Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
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Evaluation Summary:
The study by Koch et al presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 17 newly sequenced genomes and transcriptomes, which are used to estimate the tree topology and divergence times of major groups of echinoids. The molecular clock-estimated times of origin of particular echinoid lineages predate the lineages' appearance on the fossil record by tens of millions of years, prompting re-evaluation of the early evolution of echinoid diversity.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)”
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Abstract
Echinoids are key components of modern marine ecosystems. Despite a remarkable fossil record, the emergence of their crown group is documented by few specimens of unclear affinities, rendering their early history uncertain. The origin of sand dollars, one of its most distinctive clades, is also unclear due to an unstable phylogenetic context. We employ 18 novel genomes and transcriptomes to build a phylogenomic dataset with a near-complete sampling of major lineages. With it, we revise the phylogeny and divergence times of echinoids, and place their history within the broader context of echinoderm evolution. We also introduce the concept of a chronospace – a multidimensional representation of node ages – and use it to explore methodological decisions involved in time calibrating phylogenies. We find the choice of clock model to have the strongest impact on divergence times, while the use of site-heterogeneous models and alternative node prior distributions show minimal effects. The choice of loci has an intermediate impact, affecting mostly deep Paleozoic nodes, for which clock-like genes recover dates more congruent with fossil evidence. Our results reveal that crown group echinoids originated in the Permian and diversified rapidly in the Triassic, despite the relative lack of fossil evidence for this early diversification. We also clarify the relationships between sand dollars and their close relatives and confidently date their origins to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their rich fossil record.
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Evaluation Summary:
The study by Koch et al presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 17 newly sequenced genomes and transcriptomes, which are used to estimate the tree topology and divergence times of major groups of echinoids. The molecular clock-estimated times of origin of particular echinoid lineages predate the lineages' appearance on the fossil record by tens of millions of years, prompting re-evaluation of the early evolution of echinoid diversity.
(This preprint has been reviewed by eLife. We include the public reviews from the reviewers here; the authors also receive private feedback with suggested changes to the manuscript. Reviewer #1 agreed to share their name with the authors.)”
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Reviewer #1 (Public Review):
This study presents new phylogenomic and molecular clock analyses of echinoids. The manuscript is very well written and presented; the figures are informative and clear. The introduction nicely sums up the main questions for readers not acquainted with echinoids, which adds further value to this study that is relevant for a wide readership.
The phylogenomic dataset includes data for several new lineages, which allows the authors to clarify several unsettled relationships in the echinoid tree of life. Molecular clock analyses explore the effect of several key methodological decisions (clock model, complexity of evolutionary model, gene sampling). This is done using a new interesting approach implemented in the tool 'chronospace'. The new approach to exploring the sensitivity of molecular clock analysis is …
Reviewer #1 (Public Review):
This study presents new phylogenomic and molecular clock analyses of echinoids. The manuscript is very well written and presented; the figures are informative and clear. The introduction nicely sums up the main questions for readers not acquainted with echinoids, which adds further value to this study that is relevant for a wide readership.
The phylogenomic dataset includes data for several new lineages, which allows the authors to clarify several unsettled relationships in the echinoid tree of life. Molecular clock analyses explore the effect of several key methodological decisions (clock model, complexity of evolutionary model, gene sampling). This is done using a new interesting approach implemented in the tool 'chronospace'. The new approach to exploring the sensitivity of molecular clock analysis is very relevant and the new tool seems very promising for the community. Perhaps I missed the exploration of yet another key decision in molecular clock analyses: the effect of different prior probability distributions for fossil calibrations.
Overall, the data are thoroughly explored and the conclusions reached by the authors are strongly supported by their data. Results are relevant towards better understanding the evolutionary history of echinoids and provide interesting clues for re-evaluating their fossil record. The new tool 'chronospace' is likely to be highly adopted by the phylogenomics community.
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Reviewer #2 (Public Review):
In this paper Koch et al. present an updated phylogeny of Echinoids. The novelty here lies on the author's inclusion of 17 newly sequenced genomes. This new data, together with previous molecular data matrices are then used to estimate the tree topology and divergence times under various software, substitution models, priors, etc. The impact of these analysis set-ups is assessed by using multivariate statistics. This approach is original and helps visualise the data (but certainly discarding a lot of information as all PCA-like methods do). The importance of this approach appears overstated.
The work shows attention to detail, is extensive and the figures are well presented. The text appears long in places and could be shortened to make a tighter narrative.
The authors find relaxed rate models …
Reviewer #2 (Public Review):
In this paper Koch et al. present an updated phylogeny of Echinoids. The novelty here lies on the author's inclusion of 17 newly sequenced genomes. This new data, together with previous molecular data matrices are then used to estimate the tree topology and divergence times under various software, substitution models, priors, etc. The impact of these analysis set-ups is assessed by using multivariate statistics. This approach is original and helps visualise the data (but certainly discarding a lot of information as all PCA-like methods do). The importance of this approach appears overstated.
The work shows attention to detail, is extensive and the figures are well presented. The text appears long in places and could be shortened to make a tighter narrative.
The authors find relaxed rate models (autocorrelated vs independent rates) have a big impact on time estimates. This is an important result. So, which model is right? Perhaps a Bayesian model selection analysis on a subset of the data may shed light on this issue. Then the authors could focus their discussion of time estimates on the sets of results obtained under the best fitting rate model.
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