Cytogenetics of the elasmobranchs: genome evolution and phylogenetic implications

Schwartz, Frank J.; Maddock, Michael B.

doi:10.1071/mf01139

Cited by 24 publications

(16 citation statements)

References 23 publications

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“…Phylogenetically, they are considered a monophyletic group in a sister relationship to sharks (Dunn & Morrissey, 1995;Schwartz & Maddock, 2002;Douady et al, 2003;Winchell et al, 2004;Aschliman et al, 2012a;Naylor et al, 2012;Last et al, 2016). The earliest unambiguous fossil remains of the group come from the Early Jurassic (Toarcian) (Cappetta, 2012).…”

Section: Introductionmentioning

confidence: 99%

Radiation and Divergence Times of BatoideaCitation for this article: Villalobos-Segura, E., and C. J. Underwood. 2020. Radiation and divergence times of Batoidea. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2020.1777147.

Villalobos-Segura

Underwood

2020

Journal of Vertebrate Paleontology

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We present a time-scaled analysis based on morphological characters to estimate the divergence ages for the major batoids clades. Two approaches were used: Tip-dating, which allows the extinct taxa to be included as terminals, assessing the phylogenetic relations and their divergence time simultaneously; and basic and minimum branch length ("a posteriori" methods) that date a pre-existing unscaled topology, given a set of stratigraphic data for the taxa involved.We used stratigraphic indexes to compare the divergence ages recovered by both methods. The tip-dating approach obtained a more resolved topology and slightly better stratigraphic indexes scores than the other methods. Overall the tip-dating analysis recovered slightly earlier divergence ages than the rest of the time dating analyses and the known fossil record of the groups. However, these divergence ages were not as old as those estimated by molecular analysis. Our results suggest the diversity increase through the Late Jurassic-Early Cretaceous might not be gradual, and that Early Cretaceous diversity could be significantly higher. As several divergence events are placed in the Early Cretaceous, there is a suggestion that an active period of cladogenesis leads to the Late Cretaceous high diversity. The last divergence events recovered by the present analysis occurred in the Paleogene and led to the extant groups of batoids.

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Section: Introductionmentioning

confidence: 99%

Radiation and Divergence Times of BatoideaCitation for this article: Villalobos-Segura, E., and C. J. Underwood. 2020. Radiation and divergence times of Batoidea. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2020.1777147.

Villalobos-Segura

Underwood

2020

Journal of Vertebrate Paleontology

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“…We also estimated genome sizes using DNA sequences with the k-mer-based method 38 as supplementary references. For the thorny skate Amblyraja radiata whose nuclear DNA content was previously estimated to be 4.25 Gb 39 , the total sequence length of the publicly available genome assembly 31 (sAmbRad1.1.pri; GCF_010909765.2) amounts to only 2.56 Gbp. Our k-mer-based estimate of its genome size using raw sequence reads resulted in an even smaller value of approximately 1.7 Gbp.…”

Section: Resultsmentioning

confidence: 99%

Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

Kadota

Tatsumi

Yamaguchi

et al. 2023

Preprint

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Estimate of nuclear DNA content serves as an independent tool for validating the completeness of whole genome sequences and investigating the among-species variation of genome sizes, but for some species, the requirement of fresh cells makes this tool highly inaccessible. Here we focused on elasmobranch species (sharks and rays), and using flow cytometry or quantitative PCR (qPCR), estimated the nuclear DNA contents of brownbanded bamboo shark, white spotted bamboo shark, zebra shark, small-spotted catshark, sandbar shark, slendertail lanternshark, megamouth shark, red stingray, and ocellate spot skate. Our results revealed their genome sizes spanning from 3.40 pg (for ocellate spot skate) to 13.34 pg (for slendertail lanternshark), in accordance with the huge variation of genome sizes already documented for elasmobranchs. Our improved qPCR-based method enabled accurate genome size estimation without using live cells, which has been a severe limitation with elasmobranchs. These findings and our methodology are expected to contribute to better understanding of the diversity of genome sizes in elasmobranchs even including species with limited availability of fresh tissue materials. It will also help validate the completeness of already obtained or anticipated whole genome sequences.

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“…Standardized genome size C-values (haploid DNA content per cell measured in picograms, pg/n) were collected from Animal Genome Size Database, Release 2.0 30 and the literature 6,12,31 (and references therein), excluding values from potential triploid cytotypes or hypertrophic cells. Measurement technique was shown not to signi cantly in uence species-speci c genome size estimations across vertebrates (mixed-effects ANOVA [ xed effect: measurement technique; random effect: species]: F = 0.65, p = 0.597, n estimates = 20, n groups = 5; R package nlme v. 3.1.152 32 ; data from Animal Genome Size Database).…”

Section: Data Compilationmentioning

confidence: 99%

“…Multiples of 1.45 pg in chondrichthyan genome size variation have also been reported in more recent studies 8 . Although these patterns may have been a sampling artefact, comparisons of shark karyotypes have hinted at the general signi cance of polyploidy early in the diversi cation of this group 6,12 . However, recent genome-wide analyses have rejected this idea 13,14 , making the further study of shark karyotype evolution of such discontinuous patterns well warranted.…”

Section: Introductionmentioning

confidence: 99%

A pluralistic view on the evolutionary forces shaping genome size diversity in sharks

Sáez,

Hofreiter,

Straube

2023

Preprint

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Among vertebrates, sharks exhibit both large and heterogeneous genome sizes ranging from 2.86 to 17.05 pg. Aiming for a better understanding of the patterns and causalities of shark genome size evolution, we applied phylogenetic comparative methods to published genome-size estimates for 66 species representing the main phylogenetic lineages, life-histories and ecological traits. The 6-fold range of genome size variation was strongly traceable throughout the phylogeny, with a major expansion preceding shark diversification during the late Paleozoic and an ancestral state (6.37 pg) close to the present-day average (6.74 pg). Subsequent deviations from this average occurred at higher rates in squalomorph than in galeomorph sharks and were unconnected to evolutionary changes in the karyotype architecture, which were dominated by ascending disploidy events. Genome size was positively correlated with cell and nucleus sizes and negatively with metabolic rate. The metabolic constraints on increasing genome size also manifested at higher phenotypic scales, with large genomes associated with slow lifestyles, boreal latitudes, and purely marine waters. Moreover, large genome sizes were also linked to non-placental reproductive modes, which may entail metabolically less demanding embryological developments. Contrary to ray-finned fishes, genome size was associated neither with the taxonomic diversity of affected clades nor low genetic diversity.

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Cytogenetics of the elasmobranchs: genome evolution and phylogenetic implications

Cited by 24 publications

References 23 publications

Radiation and Divergence Times of BatoideaCitation for this article: Villalobos-Segura, E., and C. J. Underwood. 2020. Radiation and divergence times of Batoidea. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2020.1777147.

Radiation and Divergence Times of BatoideaCitation for this article: Villalobos-Segura, E., and C. J. Underwood. 2020. Radiation and divergence times of Batoidea. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2020.1777147.

Shark and ray genome size estimation: methodological optimization for inclusive and controllable biodiversity genomics

A pluralistic view on the evolutionary forces shaping genome size diversity in sharks

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