Evolution News - Science Got it Wrong, But Not The Way Creationists Like to Imagine.

The sand dollar Mellitella stokesii.

Image credit: Rich Mooi (CC BY 4.0)

Study reconsiders early evolution of sea urchins | eLife

In yet another example of how science constantly re-examines, reassesses and revises its understanding, according to an open access paper published in eLife, scientists had got the evolution of sea urchins wrong.

Now, calm down Creationists and don't get over-excited! They didn't get it wrong in the way you've been fooled into believing. There is absolutely no threat to the fundamental biological science of evolution; what they got wrong, according to this paper, is the details. The scientists are in no doubt that the processes involved on evolutionary diversification are as stated in the theory.

As the eLife press release explains:

New insight on the origins and early evolution of echinoids, a group that includes the sea urchins, the sand dollars, and their relatives, has been published today in the journal eLife.

There are still debates among scientists about when the ancestors of echinoids emerged and what role the mass extinction event that occurred between the Permian and Triassic periods may have played in their evolution. We set out to help resolve these debates by combining genomic and paleontological data to disentangle their evolutionary relationships. The extraordinary fossil record of echinoids and the ease with which these fossils can be incorporated in phylogenetic analyses make them an ideal system to explore their early evolution using this approach.

Dr Nicolás Mongiardino Koch, first author
Formerly at Yale University, New Haven, Connecticut, USA.
Now at Scripps Institution of Oceanography
UC San Diego, USA

The study suggests that modern echinoids emerged approximately 300 million years ago, survived the Permo-Triassic mass extinction event – the most severe biodiversity crisis in Earth’s history – and rapidly diversified in its aftermath. These findings help address a gap in knowledge caused by the relative lack of fossil evidence for this early diversification.

There are more than 1,000 living species of echinoids, including sea urchins, heart urchins, sand dollars and sea biscuits, which live across different ocean environments ranging from shallow waters to abysses. Throughout history, the hard spine-covered skeletons of these creatures have left an impressive number of fossils. However, despite this remarkable fossil record, their emergence is documented by few fossil specimens with unclear affinities to living groups, making their early history uncertain.

Our work greatly expands the genomic data available for echinoids and helps resolve some of the long-standing questions around their evolutionary history. Together, the results suggest that we need to re-evaluate the echinoid fossil record, with future studies of overlooked fossil remnants potentially providing further support to our findings.

Professor Greg Rouse, senior author
Professor of Marine Biology
Scripps Institution of Oceanography
UC San Diego, USA

Mongiardino Koch and the team built upon available molecular resources with 18 novel genomic datasets, creating the largest existing molecular matrix for echinoids. Using this dataset, they were able to reconstruct the phylogenetic relationships and divergence times of the major lineages of living echinoids and place their diversification within broader evolutionary history. They did so by applying a ‘molecular clock’ technique to their dataset, whereby the rate at which mutations accumulated in the echinoid genomes is translated into geological time with the use of fossil evidence, allowing researchers to determine when different lineages first diversified.

Their analyses suggest that the ancestors of modern echinoids likely emerged during the Early Permian, and rapidly diversified during the Triassic period in the aftermath of a mass extinction event, even though this evolutionary radiation does not seem to have been captured by the fossil record.

Additionally, the results suggest that sand dollars and sea biscuits likely emerged much earlier than thought, during the Cretaceous period about 40 to 50 million years before the first documented fossils of these creatures. The authors say this result is remarkable, as the tough skeleton of the sand dollars, their buried lifestyles, and their extremely distinct morphologies imply that their fossil record should faithfully reflect their true evolutionary history.

This is just another example of how the study of DNA and genetics has confirmed Darwin's basic idea and extended our understanding of how species evolved and diversified from common ancestors. Darwin knew nothing of how information was passed to the next generation but he knew that it must be and that it included small variations of which natural selection could favour or disfavour, giving rise to ever-greater adaptation and fitness to survive and reproduce in the selective environment.

The scientists explain more in the abstract to their eLife paper, as does the journal editor in the editor's evaluation:

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.

Editor's evaluation

The study by Mongiardino Koch et al., presents new phylogenomic and molecular clock analyses of echinoids. The study uses state of the art phylogenetic approaches and includes 18 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.

