Resolving tricky nodes in the tree of life through amino acid recoding

Giacomelli, Mattia; Rossi, Maria Eleonora; Lozano‐Fernandez, Jesus; Feuda, Roberto; Pisani, Davide

doi:10.1016/j.isci.2022.105594

Cited by 19 publications

(12 citation statements)

References 70 publications

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“…Our findings indicate that at the very least it is possible to recover Porifera-sister trees under CAT-GTR+G4: (1) without applying data recoding techniques and (2) with either Choanoflagellate or non-Choanoflagellate outgroups. This contradicts with previous assumptions that Porifera-sister could only be recovered under recoding techniques or with certain approaches to outgroup inclusion (Halanych et al 2016;Li et al 2021;Hernandez and Ryan 2021;Giacomelli et al 2022). While this study does not examine the merits or otherwise of data recoding, it appears a reasonable recourse to handling data heterogeneity if applied carefully.…”

Section: Discussioncontrasting

confidence: 78%

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny

McCarthy

Mulhair

Siu-Ting

et al. 2023

Molecular Biology and Evolution

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There is conflicting evidence as to whether Porifera (sponges) or Ctenophora (comb jellies) comprise the root of the animal phylogeny. Support for either a Porifera-sister or Ctenophore-sister tree has been extensively examined in the context of model selection, taxon sampling, and outgroup selection. The influence of dataset construction is comparatively understudied. We re-examine five animal phylogeny datasets that have supported either root hypothesis using an approach designed to enrich orthologous signal in phylogenomic datasets. We find that many component orthogroups in animal datasets fail to recover major lineages as monophyletic with the exception of Ctenophora, regardless of the supported root. Enriching these datasets to retain orthogroups recovering ≥3 major lineages reduces dataset size by up to 50% while retaining underlying phylogenetic information and taxon sampling. Site-heterogeneous phylogenomic analysis of these enriched datasets recovers both Porifera-sister and Ctenophora-sister positions, even with additional constraints on outgroup sampling. Two datasets which previously supported Ctenophora-sister support Porifera-sister upon enrichment. All enriched datasets display improved model fitness under posterior predictive analysis. While not conclusively rooting animals at either Porifera or Ctenophora, we do see an increase in signal for Porifera-sister and a decrease in signal for Ctenophore-sister when data are filtered for orthologous signal. Our results indicate that dataset size and construction as well as model fit influence animal root inference.

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Section: Discussioncontrasting

confidence: 78%

Improving Orthologous Signal and Model Fit in Datasets Addressing the Root of the Animal Phylogeny

McCarthy

Mulhair

Siu-Ting

et al. 2023

Molecular Biology and Evolution

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“…All extant ctenophore species have well-developed neuronal and muscular systems, which might co-evolve independently ( Moroz, 2015 ). The recently proposed most basal position of ctenophores (as the sister group to all other animals) is still highly debated ( Whelan et al, 2015 , 2017 ; Halanych et al, 2016 ; Telford et al, 2016 ; Laumer et al, 2019 ; Fernandez and Gabaldon, 2020 ; Kapli and Telford, 2020 ; Li et al, 2021 ; Redmond and McLysaght, 2021 ; Giacomelli et al, 2022 ). Nevertheless, the presence or absence of specific signaling pathways in the ctenophore lineage reshapes our general understanding of neuronal and animal evolution.…”

Section: Introductionmentioning

confidence: 99%

Nitric oxide signaling in ctenophores

2023

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Nitric oxide (NO) is one of the most ancient and versatile signal molecules across all domains of life. NO signaling might also play an essential role in the origin of animal organization. Yet, practically nothing is known about the distribution and functions of NO-dependent signaling pathways in representatives of early branching metazoans such as Ctenophora. Here, we explore the presence and organization of NO signaling components using Mnemiopsis and kin as essential reference species. We show that NO synthase (NOS) is present in at least eight ctenophore species, including Euplokamis and Coeloplana, representing the most basal ctenophore lineages. However, NOS could be secondarily lost in many other ctenophores, including Pleurobrachia and Beroe. In Mnemiopsis leidyi, NOS is present both in adult tissues and differentially expressed in later embryonic stages suggesting the involvement of NO in developmental mechanisms. Ctenophores also possess soluble guanylyl cyclases as potential NO receptors with weak but differential expression across tissues. Combined, these data indicate that the canonical NO-cGMP signaling pathways existed in the common ancestor of animals and could be involved in the control of morphogenesis, cilia activities, feeding and different behaviors.

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“…The long ancestral ctenophore branch (i.e., the internal branch leading to the extant ctenophores in the animal tree of life) has been suggested to cause LBA between Ctenophora and non-animal outgroups, producing tree topologies supporting Ctenophora as sister to all other animals 1,7,8,10,12 . We contend that the longer this branch is (i.e., the more substitutions per site along this branch) in a given dataset (branch length may vary due to substitution model applied, differing gene and site content, variation in alignment and orthology errors, etc.)…”

Section: Ancestral Ctenophora Branch Length As An Lba Severity Measurementioning

confidence: 99%

“…First, we disagree that we inappropriately dismissed Hernandez and Ryan's 11 concerns about recoding given our above points on the recovery of Deuterostomia and Chordata in our test datasets and evidence that W&H's issues with recoded analyses in R&M do not in fact derive from recoding. Other simulation studies have supported recoding 12 , or are at least ambivalent 13 , and as we advocated in R&M, 'a fuller understanding of the implications of recoding is needed' 1 . Second, our claim that REA and WEA15 contain paralog contamination referenced other work 7 and personal communication was limited to WEA17 1 , which has now been shown to support Porifera-sister without recoding when orthogroups with poor orthologous signal (i.e., inability to recover major animal lineages at the gene tree level) are excluded 14 .…”

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confidence: 96%