Substitution rate variation in a robust procellariiform seabird phylogeny is not solely explained by body mass, flight efficiency, population size or life history traits
Creators: name: Estandia, Andrea
name: Chesser, Terry
name: James, Helen
name: Levy, Max
name: Ferrer-Obiol, Joan
name: Bretagnolle, Vincent
name: González-Solís, Jacob
name: Welch, Andreanna
Publisher: name: Zenodo
Year: 2021
Subjects: rate heterogeneity
Ultraconserved Elements
molecular clock
life history traits
flight
Procellariiformes

description: Molecular substitution rates vary among branches, which can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Body mass is often assumed to be a major driver of substitution rate, though other factors such as population size, life history traits, and flight demands are also thought to have an influence. Birds of the order Procellariiformes—which encompasses petrels, storm-petrels and albatrosses—show a striking 900-fold difference in body mass between the smallest and largest members, divergent life history traits, and substantial heterogeneity in mitochondrial substitution rates. Here, we used genome-scale nuclear DNA sequence data from 4365 ultraconserved element loci (UCEs) in 51 procellariiform species to examine whether phylogenetic reconstruction using genome-wide datasets is robust to the presence of rate heterogeneity, and to identify predictors of substitution rate variation. Our results provide a backbone phylogeny for procellariiform seabirds and resolves several controversies about the evolutionary history of the order, demonstrating that albatrosses are basal, storm-petrels are paraphyletic and diving petrels nestled within the Procellariidae. We find evidence of rate variation; however, all phylogenetic analyses using both concatenation and multispecies coalescent approaches recovered the same branching topology, including analyses implementing different clock models, and analyses of the most and least clock-like loci. Overall, we find that rate heterogeneity is little impacted by body mass, population size, age at first breeding, and longevity but moderately correlated with hand-wing index, a proxy for wing shape and flight efficiency. Given our results and the context of the broader literature, perhaps it is time that we begin to question the prevailing assumption that one or a few traits largely explain rate variation and accept instead that substitution rate may be the product of weak interactions among many, potentially taxon-specific, variables. --
description: Supplementary material for <em>Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny is not Solely Explained by Body Mass, Flight Efficiency, Population Size or Life History Traits</em>. Raw data is deposited in Genbank under accession PRJNA749710 Code to reproduce all analyses can be found here: https://github.com/andreaestandia/procellariiform_backbone This repository contains: Supplementary Information text and Supplementary figures Supplementary tables UCE contigs Alignments and charsets used for: RAxML IQtree Exabayes ASTRAL BEAST Trees produced by the programs mentioned in section 4 Partitioning info Coevol 1.4b input files (phenotypes and calibrations. Alignments in 4_alignments folder) and output files Funding provided by: Smithsonian Institution<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000014<br>Award Number: Wetmore Endowment FundFunding provided by: Durham University<br>Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001314<br>Award Number:
description: We collected blood and tissue samples in the field or from museum loans for 51 procellariiform seabirds and sequenced the DNA extracts targeting 5000 ultraconserved elements. We built phylogenies using a variety of approaches and explore substitution rate variation among lineages. We tested for correlations among substitution rate and body mass, life history variables, population size, and hand-wing index.