A case of hermaphroditism in the gonochoristic sea urchin, <i>Strongylocentrotus purpuratus</i>, reveals key mechanisms of sex determination

Pieplow, Cosmo; Furze, Aidan R; Wessel, Gary M.

doi:10.1093/biolre/ioad036

Cited by 2 publications

(1 citation statement)

References 53 publications

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“…The 21 largest scaffolds correspond to the 21 S. purpuratus chromosomes (2 n = 42) and represent 90% of the 921,855,793 bases in the S. purpuratus reference genome assembly (Spur_5.0). Although it is known that S. purpuratus has a genetically based sex determination, sex chromosomes have yet to be identified ( Pieplow et al 2023 ). PhyloNet-HMM only allows for DNA base characters in the input sequence alignments, so all indels were excluded, and only variable sites where all four samples had genotypes passing filter were used.…”

Section: Methodsmentioning

confidence: 99%

Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species

Glasenapp,

Pogson

2024

Genome Biology and Evolution

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A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, nonsister sea urchin species: Strongylocentrotus pallidus and Strongylocentrotus droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% to 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. One striking result was the overrepresentation of hyalin genes in the identified introgressed regions despite observing considerable overall evidence of selection against introgression. There was a negative correlation between introgression and chromosome gene density, and two chromosomes were observed with considerably reduced introgression. Relative to the nonintrogressed genome-wide background, introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN, dS, dN/dS) than random samples of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.

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Section: Methodsmentioning

confidence: 99%

Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species

Glasenapp,

Pogson

2024

Genome Biology and Evolution

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Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species

Glasenapp,

Pogson

2023

Preprint

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A growing number of recent studies have demonstrated that introgression is common across the tree of life. However, we still have a limited understanding of the fate and fitness consequence of introgressed variation at the whole-genome scale across diverse taxonomic groups. Here, we implemented a phylogenetic hidden Markov model to identify and characterize introgressed genomic regions in a pair of well-diverged, non-sister sea urchin species:Strongylocentrotus pallidusandS. droebachiensis. Despite the old age of introgression, a sizable fraction of the genome (1% - 5%) exhibited introgressed ancestry, including numerous genes showing signals of historical positive selection that may represent cases of adaptive introgression. There were two chromosomes with considerably reduced introgression and a negative correlation between introgression and gene density, consistent with selection against introgression. Testing for nonrandom patterns among introgressed regions relative to the non-introgressed genome-wide background revealed that introgressed regions had significantly reduced nucleotide divergence (dXY) and overlapped fewer protein-coding genes, coding bases, and genes with a history of positive selection. Additionally, genes residing within introgressed regions showed slower rates of evolution (dN,dS,dN/dS) than random distributions of genes without introgressed ancestry. Overall, our findings are consistent with widespread selection against introgressed ancestry across the genome and suggest that slowly evolving, low-divergence genomic regions are more likely to move between species and avoid negative selection following hybridization and introgression.

show abstract

A case of hermaphroditism in the gonochoristic sea urchin, Strongylocentrotus purpuratus, reveals key mechanisms of sex determination

Cited by 2 publications

References 53 publications

Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species

Selection Shapes the Genomic Landscape of Introgressed Ancestry in a Pair of Sympatric Sea Urchin Species

Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species

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