Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life

Mulhair, Peter O.; McCarthy, Charley G. P.; Siu-Ting, Karen; Creevey, Christopher J.; O’Connell, Mary J.

doi:10.1016/j.cub.2022.10.036

Cited by 16 publications

(31 citation statements)

References 62 publications

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“…Such chromosomal fusion-with-mixing events may help to resolve the phylogenetic positions of animal groups with weak phylogenetic signals based on sequence divergence. For example, Xenacoelomorpha, a group comprising xenoturbellids and acoelomorphs, have been placed as early branching bilaterians (Nephrozoa hypothesis) or as a sister group of ambulacrarians (Xenambulacraria hypothesis) 10, 11, 37, 38 . To find support for either hypothesis, we examined the recently available chromosome-level genome assembly of Xenoturbella bocki 39 , which belongs to xenoturbellids.…”

Section: Resultsmentioning

confidence: 99%

“…After chromosomal fusion with extensive mixing, it is unlikely that genes in a fused chromosome would be sorted to reassemble back into individual chromosomes with the original makeup 17,18 , and, such irreversible chromosomal fusion-with-mixing events can be used as polarized traits for probing deep phylogenetic relationships of animals 17,18 . Recent phylogenomic studies have provided evidence to support the sister-group relationship between Ambulacraria and Xenacoelomorpha, and some even questioned the monophyletic grouping of Deuterostomia [8][9][10][11] (Fig. 3a).…”

Section: Lineage-specific Chromosomal Fusion Events In Major Animal G...mentioning

confidence: 99%

“…While subsequent phylogenomic studies have reinforced support for the ambulacrarian clade, some have suggested a sister group relationship between Ambulacraria and Xenacoelomorpha (a group of marine worms lacking definitive coeloms) and even questioned the monophyletic grouping of the Deuterostomia [8][9][10][11] . Due to the long evolutionary history of deuterostome lineages and the difficulties in assigning definitive stem fossils during the early diversification of the group, it remains challenging to postulate the ancestral condition of their common ancestor, let alone to decipher the genomic basis underlying the origins of diverse body plans and phylogenetic affiliations.…”

Section: Introductionmentioning

confidence: 99%

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Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution

Lin,

Marlétaz,

Pérez-Posada

et al. 2023

Preprint

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Deuterostomes are an animal superphylum that includes Hemichordata and Echinodermata (together Ambulacraria) and Chordata. The diversity of deuterostome body plans has made it challenging to reconstruct their ancestral condition and to decipher the genetic changes that drove the diversification of deuterostome lineages. Here, we generate chromosome-level genome assemblies of two hemichordate species,Ptychodera flavaandSchizocardium californicum, and use comparative genomic approaches to infer the chromosomal architecture of the deuterostome common ancestor and delineate lineage-specific chromosomal modifications. We show that hemichordate chromosomes (1N=23) exhibit remarkable chromosome-scale macrosynteny when compared to other deuterostomes, and can be derived from 24 deuterostome ancestral linkage groups (ALGs). These deuterostome ALGs in turn match previously inferred bilaterian ALGs, consistent with a relatively short transition from the last common bilaterian ancestor to the origin of deuterostomes. Based on this deuterostome ALG complement, we deduced chromosomal rearrangement events that occurred in different lineages. For example, a fusion-with-mixing event produced an Ambulacraria-specific ALG that subsequently split into two chromosomes in extant hemichordates, while this homologous ALG further fused with another chromosome in sea urchins. Orthologous genes distributed in these rearranged chromosomes are enriched for functions in various developmental processes. We found that the deeply conserved Hox clusters are located in highly rearranged chromosomes but have lower densities of transposable elements within the clusters. We also provide evidence that the deuterostome-specific pharyngeal gene cluster was established via the combination of three pre-assembled microsyntenic blocks. We suggest that since chromosomal rearrangement events and formation of new gene clusters may change the regulatory controls of developmental genes, these events may have contributed to the evolution of diverse body plans among deuterostomes.

