Family matters: The first molecular phylogeny of the Onchidorididae Gray, 1827 (Mollusca, Gastropoda, Nudibranchia)

Hallas, Joshua M.; Gosliner, Terrence M.

doi:10.1016/j.ympev.2015.03.015

Cited by 20 publications

(24 citation statements)

References 38 publications

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“…For example, we only recovered a monophyletic Onchidoridoidea in our CA phylogenetic estimate. By contrast, Hallas & Gosliner [ 62 ] recovered a mostly resolved monophyletic Onchidoridoidea with significant pp and bs support. Their taxonomic sampling, however, was much more focused and included histone 3 as an additional molecular marker.…”

Section: Discussionmentioning

confidence: 96%

“…Genomic DNA was extracted using the Qiagen DNeasy Blood & Tissue extraction kit (Valencia, CA). Amplification and sequencing for targeted gene fragments 16S, 18S, 28S and cytochrome c oxidase subunit I (COI) followed protocols used by Hallas & Gosliner [ 62 ]. Amplified fragments were sequenced at the Center for Comparative Genomics located at the California Academy of Sciences and National Scientific Center of Marine Biology.…”

Section: Methodsmentioning

confidence: 99%

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Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

2017

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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.

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Section: Discussionmentioning

confidence: 96%

Section: Methodsmentioning

confidence: 99%

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

2017

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“…Onchidoris species were most different from Cadlina and Aldisa , which is perhaps expected due to their phylogenetic position (Hallas & Gosliner, ). Both Onchidoris species had multiple layers of large spicules in the mantle edge, body wall and foot rather than tracts of smaller spicules.…”

Section: Discussionmentioning

confidence: 91%

“…They are often rejected by predators and are generally associated with well‐defended prey, such as sponges (Thompson, ; Todd, ). Therefore, dorids are a key taxon for studying the evolution and interaction of chemical defence, colour patterns and feeding specialization (Cimino & Gavagnin, ; Faulkner & Ghiselin, ; Hallas & Gosliner, ; Karuso, ; Rudman & Bergquist, ; Valdés, ; Wägele, Ballesteros, & Avila, ; Wägele & Klussmann‐Kolb, ). However, a robust phylogeny has proven elusive (Bouchet et al., ), therefore inhibiting formal tests of these hypotheses.…”

Section: Introductionmentioning

confidence: 99%

“…First, dorids have traditionally been divided into four suborders (Bouchet et al., ) with most defence and feeding studies carried out on the Cryptobranchia (Cimino & Gavagnin, ), a group which can withdraw their gill into a specialized pocket. However, recent work has questioned the monophyly of the Cryptobranchia (Hallas, Chichvarkhin, & Gosliner, ; Hallas & Gosliner, ; Martynov & Schrödl, ). Second, the genus Cadlina has been found to be closely related to Aldisa (Johnson, ), breaking the previously thought relationship between Cadlina and the chromodorids, the latter of which have the best‐described chemical defences (Cimino & Gavagnin, ).…”

Section: Introductionmentioning

confidence: 99%

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Micro‐computed tomography of spicule networks in three genera of dorid sea‐slugs (Gastropoda: Nudipleura: Doridina) shows patterns of phylogenetic significance

et al. 2018

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Dorid nudibranchs (Gastropoda: Nudipleura) are a key taxon for studying the evolution and interaction of chemical defence, colour patterns and feeding specialization, but we lack a robust phylogeny for hypothesis testing. To provide new morphological characters, we investigated the extensive interior spicule networks of several dorid taxa. We compared traditional staining methods versus micro‐computed tomography (μCT) of 31 specimens representing 10 species of Aldisa, Cadlina and Onchidoris. We found that μCT offered a nondestructive view of sufficient resolution to study the gross morphology of networks, although images of fine structures were too grainy to allow robust comparisons. Network form did not vary within species and was consistent within genera. The three genera varied in several obvious characters, such as the presence of a pleural sinus channel, large dorsal spicules and multispicular tracts, as well as in relative size, shape and orientation of spicules. These characters, combined with those from the literature, supported recent molecular phylogenies that group Cadlina with Aldisa, and that question the monophyly of the Cryptobranchia. This suggests that these network forms will prove a fruitful source of phylogenetic characters with at least genus‐level resolution.

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First record of the Aeolid Anteaeolidiella fijensis (Nudibranchia, Aeolidiidae) from India

et al. 2016

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Family matters: The first molecular phylogeny of the Onchidorididae Gray, 1827 (Mollusca, Gastropoda, Nudibranchia)

Cited by 20 publications

References 38 publications

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

Aligning evidence: concerns regarding multiple sequence alignments in estimating the phylogeny of the Nudibranchia suborder Doridina

Micro‐computed tomography of spicule networks in three genera of dorid sea‐slugs (Gastropoda: Nudipleura: Doridina) shows patterns of phylogenetic significance

First record of the Aeolid Anteaeolidiella fijensis (Nudibranchia, Aeolidiidae) from India

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