Investigating Sources of Conflict in Deep Phylogenomics of Vetigastropod Snails

Abstract

Phylogenetic analyses may suffer from multiple sources of error leading to conflict between genes and methods of inference. The evolutionary history of the mollusc clade Vetigastropoda makes them susceptible to these conflicts, their higher level phylogeny remaining largely unresolved. Originating over 350 million years ago, vetigastropods were the dominant marine snails in the Paleozoic. Multiple extinction events and new radiations have resulted in both very long and very short branches and a large extant diversity of over 4000 species. This is the perfect setting of a hard phylogenetic question in which sources of conflict can be explored. We present 41 new transcriptomes across the diversity of vetigastropods (62 terminals total), and provide the first genomic-scale phylogeny for the group. We find that deep divergences differ from previous studies in which long branch attraction was likely pervasive. Robust results leading to changes in taxonomy include the paraphyly of the order Lepetellida and the family Tegulidae. Tectinae subfam. nov. is designated for the clade comprising Tectus, Cittarium and Rochia. For two early divergences, topologies disagreed between concatenated analyses using site heterogeneous models vs. concatenated partitioned analyses and summary coalescent methods. We investigated rate and composition heterogeneity among genes, as well as missing data by locus and by taxon, none of which had an impact on the inferred topologies. We also found no evidence for ancient introgression throughout the phylogeny. We further tested whether uninformative genes and over-partitioning were responsible for this discordance by evaluating the phylogenetic signal of individual genes using likelihood mapping, and by analyzing the most informative genes with a full multispecies coalescent model. We find that most genes are not informative at the two conflicting nodes, but neither this nor gene-wise partitioning are the cause of discordant results. New method implementations that simultaneously integrate amino acid profile mixture models and the multispecies coalescent might be necessary to resolve these and other recalcitrant nodes in the Tree of Life.

Taxonomy and diversity of slit‐band gastropods (Order Pleurotomariida) and some slit bearing Caenogastropoda from the Pennsylvanian of the USA

“…2014; Cunha et al . 2021), which is more consistent with the fossil record that indicates a greater geological age for the group. Aktipis & Giribet (2012) also found Pleurotomarioidea in a basal position but outside the Vetigastropoda.…”

Confusion will be my epitaph: genome-scale discordance stifles phylogenetic resolution of Holothuroidea

“…Finally, exploring a range of inference methods, which vary in their realism, complexity, susceptibility to errors, and ( potentially) relative fit, can also be used to justify favouring one among several alternative hypotheses [76][77][78]. However, even after exhaustive testing of these options, a robust resolution for some nodes on the tree of life remains elusive [79][80][81][82], awaiting the discovery of novel phylogenetic markers, improved taxon sampling or methodological developments.…”

“…Alternatively, neoholothuriid evolution might be better explained by ancient events of reticulation, as produced by processes such as ancient hybridization and incomplete lineage sorting. Finding direct evidence to substantiate these claims is complicated by the relatively sparse sampling attained by this study, the limited genomic resources available for the clade, and the lack of available methods that can simultaneously address both of these processes [ 79 ]. We suggest that Neoholothuriida constitutes a case of an ancient and rapid radiation, and further progress in its resolution could benefit from targeting data whose evolutionary history proves easier to model.…”

Confusion will be my epitaph: Genome-scale discordance stifles phylogenetic resolution of Holothuroidea

“…Finally, exploring a range of inference methods, which vary in their realism, complexity, susceptibility to errors, and (potentially) relative fit, can also be used to justify favoring one among several alternative hypotheses [70][71][72]. However, even after exhaustive testing of these options, a robust resolution for some nodes on the tree of life remains elusive [73][74][75][76], awaiting the discovery of novel phylogenetic markers, improved taxon sampling, or methodological developments.…”