The complete mitochondrial genome of the sea urchin, <i>Echinometra</i> sp. EZ

Ketchum, Remi N.; DeBiasse, Melissa B.; Ryan, Joseph F.; Burt, John A.; Reitzel, Adam M.

doi:10.1080/23802359.2018.1532335

Cited by 12 publications

(8 citation statements)

References 14 publications

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“…RESL and bPTP were the only methods to split Echinometra mathaei in three or more putative species. This is in accordance with the distinct species identified within Echinometra mathaei using ecological distribution, test morphology, gonadal spicules, gametes and cross-fertilization experiments (60–64). These cases show the difficulty to interpret the different species delimitation methods in absence of additional lines of evidence and when distances among species are relatively small.…”

Section: Discussionsupporting

confidence: 88%

DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

Sonet

Smitz

Vangestel

et al. 2022

Preprint

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Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5’ end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.

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Section: Discussionsupporting

confidence: 88%

DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

Sonet

Smitz

Vangestel

et al. 2022

Preprint

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“…2015 ). Until a recently published mitochondrial genome became available ( Ketchum et al. 2018 ), E .…”

Section: Discussionmentioning

confidence: 99%

“…The most abundant sea urchin in the PAG is Echinometra sp. EZ , previously thought to be Echinometra mathaei ( Ketchum et al. 2018 ) .…”

Section: Introductionmentioning

confidence: 99%

Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient

Ketchum

Smith

DeBiasse

et al. 2020

Genome Biology and Evolution

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Extreme environmental gradients represent excellent study systems to better understand the variables that mediate patterns of genomic variation between populations. They also allow for more accurate predictions of how future environmental change might affect marine species. The Persian/Arabian Gulf is extreme in both temperature and salinity while the adjacent Gulf of Oman has conditions more typical of tropical oceans. The sea urchin Echinometra sp. EZ inhabits both of these seas and plays a critical role in coral reef health as a grazer and bioeroder, but, to date, there have been no population genomic studies on this or any urchin species in this unique region. E. sp. EZ’s life history traits (e.g., large population sizes, large reproductive clutches, and long life spans), in theory, should homogenize populations unless non-neutral processes are occurring. Here, we generated a draft genome and a restriction-site associated DNA sequencing dataset from seven populations along an environmental gradient across the Persian/Arabian Gulf and the Gulf of Oman. The estimated genome size of E. sp. EZ was 609 Mb and the heterozygosity was amongst the highest recorded for an echinoderm at 4.5%. We recovered 918 high quality SNPs from 85 individuals which we then used in downstream analyses. Population structure analyses revealed a high degree of admixture between all sites, although there was population differentiation and significant pairwise FST values between the two seas. Preliminary results suggest migration is bidirectional between the seas and nine candidate loci were identified as being under putative natural selection, including one collagen gene. This study is the first to investigate the population genomics of a sea urchin from this extreme environmental gradient and is an important contribution to our understanding of the complex spatial patterns that drive genomic divergence.

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“…First, adult Echinometra sp. EZ (Ketchum, DeBiasse et al, 2018) were sampled in August 2017 and February 2018 from six sites along the Arabian Peninsula (Table S1, Supporting Information) for a total of 183 samples (Figure 1). This dataset is referred to as the "summer-winter spatial series."…”

Section: Sample Collectionmentioning

confidence: 99%

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

Ketchum

Smith

Vaughan³

et al. 2021

Molecular Ecology

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The complete mitochondrial genome of the sea urchin, Echinometra sp. EZ

Cited by 12 publications

References 14 publications

DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy

Population Genomic Analyses of the Sea Urchin Echinometra sp. EZ across an Extreme Environmental Gradient

Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

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