Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea
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Confusion will be my epitaph : genome-scale discordance stifles phylogenetic resolution of Holothuroidea. / Koch, Nicolás Mongiardino; Tilic, Ekin; Miller, Allison K.; Stiller, Josefin; Rouse, Greg W.
In: Proceedings of the Royal Society B: Biological Sciences, Vol. 290, No. 2002, 20230988, 2023.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Confusion will be my epitaph
T2 - genome-scale discordance stifles phylogenetic resolution of Holothuroidea
AU - Koch, Nicolás Mongiardino
AU - Tilic, Ekin
AU - Miller, Allison K.
AU - Stiller, Josefin
AU - Rouse, Greg W.
PY - 2023
Y1 - 2023
N2 - Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest oceanic trenches. Their reduced skeletons and limited number of phylogenetically informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with 13 novel transcriptomes. Using a highly curated dataset of 1100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favour one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.
AB - Sea cucumbers (Holothuroidea) are a diverse clade of echinoderms found from intertidal waters to the bottom of the deepest oceanic trenches. Their reduced skeletons and limited number of phylogenetically informative traits have long obfuscated morphological classifications. Sanger-sequenced molecular datasets have also failed to constrain the position of major lineages. Noteworthy, topological uncertainty has hindered a resolution for Neoholothuriida, a highly diverse clade of Permo-Triassic age. We perform the first phylogenomic analysis of Holothuroidea, combining existing datasets with 13 novel transcriptomes. Using a highly curated dataset of 1100 orthologues, our efforts recapitulate previous results, struggling to resolve interrelationships among neoholothuriid clades. Three approaches to phylogenetic reconstruction (concatenation under both site-homogeneous and site-heterogeneous models, and coalescent-aware inference) result in alternative resolutions, all of which are recovered with strong support and across a range of datasets filtered for phylogenetic usefulness. We explore this intriguing result using gene-wise log-likelihood scores and attempt to correlate these with a large set of gene properties. While presenting novel ways of exploring and visualizing support for alternative trees, we are unable to discover significant predictors of topological preference, and our efforts fail to favour one topology. Neoholothuriid genomes seem to retain an amalgam of signals derived from multiple phylogenetic histories.
U2 - 10.1098/rspb.2023.0988
DO - 10.1098/rspb.2023.0988
M3 - Journal article
C2 - 37434530
VL - 290
JO - Proceedings of the Royal Society B: Biological Sciences
JF - Proceedings of the Royal Society B: Biological Sciences
SN - 0962-8452
IS - 2002
M1 - 20230988
ER -
ID: 359251000