New patellogastropod mitogenomes help counteracting long-branch attraction in the deep phylogeny of gastropod mollusks

Uribe, Juan E.; Irisarri, Iker; Templado, José; Zardoya, Rafael

doi:10.1016/j.ympev.2018.12.019

Cited by 57 publications

(65 citation statements)

References 80 publications

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“…The fact that all protein-coding and rRNA genes are consistently encoded by the same strands in all sequenced chitons might have reduced the chance for rate and compositional heterogeneities among lineages. Less rearranged, slower evolving mitogenomes have been shown to produce more accurate phylogenies [46]. Despite the presence of non-stationary amino acid composition in our data (see Results), our phylogenetic analyses recovered fairly robust and congruent tree topologies, regardless of the applied models and inference methods, with only four unsettled branches left (Fig.…”

Section: Utility Of Mitogenomes For Resolving the Chiton Phylogenymentioning

confidence: 68%

“…Despite these known analytical challenges, mitogenomes have been successfully used to reconstruct robust phylogenies in many animal groups, including mollusks (e.g., [7,26,45,46]). However, the thus far seven available chiton mitogenomes only represent a small glimpse of the diversity of the group and representatives of major lineages, remarkably Lepidopleurida and Callochitonidae, have been missing.…”

Section: Introductionmentioning

confidence: 99%

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A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

et al. 2020

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Background: Polyplacophora, or chitons, have long fascinated malacologists for their distinct and rather conserved morphology and lifestyle compared to other mollusk classes. However, key aspects of their phylogeny and evolution remain unclear due to the few morphological, molecular, or combined phylogenetic analyses, particularly those addressing the relationships among the major chiton lineages. Results: Here, we present a mitogenomic phylogeny of chitons based on 13 newly sequenced mitochondrial genomes along with eight available ones and RNAseq-derived mitochondrial sequences from four additional species. Reconstructed phylogenies largely agreed with the latest advances in chiton systematics and integrative taxonomy but we identified some conflicts that call for taxonomic revisions. Despite an overall conserved gene order in chiton mitogenomes, we described three new rearrangements that might have taxonomic utility and reconstructed the most likely scenario of gene order change in this group. Our phylogeny was time-calibrated using various fossils and relaxed molecular clocks, and the robustness of these analyses was assessed with several sensitivity analyses. The inferred ages largely agreed with previous molecular clock estimates and the fossil record, but we also noted that the ambiguities inherent to the chiton fossil record might confound molecular clock analyses. Conclusions: In light of the reconstructed time-calibrated framework, we discuss the evolution of key morphological features and call for a continued effort towards clarifying the phylogeny and evolution of chitons.

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Section: Utility Of Mitogenomes For Resolving the Chiton Phylogenymentioning

confidence: 68%

Section: Introductionmentioning

confidence: 99%

A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

et al. 2020

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“…Considering that the focus of our present analyses is the inter-relationships within Staphylininae, such a wide sampling of outgroup taxa does not appear necessary. In fact, the inclusion of distantly related outgroups can lead to long branch attraction [28,29]. Moreover, incomplete gene sampling for the genera Pseudopsis and Olisthaerus could obscure character polarity and lead to misleading topologies [3].…”

Section: Outgroup Selectionmentioning

confidence: 99%

New Data, Old Story: Molecular Data Illuminate the Tribal Relationships among Rove Beetles of the Subfamily Staphylininae (Coleoptera: Staphylinidae)

