DOI: 10.5061/dryad.xgxd254gs
title: Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

description: Ray-finned fishes (Actinopterygii) are the largest and most diverse group
 of vertebrates, comprising over half of all living vertebrate species.
 Phylogenetic relationships between ray-finned fishes have historically
 pivoted on the study of morphology, which has notoriously failed to
 resolve higher-order relationships, such as within the percomorphs. More
 recently, comprehensive genomic analyses have provided further resolution
 of actinopterygian phylogeny, including higher-order relationships. Such
 analyses are rightfully regarded as the ‘gold standard’ for phylogenetics.
 However, DNA retrieval requires modern or well-preserved tissue and is
 less likely to be preserved in archaeological or fossil specimens. In
 contrast some proteins, such as collagen, are phylogenetically informative
 and can survive into deep time. Here, we test the utility of collagen type
 I amino acid sequences for phylogenetic estimation of ray-finned fishes.
 We estimate topology using Bayesian approaches and compare the congruence
 of our estimated trees with published genomic phylogenies. Furthermore, we
 apply a Bayesian molecular clock approach and compare estimated divergence
 dates with previously published genomic clock analyses. Our
 collagen-derived trees exhibit 77% of node positions as congruent with
 recent genomic-derived trees, with the majority of discrepancies occurring
 in higher-order node positions, almost exclusively within the Percomorpha.
 Our molecular clock trees present divergence times that are fairly
 comparable with genomic-based phylogenetic analyses. We estimate the mean
 node age of Actinopteri at ~293 million years (Ma), the base of Teleostei
 at ~211 Ma and the radiation of percomorphs beginning at ~141 Ma (~350 Ma,
 ~250–283 Ma and ~120–133 Ma in genomic trees, respectively). Finally, we
 show that the average rate of collagen (I) sequence evolution is 0.9 amino
 acid substitutions for every million years of divergence, with the α3 (I)
 sequence evolving the fastest, followed by the α2 (I) chain. This is the
 quickest rate known for any vertebrate group. We demonstrate that
 phylogenetic analyses using collagen type I amino acid sequences generate
 tangible signals for actinopterygians that are highly congruent with
 recent genomic-level studies. However, there is limited congruence within
 percomorphs, perhaps due to clade-specific functional constraints acting
 upon collagen sequences. Our results provide important insights for future
 phylogenetic analyses incorporating extinct actinopterygian species via
 collagen (I) sequencing.
description: 1. Bayesian topology analysis – Bayesian phylogenetic trees were
 estimated using MrBayes software (v3.2.7). A collagen (I) sequence dataset
 was run in PartitionFinder2 using the ‘MrBayes only’ option, and testing
 both linked and unlinked branch lengths. 2. Tree space
 visualisation – Tree space was visualised in R using a custom
 script utilising the phylogenetic packages phangorn(), Quartet(), vegan()
 and ade4(). 3. Bayesian clock analysis – The rate of
 sequence evolution per collagen (I) α-chain was investigated in MrBayes
 using both a uniform and birth-death clock prior.