Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia)
Within Polynoidae, a diverse aphroditiform family, the subfamily Macellicephalinae comprises anchialine cave-dwelling and deep-sea scaleworms. In this study, Lepidonotopodinae is synonymized with Macellicephalinae, and the tribe Lepidonotopodini is applied to a well-supported clade inhabiting deep-s...
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2024-11-01
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| author | Avery S. Hiley Nicolás Mongiardino Koch Greg W. Rouse |
| author_facet | Avery S. Hiley Nicolás Mongiardino Koch Greg W. Rouse |
| author_sort | Avery S. Hiley |
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| description | Within Polynoidae, a diverse aphroditiform family, the subfamily Macellicephalinae comprises anchialine cave-dwelling and deep-sea scaleworms. In this study, Lepidonotopodinae is synonymized with Macellicephalinae, and the tribe Lepidonotopodini is applied to a well-supported clade inhabiting deep-sea chemosynthetic-based ecosystems. Newly sequenced “genome skimming” data for 30 deep-sea polynoids and the comparatively shallow living <i>Eulagisca gigantea</i> is used to bioinformatically assemble their mitogenomes. When analyzed with existing scaleworm mitogenomes, deep-sea scaleworms exhibit increased gene order rearrangement events compared to shallow-water relatives. Additionally, comparative analyses of shallow-water vs. deep-sea polynoid substitution rates in mitochondrial protein-coding genes show an overall relaxed purifying selection and a positive selection of several amino acid sites in deep-sea species, indicating that polynoid mitogenomes have undergone selective pressure to evolve metabolic adaptations suited to deep-sea environments. Furthermore, the inclusion of skimming data for already known Lepidonotopodini species allowed for an increased coverage of DNA data and a representation of the taxa necessary to create a more robust phylogeny using 18 genes, as opposed to the six genes previously used. The phylogenetic results support the erection of <i>Cladopolynoe</i> gen. nov., <i>Mamiwata</i> gen. nov., <i>Photinopolynoe</i> gen. nov., <i>Stratigos</i> gen. nov., and <i>Themis</i> gen. nov., and emended diagnoses for <i>Branchinotogluma, Branchipolynoe</i>, <i>Lepidonotopodium</i>, and <i>Levensteiniella</i>. |
| format | Article |
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| spelling | doaj-art-cdb19491b9c24ec5877ae83ffa0ff9912024-12-27T14:11:54ZengMDPI AGBiology2079-77372024-11-01131297910.3390/biology13120979Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia)Avery S. Hiley0Nicolás Mongiardino Koch1Greg W. Rouse2Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USAScripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USAScripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202, USAWithin Polynoidae, a diverse aphroditiform family, the subfamily Macellicephalinae comprises anchialine cave-dwelling and deep-sea scaleworms. In this study, Lepidonotopodinae is synonymized with Macellicephalinae, and the tribe Lepidonotopodini is applied to a well-supported clade inhabiting deep-sea chemosynthetic-based ecosystems. Newly sequenced “genome skimming” data for 30 deep-sea polynoids and the comparatively shallow living <i>Eulagisca gigantea</i> is used to bioinformatically assemble their mitogenomes. When analyzed with existing scaleworm mitogenomes, deep-sea scaleworms exhibit increased gene order rearrangement events compared to shallow-water relatives. Additionally, comparative analyses of shallow-water vs. deep-sea polynoid substitution rates in mitochondrial protein-coding genes show an overall relaxed purifying selection and a positive selection of several amino acid sites in deep-sea species, indicating that polynoid mitogenomes have undergone selective pressure to evolve metabolic adaptations suited to deep-sea environments. Furthermore, the inclusion of skimming data for already known Lepidonotopodini species allowed for an increased coverage of DNA data and a representation of the taxa necessary to create a more robust phylogeny using 18 genes, as opposed to the six genes previously used. The phylogenetic results support the erection of <i>Cladopolynoe</i> gen. nov., <i>Mamiwata</i> gen. nov., <i>Photinopolynoe</i> gen. nov., <i>Stratigos</i> gen. nov., and <i>Themis</i> gen. nov., and emended diagnoses for <i>Branchinotogluma, Branchipolynoe</i>, <i>Lepidonotopodium</i>, and <i>Levensteiniella</i>.https://www.mdpi.com/2079-7737/13/12/979chemosynthetic-based ecosystemsdeep seagene order rearrangementLepidonotopodiniMacellicephalinaemitogenomes |
| spellingShingle | Avery S. Hiley Nicolás Mongiardino Koch Greg W. Rouse Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia) Biology chemosynthetic-based ecosystems deep sea gene order rearrangement Lepidonotopodini Macellicephalinae mitogenomes |
| title | Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia) |
| title_full | Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia) |
| title_fullStr | Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia) |
| title_full_unstemmed | Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia) |
| title_short | Phylogenetics of Lepidonotopodini (Macellicephalinae, Polynoidae, Annelida) and Comparative Mitogenomics of Shallow-Water vs. Deep-Sea Scaleworms (Aphroditiformia) |
| title_sort | phylogenetics of lepidonotopodini macellicephalinae polynoidae annelida and comparative mitogenomics of shallow water vs deep sea scaleworms aphroditiformia |
| topic | chemosynthetic-based ecosystems deep sea gene order rearrangement Lepidonotopodini Macellicephalinae mitogenomes |
| url | https://www.mdpi.com/2079-7737/13/12/979 |
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