Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers

Brosseau, Olivier; Murienne, Jérôme; Pichon, Delphine; Vidal, Nicolás; Eléaume, Marc; Améziane, Nadia

doi:10.1007/s13127-012-0087-1

Cited by 10 publications

(6 citation statements)

References 41 publications

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“…Cidaroids form the sister group to all other crown group echinoids (Euechinoidea). Some aspects of the relationships among sampled cidaroids are consistent with previous molecular ( Brosseau et al, 2012 ) and morphological studies ( Kroh and Smith, 2010 ), including an initial split between Histocidaris and the remaining taxa, representing the two main branches of extant cidaroids ( Kroh, 2020 ; Kroh and Mooi, 2020 ). Others, such as the nested position of Prionocidaris baculosa within the genus Eucidaris, not only implies paraphyly of this genus but also suggests the need for a taxonomic reorganization of the family Cidaridae.…”

Section: Discussionsupporting

confidence: 83%

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Koch

Thompson

Hiley

et al. 2022

eLife

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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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Section: Discussionsupporting

confidence: 83%

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Koch

Thompson

Hiley

et al. 2022

eLife

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“…Cidaroids form the sister group to all other crown group echinoids (Euechinoidea). Some aspects of the relationships among sampled cidaroids are consistent with previous molecular [49] and morphological studies [19], including an initial split between Histocidaris and the remaining taxa, representing the two main branches of extant cidaroids [5, 35]. Others, such as the nested position of Prionocidaris baculosa within the genus Eucidaris, not only implies paraphyly of this genus but also suggests the need for a taxonomic reorganization of the family Cidaridae.…”

Section: Discussionsupporting

confidence: 80%

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Koch

Thompson

Hatch

et al. 2021

Preprint

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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 seventeen novel genomes and transcriptomes to build a dataset with a near-complete sampling of major lineages and use it to revise the phylogeny and divergence times of echinoids. We introduce the concept of a chronospace - a multidimensional representation of node ages - and use it to explore the effects of using alternative gene samples, models of molecular evolution, and clock priors. We find the choice of clock model to have the strongest impact on divergence times, while gene sampling and the use of site-heterogeneous models show little effects. Crown group echinoids originated in the Permian and diversified rapidly in the Triassic. We clarify the relationships among sand dollars and their close relatives, showing that Apatopygus represents a relict lineage with a deep Jurassic origin. Sand dollars are confidently dated to the Cretaceous, implying ghost ranges spanning approximately 50 million years, a remarkable discrepancy with their fossil record.

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“…These results are consistent with those reported previous studies (e.g. Jeffery et al, 2003;Brosseau et al, 2012), suggesting that mitochondrial DNA independent regions that comprise several hundred to a thousand bases contain insufficient information to examine phylogenetic relationships among higher-level clades, such as orders. In a phylogenetic tree constructed using all the protein-coding regions, the two clades were swapped with each other between the two analysis methods.…”

Section: Phylogeny Of the Sea Urchinssupporting

confidence: 92%

<strong>Effective DNA extraction methods for mitochondrial phylogenomics of the sea urchins</strong>

et al. 2019

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In the present study, we evaluated the efficiency of a minimally destructive and a destructive mitochondrial DNA extraction method. The first method extracted total DNA from epidermis and muscles of the spines and yielded varying PCR efficiency values that are dependent on the template concentration, which could be attributed to contamination by pigment and/or genomic DNA in the tissue. The second method extracted mitochondrial DNA from fractionated mitochondria obtained from tissues and coelomic fluid inside the test. Using this method, PCR products and purified mitochondrial DNA were used for sequencing on a next generation sequencer (Ion PGM). Direct sequencing of the purified mitochondrial DNA led to complete recovery of the mitochondrial genomes; however, contaminants were present. PCR failure was commonly encountered using the first method but was absent using the second method. The two extraction methods were compared to the commonly used destructive method that extracted total DNA from gonad or coelomic fluid inside the test. PCR results indicated that the destructive method exhibited similar performance as the first method. The present study generated 11 complete and one partial mitochondrial genome sequences for 12 species. The complete mitochondrial sequences from the order Cidaroida were sequenced for the first time. Phylogenetic trees constructed based on individual genes showed various topologies. Phylogenetic relationships estimated from all protein-coding regions of the mitochondrial genome were consistent with the order-level relationships estimated from molecular and morphological data in previous studies.

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Phylogeny of Cidaroida (Echinodermata: Echinoidea) based on mitochondrial and nuclear markers

Cited by 10 publications

References 41 publications

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

Phylogenomic analyses of echinoid diversification prompt a re-evaluation of their fossil record

<strong>Effective DNA extraction methods for mitochondrial phylogenomics of the sea urchins</strong>

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