Tihelka

Thayer

Newton

et al. 2020

Insects

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The megadiverse subfamily Staphylininae traditionally belonged to the best-defined rove beetle taxa, but the advent of molecular phylogenetics in the last decade has brought turbulent changes to the group’s classification. Here, we reevaluate the internal relationships among the tribes of Staphylininae by implementing tree inference methods that suppress common sources of systematic error. In congruence with morphological data, and in contrast to some previous phylogenetic studies, we unambiguously recover Staphylininae and Paederinae as monophyletic in the traditional sense. We show that the recently proposed subfamily Platyprosopinae (Arrowinus and Platyprosopus) is a phylogenetic artefact and reinstate Arrowinus as a member of Arrowinini stat. res. and Platyprosopus as a member of Platyprosopini stat. res. We show that several recent changes to the internal classification of the subfamily are phylogenetically unjustified and systematically unnecessary. We, therefore, reestablish Platyprosopini, Staphylinini, and Xantholinini as tribes within Staphylininae (all stat. res.) and recognize Coomaniini as a tribe (stat. nov.) rather than subfamily. Consequently, the traditional ranks of the subtribes Acylophorina, Afroquediina, Amblyopinina, Antimerina, †Baltognathina, Cyrtoquediina, Erichsoniina, Hyptiomina, Indoquediina, Quediina, and Tanygnathinina are restored (all stat. res.). We review the current classification of Staphylininae and discuss sources of incongruence in multigene phylogenies.

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“…Organismal scope or featured taxon Cunha & Giribet (2019) yes Gastropods Laumer et al (2019) yes Animals Lemer et al (2019) yes Bivalves Lozano-Fernandez et al (2019) yes Chelicerates Marlétaz et al (2019) yes Spiralia Philippe et al (2019) yes Bilateria Narayanan Kutty et al (2019) no Calyptratae Uribe et al (2019) no Gastropods Wolfe et al (2019) no Decapod crustaceans Zverkov et al (2019) no Dicyemida and Orthonectida Aouad et al (2018) yes Archaea Laumer et al (2018) yes Placozoa Otero-Bravo et al (2018) yes Pantoea Puttick et al (2018) yes Land plants Schwentner et al (2018) yes Pancrustacea Sousa et al (2018) yes Land plants Bennett & Mao (2018) no Fulgoroidea symbionts Eitel et al (2018) no Placozoa Manzano-Marín et al (2018) no Cinara strobi symbionts Feuda et al (2017) yes Animals Szabó et al (2017) yes Pseudococcidae symbionts Williams et al (2017) yes Archaea Schwentner et al (2017) no Pancrustacea Shin et al (2017) no Curculionoidea Simion et al (2017) no Animals Yoshida et al (2017) no Tardigrades Leliaert et al (2016) yes Viridiplantae Zhang et al (2016) yes Roseobacter CHAB-I-5 lineage He et al (2016) no Rhizaria Song et al (2016) no Holometabola Domman et al (2015) yes Plastids Luo (2015) yes SAR11 Petitjean et al (2015) yes Archaea Borowiec et al (2015) no Animals Derelle et al (2015) no Eukaryotes Wang & Wu (2015) no Mitochondria…”

Section: Citationmentioning

confidence: 99%

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

Hernandez

Ryan

2019

Preprint

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Six-state amino acid recoding strategies are commonly applied to combat the effects of compositional heterogeneity and substitution saturation in phylogenetic analyses. While these methods have been endorsed from a theoretical perspective, their performance has never been extensively tested. Here, we test the effectiveness of 6-state recoding approaches by comparing the performance of analyses on recoded and non-recoded datasets that have been simulated under gradients of compositional heterogeneity or saturation. In all of our simulation analyses, non-recoding approaches greatly outperformed 6-state recoding approaches. Our results suggest that 6-state recoding strategies are not effective in the face of high saturation. Further, while recoding strategies do buffer the effects of compositional heterogeneity, the loss of information that accompanies 6-state recoding outweighs its benefits, even in the most compositionally heterogeneous datasets. In addition, we evaluate recoding schemes with 9, 12, 15, and 18 states and show that these all outperform 6-state recoding. Our results have important implications for the more than 70 published papers that have incorporated 6-state recoding, many of which have significant bearing on relationships across the tree of life.

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New patellogastropod mitogenomes help counteracting long-branch attraction in the deep phylogeny of gastropod mollusks

Cited by 57 publications

References 80 publications

A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

A mitogenomic phylogeny of chitons (Mollusca: Polyplacophora)

New Data, Old Story: Molecular Data Illuminate the Tribal Relationships among Rove Beetles of the Subfamily Staphylininae (Coleoptera: Staphylinidae)

Six-state amino acid recoding is not an effective strategy to offset the effects of compositional heterogeneity and saturation in phylogenetic analyses

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