Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes
Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirur...
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Ecology and Evolution |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fevo.2021.769565/full |
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| author | Mohammed Ahmed Nickellaus G. Roberts Funmilola Adediran Ashleigh B. Smythe Kevin M. Kocot Oleksandr Holovachov |
| author_facet | Mohammed Ahmed Nickellaus G. Roberts Funmilola Adediran Ashleigh B. Smythe Kevin M. Kocot Oleksandr Holovachov |
| author_sort | Mohammed Ahmed |
| collection | DOAJ |
| description | Phylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida. |
| first_indexed | 2024-12-20T09:17:42Z |
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| issn | 2296-701X |
| language | English |
| last_indexed | 2024-12-20T09:17:42Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Ecology and Evolution |
| spelling | doaj.art-3f279a52cba2468ea33eac9b61b0cddf2022-12-21T19:45:22ZengFrontiers Media S.A.Frontiers in Ecology and Evolution2296-701X2022-01-01910.3389/fevo.2021.769565769565Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and MitogenomesMohammed Ahmed0Nickellaus G. Roberts1Funmilola Adediran2Ashleigh B. Smythe3Kevin M. Kocot4Oleksandr Holovachov5Department of Zoology, Swedish Museum of Natural History, Stockholm, SwedenDepartment of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, AL, United StatesDepartment of Zoology, Stockholm University, Stockholm, SwedenDepartment of Biology, Virginia Military Institute, Lexington, VA, United StatesDepartment of Biological Sciences and Alabama Museum of Natural History, The University of Alabama, Tuscaloosa, AL, United StatesDepartment of Zoology, Swedish Museum of Natural History, Stockholm, SwedenPhylogenetic relationships within many lineages of the phylum Nematoda remain unresolved, despite numerous morphology-based and molecular analyses. We performed several phylogenomic analyses using 286 published genomes and transcriptomes and 19 new transcriptomes by focusing on Trichinellida, Spirurina, Rhabditina, and Tylenchina separately, and by analyzing a selection of species from the whole phylum Nematoda. The phylogeny of Trichinellida supported the division of Trichinella into encapsulated and non-encapsulated species and placed them as sister to Trichuris. The Spirurina subtree supported the clades formed by species from Ascaridomorpha and Spiruromorpha respectively, but did not support Dracunculoidea. The analysis of Tylenchina supported a clade that included all sampled species from Tylenchomorpha and placed it as sister to clades that included sampled species from Cephalobomorpha and Panagrolaimomorpha, supporting the hypothesis that postulates the single origin of the stomatostylet. The Rhabditina subtree placed a clade composed of all sampled species from Diplogastridae as sister to a lineage consisting of paraphyletic Rhabditidae, a single representative of Heterorhabditidae and a clade composed of sampled species belonging to Strongylida. It also strongly supported all suborders within Strongylida. In the phylum-wide analysis, a clade composed of all sampled species belonging to Enoplia were consistently placed as sister to Dorylaimia + Chromadoria. The topology of the Nematoda backbone was consistent with previous studies, including polyphyletic placement of sampled representatives of Monhysterida and Araeolaimida.https://www.frontiersin.org/articles/10.3389/fevo.2021.769565/fullroundwormsevolutiontranscriptomegenomeparasitismclassification |
| spellingShingle | Mohammed Ahmed Nickellaus G. Roberts Funmilola Adediran Ashleigh B. Smythe Kevin M. Kocot Oleksandr Holovachov Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes Frontiers in Ecology and Evolution roundworms evolution transcriptome genome parasitism classification |
| title | Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes |
| title_full | Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes |
| title_fullStr | Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes |
| title_full_unstemmed | Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes |
| title_short | Phylogenomic Analysis of the Phylum Nematoda: Conflicts and Congruences With Morphology, 18S rRNA, and Mitogenomes |
| title_sort | phylogenomic analysis of the phylum nematoda conflicts and congruences with morphology 18s rrna and mitogenomes |
| topic | roundworms evolution transcriptome genome parasitism classification |
| url | https://www.frontiersin.org/articles/10.3389/fevo.2021.769565/full |
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