Biology subjects

O'Hara, T. D.

Publications and source records attributed to O'Hara, T. D..

3 recordsLinked to original sources

bioRxiv2023

Brooding brittle-star is a global hybrid polyploid swarm

The widespread and abundant brooding brittle-star (Amphipholis squamata) is a simultaneous hermaphrodite with a complex mitochondrial phylogeography of multiple divergent overlapping mtDNA lineages and can exhibit high levels of inbreeding or clonality and unusual sperm morphology. We use exon-capture and transcriptome data to show that the nuclear genome comprises multiple (>3) divergent ({pi} > 6%) expressed components spread across the mitochondrial lineages, and encompassing several other genera, including diploid dioecious dimorphic species. We also report a massive sperm genome size in A. squamata, an order of magnitude larger than in the sperm of other brittle-star species, consistent with our genetic measures of elevated and variable ploidy (>6). We propose that A. squamata (and related taxa) is a hybrid polyploid complex with many independent hybrid origins, variable ploidy, and complex patterns of parental subgenomes. We hypothesize that A. squamata has facultative sperm-dependent asexual reproduction, where sperm is required for embryogenesis but the egg and sperm only occasionally undergo fertilisation, a process that has been associated with the formation of polyploid hybrid swarms in other taxa [1]. Unique amongst known marine allopolyploids, the A. squamata complex inhabits an extensive bathymetric as well as geographic range. A. squamata is a much-studied animal amenable to laboratory culture: appreciating it as a hybrid polyploid complex makes it even more interesting to the study of evolutionary biology.

evolutionary biology↗

bioRxiv2019

Convergent evolution and structural adaptation in the eukaryotic chaperonin CCTα of deep-sea brittle stars

The deep ocean is the largest biome on Earth and yet it is among the least studied environments of our planet. Life at great depths requires several specific adaptations, however their molecular mechanisms remain understudied. We examined patterns of positive selection in 416 genes from four brittle star (Ophiuroidea) families displaying replicated events of deep-sea colonization (288 individuals from 216 species). We found consistent signatures of molecular convergence in functions related to protein biogenesis, including protein folding and translation. Five genes were recurrently positively selected, including CCTα (Chaperonin Containing TCP-1 subunit α), which is essential for protein folding. Molecular convergence was detected at the functional and gene levels but not at the amino-acid level. Pressure-adapted proteins are expected to display higher stability to counteract the effects of denaturation. We thus examined in silico local protein stability of CCTα across the ophiuroid tree of life (967 individuals from 725 species) in a phylogenetically-corrected context and found that deep sea-adapted proteins display higher stability within and next to the substrate-binding region, which was confirmed by in silico global protein stability analyses. This suggests that CCTα not only displays structural but also functional adaptations to deep water conditions. The CCT complex is involved in the folding of ∼10% of newly synthesized proteins and has previously been categorized as ‘cold-shock’ protein in numerous eukaryotes. We thus propose that adaptation mechanisms to cold and deep-sea environments may be linked and highlight that efficient protein biogenesis, including protein folding and translation, are key metabolic deep-sea adaptations.Competing Interest StatementThe authors have declared no competing interest.View Full Text

evolutionary biology↗

bioRxiv2017

Ophiuroid Phylotranscriptomics Enables Discovery Of Novel Echinoderm Representatives Of Bilaterian Neuropeptide Families And Reconstruction Of Neuropeptide Precursor Evolution Over ~270 Million Years

BackgroundNeuropeptides are a diverse class of intercellular signaling molecules that mediate neuronal regulation of many physiological and behavioural processes, including feeding, reproduction and locomotion. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signaling. Here we report a phylo-transcriptomic analysis of neuropeptide precursors in over fifty species of brittle stars (Class Ophiuroidea; Phylum Echinodermata).\n\nResultsDetailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae, Amphiura filiformis and Ophiopsila aranea, enabled the first comprehensive identification of neuropeptide precursors in ophiuroids. Representatives of over thirty bilaterian neuropeptide precursor families were identified, some of which occur as paralogs (e.g. thyrotropin-releasing hormone, corticotropin-releasing hormone, cholecystokinin, somatostatin and pedal peptide). Furthermore, homologs of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally-related, neuropeptides. Here we performed an unprecedented investigation of the evolution of neuropeptide copy-number over a period of ~270 million years by analysing sequence data from over fifty ophiuroid species, with reference to a robust phylogeny. Interestingly, the number of neuropeptide copies in the majority of precursors was constant across all the species examined, but examples of clade-specific losses/gains of neuropeptides were also observed.\n\nConclusionsWe report here the most comprehensive analysis to date of neuropeptide precursors in the phylum Echinodermata, with novel representatives of several bilaterian neuropeptide families discovered for the first time in echinoderms. Furthermore, analysis of precursor proteins comprising multiple copies of identical or related neuropeptides across ~270 million years of ophiuroid evolution indicates that the composition of neuropeptide \"cocktails\" is functionally important, but with plasticity over long evolutionary time scales.

neuroscience↗