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

Koch, Nicolás Mongiardino; Ekin, Tilic; Miller, Allison K.; Stiller, Josefin; Rouse, Greg W.

doi:10.1098/rspb.2023.0988

Cited by 4 publications

(1 citation statement)

References 94 publications

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“…This is in fact the expected behavior if topological incongruence is driven by biological factors such as ILS (Mendes & Hahn 2016). While some have argued that deep recalcitrant nodes are linked to ancient events of ILS (e.g., Cai et al 2021;Hime et al 2021;Mongiardino Koch et al 2023;Song et al 2023), it has also been suggested that topological incongruence at deep timescales is more likely to be caused by methodological issues related to loss of signal and model inadequacy (Gatesy & Springer 2014;Richards et al 2018). While our analyses were not designed to test this phenomenon, our results are contrary to those expected if ILS was the main driver of topological conflict at ancient nodes.…”

Section: Discussionmentioning

confidence: 75%

Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

Mongiardino Koch,

Milla Carmona

2024

Preprint

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Much of our understanding of the history of life hinges upon time calibration, the process of assigning absolute times to cladogenetic events. Bayesian approaches to time scaling phylogenetic trees have dramatically grown in complexity, and hinge today upon numerous methodological choices. Arriving at objective justifications for all of these is difficult and time consuming. Thus, divergence times are routinely inferred under only one or a handful of parametric conditions, often chosen arbitrarily. Progress towards building robust biological timescales necessitate the development of better methods to visualize and quantify the sensitivity of results to these decisions. Here, we present an R package that assists in this endeavor through the use of chronospaces, i.e., graphical representations summarizing variation in the node ages contained in time-calibrated trees. We further test this approach using three empirical datasets spanning widely differing timeframes. Our results reveal large differences in the impact of many common methodological decisions, with the choice of clock (uncorrelated vs. autocorrelated) and loci having strong effects on inferred ages. Other decisions have comparatively minor consequences, including the use of the computationally intensive site-heterogeneous model CAT-GTR. Notably, these conclusions are as valid for Cenozoic divergences as they are for the deepest eukaryote nodes. The packagechronospaceimplements a range of graphical and analytical tools that assist in the exploration of sensitivity and the prioritization of computational resources in the inference of divergence times.

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Section: Discussionmentioning

confidence: 75%

Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

Mongiardino Koch,

Milla Carmona

2024

Preprint

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

et al. 2023

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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.

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Larval development in the apodid sea cucumber Chiridota gigas, with a focus on coelom development and the serotonergic nervous system during metamorphosis

Sewell,

Prowse,

Selvakumaraswamy

et al. 2024

Invertebrate Biology

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A unifying feature of echinoderm larvae is the development of a left anterior coelom, which consists of an undivided left axocoel and hydrocoel. Although the axocoel is a key deuterostome trait, the presence of this coelom in holothurians has been the subject of debate. Here, we focus on the development of the coelom in a basal holothuroid, the apodid Chiridota gigas (F. Chiridotidae). The dorsal pore and dorsal duct develop first, just after gastrulation, followed by expansion into an axohydrocoel in the auricularia. The left somatocoel was first evident adjacent to the stomach ~30 days post‐fertilization. The axohydrocoel differentiated into two distinct parts: the hydrocoel adjacent to the stomach, and a thin‐walled axocoel that was mid‐dorsal between the hydrocoel and the dorsal pore. This left axocoel extended to both the anterior and posterior but did not cross the larval midline. Out‐folding of the hydrocoel to form the primary tentacles was first observed at 58 days. Transition to a doliolaria with four‐rings was rapid (24 hr) and similar to the transition in other holothurians, with the hydrocoel encircling the esophagus. This transition involved a posterior shift of elements of the auricularia ciliary band and associated nervous system. The ciliary band of the auricularia was rearranged to form transverse bands of the doliolaria larva, and at the same time, the serotonergic cells and fibers that had been at the anterior end moved with the portions of the ciliary band with which they were associated. These serotonergic cells and fibers were still present in the pentactula. The first pentactula was observed at 66 days. Coelom development in C. gigas showed two differences from that in other holothurians, including the development of the left axocoel and the extension of the anterior coelom into the preoral lobe. Description of the full larval development in C. gigas also revealed highly variable morphology in the late auricularia stage, which may aid in identifying apodid holothurians from plankton samples.

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

Cited by 4 publications

References 94 publications

Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

Chronospaces: an R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity

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

Larval development in the apodid sea cucumber Chiridota gigas, with a focus on coelom development and the serotonergic nervous system during metamorphosis

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