subclades in most recent phylogenomic studies [40,47,48], Reddy et al [39] dubbed them, together with hoatzin (Opistomorphes), "orphaned"orders due to their uncler position within Neoaves. However, both are definitely rather distant from telluravian lineage.…”