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Correlates of substitution rate variation in a robust Procellariiform seabird phylogeny

Citation

Estandia, Andrea et al. (2022), Correlates of substitution rate variation in a robust Procellariiform seabird phylogeny, Dryad, Dataset, https://doi.org/10.5061/dryad.h18931zm5

Abstract

Molecular substitution rates vary among branches and can lead to inaccurate reconstructions of evolutionary relationships and obscure the true phylogeny of affected clades. Body mass is often assumed to have a major influence on 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 and age at first breeding, but moderately impacted by longevity and hand-wing index, a proxy for wing shape and flight efficiency. Our results indicate that substitution rate may be the product of interactions among many, potentially taxon-specific, variables.

Methods

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.

Usage Notes

Supplementary material for Correlates of Substitution Rate Variation in a Robust Procellariiform Seabird Phylogeny.

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:

  1. UCE contigs

  2. Alignments and charsets used for:

    1. RAxML

    2. IQtree

    3. Exabayes

    4. ASTRAL

    5. BEAST

  3. Trees produced raw and rooted

  4. Partitioning info

  5. Coevol 1.4b input and output files, and files used for plots

  6. BEAST XML files

  7. Main figures in pdf and png formats

  8. Supplementary tables and supplementary material

Funding

Smithsonian Institution, Award: Wetmore Endowment Fund

Durham University