Mongiardino Koch, Nicolás; Thompson, Jeffrey R; Hiley, Avery S; McCowin, Marina F; Armstrong, A Frances; Coppard, Simon E; Aguilera, Felipe; Bronstein, Omri; Kroh, Andreas; Mooi, Rich; Rouse, Greg W; Rokas, Antonis; Perry, George H; Irisarri, Iker
Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record
eLife 2022;11:e72460. DOI: 10.7554/eLife.72460

Copyright: © 2022 The authors. Published by eLife Sciences Publications Ltd.
Open access
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Incidentally, if anyone is in any doubt about peer-review and imaging it's some sort of formality that waves any scientific papers through on the nod, provided they conform to some assumed dogma, like creationist articles, it is worth scrolling down to the Decision letter section, where unusually for a scientific paper the reviewers' comments appear in full, together with the authors' responses. Peer-review is not a process to ensure compliance to some assumes party line, but a constructive, critical process by experts in the field that ensure the highest standards of scientific integrity and accuracy are maintained in the articles published by scientific journals, so readers can rely on the accuracy and validity of the findings.

For examples (reviewer's comments in italics and the authors' response to them):

Reviewer #2 (Recommendations for the authors):

I found the text long in places and thus tedious to read. Particularly the introduction and the discussion. The intro could have a tighter narrative more focused on the discrepancies of the fossil record and divergence times, and on discrepancies in topology without the needed to review so much echinoid biology. The discussion appears too long. Too much effort is made on justifying the chronospace approach. This perhaps does not need to be justified at all beyond a sentence or two.

The issue of the length of the introduction and the extent to which echinoid background is developed seems to be a discrepancy between reviewers. We have decided not to modify its length, as we believe the present version is already a good compromise, as is suggested by Reviewer #1 as well. We have however reduced the length of the justification of chronospaces.

Because the clock model has such an impact, you should explore this further. PhyloBayes provides the ability to test for the various rate models using Bayes factors and you should try this. Because this analyses are computationally expensive, you can do them on a reduced amount of data. MCMCtree also allows you to test for various clock models with Bayes factors.

Given the computational burden of running a Bayes factor analysis on PhyloBayes, we had explored CorrTest instead, a different approach for selecting among competing clock models. The results of this were not reported before, but are now incorporated as Reviewer #1 also suggested this. Given that these methods did not eliminate uncertainty in terms of which clock model should be preferred, we have taken the position of exploring and reporting the sensitivity of results to all factors. All conclusions drawn in the manuscript regarding echinoderm diversification are robust even to the large effects introduced by the choice of clock models. We don’t feel the need to restrict the analyses or results to a subset of conditions when this would not modify our insights.

Additional points:

The y-axis (Δ likelihood) of panel C in Figure 2 needs to be explained in the legend. What is the benchmark likelihood?

Panel C of Figure 2 is better explained now in the caption. There is no benchmark likelihood, values larger than 0 mean support for one topology, those below 0 for the alternative.

In the figure legends, the program/models used to infer the tree and times should be indicated. From the methods it's clear that many many different methods were tested, but from the main text and the figure legends is not clear what is being summarised in the figures.

Software are now mentioned in the captions of Figures 2 and 4.

Please remove the p-value for the multivariate analysis in line 198. This is not a replicated stochastic experiment. You are simply changing priors and substitution models and hence the posterior changes. This is a deterministic mapping between data/prior and posterior.

We agree with this comment and have removed the mention to p-values.

Panel C of Figure 4: please mention in the legend the scale of the x-axis tickmarks (10 My?).

Done.

Lines 359 to 367 have little substance. There are no figures in this paper showing the correlation structure among branch lengths. For example, figure 4 shows stacked posterior distributions, like those in previous works, so isn't this work a victim of its own criticism? There is indeed a correlation structure among branches and times, which is not shown, and which is discarded in the plots shown here. To emphasise this point, here is paper's text edited: "The sensitivity of inferred ages is commonly explored by running analyses under different settings and summarizing the results in tables or by stacking chronograms in order to visualize the relative position of nodes (see for example Figure 4C here and the supplementary material figures)."

We agree with the reviewer and have removed all of the text mentioned here, as well as other parts referring to the chronospace approach. Correlation plots were shown in a previous version of the manuscript, but we agree that these sentences do not add much after these have been removed.

---

Thank you for sharing!

Tweet Link