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Section: Resultsmentioning

confidence: 99%

Section: Lineage-specific Chromosomal Fusion Events In Major Animal G...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution

Lin,

Marlétaz,

Pérez-Posada

et al. 2023

Preprint

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“…Others argue that Xenacoelomorpha is the sister group to Ambulacraria (the Xenambulacraria hypothesis) 3,[26][27][28] , implying that their morphology is degenerate (Fig. 1A).…”

Section: Introductionmentioning

confidence: 99%

“…1A). In the latter case Nephrozoa is viewed to be the result of systematic error stemming from the fast-evolving and long-branching Acoelomorpha 3,[26][27][28][29][30] .…”

Section: Introductionmentioning

confidence: 99%

Acoelomorph flatworm monophyly is a severe long branch-attraction artefact obscuring a clade of Acoela and Xenoturbellida

Redmond

2023

Preprint

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Acoelomorpha is a broadly accepted clade of bilaterian animals made up of the fast-evolving, morphologically simple, mainly marine flatworm lineages Acoela and Nemertodermatida. Phylogenomic studies support Acoelomorpha’s close relationship with the slowly evolving and similarly simplisticXenoturbella, together forming the phylum Xenacoelomorpha. The phylogenetic placement of Xenacoelomorpha amongst bilaterians is controversial, with some studies supporting Xenacoelomorpha as the sister group to all other bilaterians, implying that their simplicity may be representative of early bilaterians. Others propose that this placement is a long branch attraction artefact resulting from the fast-evolving Acoelomorpha, and instead suggest that they are the secondarily simplified sister group of the deuterostome clade Ambulacraria. Perhaps as a result of this debate, internal xenacoelomorph relationships have been somewhat overlooked at a phylogenomic scale. Here, I employ both empirical and simulation approaches to detect and overcome phylogenomic errors to reassess the relationship betweenXenoturbellaand the fast evolving acoelomorph flatworms. I conclude that subphylum Acoelomorpha is a long-branch attraction artefact obscuring a previously undiscovered clade comprisingXenoturbellaand Acoela, for which I propose the name Xenacoela. These analyses are also consistent with the Nephrozoa hypothesis deriving from systematic error, and instead generally favour a close, but unclear, relationship of Xenacoelomorpha with deuterostomes. This study provides a template for future efforts aimed at discovering and correcting unrecognised long-branch attraction artefacts throughout the tree of life.

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PhyKIT: A Multitool for Phylogenomics

Steenwyk,

Martínez‐Redondo,

Buida

et al. 2024

Current Protocols

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Multiple sequence alignments and phylogenetic trees are rich in biological information and are fundamental to research in biology. PhyKIT is a tool for processing and analyzing the information content of multiple sequence alignments and phylogenetic trees. Here, we describe how to use PhyKIT for diverse analyses, including (i) constructing a phylogenomic supermatrix, (ii) detecting errors in orthology inference, (iii) quantifying biases in phylogenomic data sets, (iv) identifying radiation events or lack of resolution using gene support frequencies, and (v) conducting evolution‐based screens to facilitate gene function prediction. Several PhyKIT functions that streamline multiple sequence alignment and phylogenetic processing—such as renaming FASTA entries or tree tips—are also discussed. These protocols demonstrate how simple command‐line operations in the unified framework of PhyKIT facilitate diverse phylogenomic data analysis and processing, from supermatrix construction and diagnosis to gaining clues about gene function. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Installing PhyKIT and syntax for usageBasic Protocol 2: Constructing a phylogenomic supermatrixBasic Protocol 3: Detecting anomalies in orthology relationshipsBasic Protocol 4: Quantifying biases in phylogenomic data matrices and related measuresBasic Protocol 5: Identifying polytomiesBasic Protocol 6: Assessing gene‐gene coevolution as a genetic screen

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Filtering artifactual signal increases support for Xenacoelomorpha and Ambulacraria sister relationship in the animal tree of life

Cited by 16 publications

References 62 publications

Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution

Chromosome-level genome assemblies of two hemichordates provide new insights into deuterostome origin and chromosome evolution

Acoelomorph flatworm monophyly is a severe long branch-attraction artefact obscuring a clade of Acoela and Xenoturbellida

PhyKIT: A Multitool for Phylogenomics

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