Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina
Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecula...
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| Format: | Article |
| Language: | English |
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The Royal Society
2017-01-01
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| Series: | Royal Society Open Science |
| Subjects: | |
| Online Access: | https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.171095 |
| _version_ | 1824034019195486208 |
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| author | Joshua M. Hallas Anton Chichvarkhin Terrence M. Gosliner |
| author_facet | Joshua M. Hallas Anton Chichvarkhin Terrence M. Gosliner |
| author_sort | Joshua M. Hallas |
| collection | DOAJ |
| description | Molecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness (PI) profiles suggest that the molecular markers tested lack the power to resolve relationships at the base of the Doridina, while being more robust at family-level classifications. This supports the lack of consistent resolution between the 19 families within the Doridina across all three alignments. Most of the 19 families were recovered as monophyletic, and instances of non-monophyletic families were consistently recovered between analyses. We conclude that the alignment of variable regions has some effect on phylogenetic estimates of the Doridina, but these effects can vary depending on the size and scope of the phylogenetic query and PI of molecular markers. |
| first_indexed | 2024-12-22T17:52:25Z |
| format | Article |
| id | doaj.art-d207729ccdc24a46b1bfddc0f81eee03 |
| institution | Directory Open Access Journal |
| issn | 2054-5703 |
| language | English |
| last_indexed | 2024-12-22T17:52:25Z |
| publishDate | 2017-01-01 |
| publisher | The Royal Society |
| record_format | Article |
| series | Royal Society Open Science |
| spelling | doaj.art-d207729ccdc24a46b1bfddc0f81eee032022-12-21T18:18:08ZengThe Royal SocietyRoyal Society Open Science2054-57032017-01-0141010.1098/rsos.171095171095Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder DoridinaJoshua M. HallasAnton ChichvarkhinTerrence M. GoslinerMolecular estimates of phylogenetic relationships rely heavily on multiple sequence alignment construction. There has been little consensus, however, on how to properly address issues pertaining to the alignment of variable regions. Here, we construct alignments from four commonly sequenced molecular markers (16S, 18S, 28S and cytochrome c oxidase subunit I) for the Nudibranchia using three different methodologies: (i) strict mathematical algorithm; (ii) exclusion of variable or divergent regions and (iii) manually curated, and examine how different alignment construction methods can affect phylogenetic signal and phylogenetic estimates for the suborder Doridina. Phylogenetic informativeness (PI) profiles suggest that the molecular markers tested lack the power to resolve relationships at the base of the Doridina, while being more robust at family-level classifications. This supports the lack of consistent resolution between the 19 families within the Doridina across all three alignments. Most of the 19 families were recovered as monophyletic, and instances of non-monophyletic families were consistently recovered between analyses. We conclude that the alignment of variable regions has some effect on phylogenetic estimates of the Doridina, but these effects can vary depending on the size and scope of the phylogenetic query and PI of molecular markers.https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.171095sequence homologymultiple sequence alignmentdorid systematicsphanerobranchiacryptobranchia |
| spellingShingle | Joshua M. Hallas Anton Chichvarkhin Terrence M. Gosliner Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina Royal Society Open Science sequence homology multiple sequence alignment dorid systematics phanerobranchia cryptobranchia |
| title | Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina |
| title_full | Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina |
| title_fullStr | Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina |
| title_full_unstemmed | Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina |
| title_short | Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina |
| title_sort | aligning evidence concerns regarding multiple sequence alignments in estimating the phylogeny of the nudibranchia suborder doridina |
| topic | sequence homology multiple sequence alignment dorid systematics phanerobranchia cryptobranchia |
| url | https://royalsocietypublishing.org/doi/pdf/10.1098/rsos.171095 |
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