Parallel Amino Acid Deletions of Prestin Protein in Two Dramatically Divergent Bat Lineages Suggest the Complexity of the Evolution of Echolocation in Bats

Min, Ren; Sun, Haijian; Bo, Shunqi; Zhang, Shuyi; Hua, Panyu

doi:10.3161/15081109acc2018.20.2.003

Cited by 3 publications

(3 citation statements)

References 19 publications

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“…However, more recent studies seem to provide less support for this hypothesis; 2) the Yinpterochiroptera-Yangochiroptera hypothesis, in which the Yangochiroptera clade includes most of Microchiroptera and the Yinpterochiroptera clade includes the rest of Microchiroptera and all of Megachiroptera. There is growing support for this hypothesis in the literature (Meganathan, et al 2012;Tsagkogeorga, et al 2013;Ren, et al 2018; Reyes-Amaya and Flores 2019).…”

Section: Applying the Methods To Two Clades Whose Root Position Is Unmentioning

confidence: 94%

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals

Naser-Khdour

Minh

Lanfear

2020

Preprint

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Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position.Availability and implementationA python script for calculating rootstrap support values is available at https://github.com/suhanaser/Rootstrap.

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Section: Applying the Methods To Two Clades Whose Root Position Is Unmentioning

confidence: 94%

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals

Naser-Khdour

Minh

Lanfear

2020

Preprint

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“…However, more recent studies seem to provide less support for this hypothesis; 2) the Yinpterochiroptera-Yangochiroptera hypothesis, in which the Yangochiroptera clade includes most of Microchiroptera and the Yinpterochiroptera clade includes the rest of Microchiroptera and all of Megachiroptera. There is growing support for this hypothesis in the literature ( Meganathan et al 2012 ; Tsagkogeorga et al 2013 ; Ren et al 2018 ; Reyes-Amaya and Flores 2019 ).…”

Section: Methodsmentioning

confidence: 95%

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals

2021

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Using time-reversible Markov models is a very common practice in phylogenetic analysis, because although we expect many of their assumptions to be violated by empirical data, they provide high computational efficiency. However, these models lack the ability to infer the root placement of the estimated phylogeny. In order to compensate for the inability of these models to root the tree, many researchers use external information such as using outgroup taxa or additional assumptions such as molecular-clocks. In this study, we investigate the utility of non-reversible models to root empirical phylogenies and introduce a new bootstrap measure, the rootstrap, which provides information on the statistical support for any given root position. Availability and implementation: rootstrap support is implemented in IQ-TREE 2 and a tutorial is available at the iqtree webpage http://www.iqtree.org/doc/Rootstrap. In addition, a python script is available at https://github.com/suhanaser/Rootstrap

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“…Here, recurrent substitutions are used as an umbrella for convergent and parallel substitutions. Bats and cetaceans have fixed a similar set of mutations with respect to their closest relatives during the emergence of echolocation [6,7,5].…”

Section: Introductionmentioning

confidence: 99%

Recurrent Sequence Evolution After Independent Gene Duplication

Dunk

Snel

2020

Preprint

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Background Convergent and parallel evolution provide unique insights into the mechanisms of natural selection. Some of the most striking convergent and parallel (collectively recurrent ) amino acid substitutions in proteins are adaptive, but there are also many that are selectively neutral. Genome-wide assessment of recurrent substitutions has only been performed for orthologs. These studies have revealed that the pervasiveness of recurrent substitutions is for a large part explained by purifying selection. At any position in a protein, only a subset of amino acids is allowed, increasing the chance of the same substitution happening in different lineages. ResultsWe developed a framework that detects patterns of recurrent differentiation in paralogs across 90 divergent eukaryotic genomes. A skew in recurrent substitutions serves as a proxy for a recurrent trend in function. We find remarkable examples of recurrent sequence evolution after independent duplication, in some cases involving more than ten different lineages where duplicates show a similar differentiation. We reveal the implicated functional patterns for the gene families Hint1/Hint2, Sco1/Sco2 and vma11/vma3. ConclusionsThe presented methodology provides a means to study the biochemical underpinning of functional differentiation between paralogs. For instance, two abundantly repeated substitutions are identified between independently derived Sco1 and Sco2 paralogs. Such identified substitutions allow direct experimental testing of the biological role of these residues for the repeated functional differentiation. The present study uncovers a diverse set of families with recurrent sequence evolution and reveals trends in the functional and evolutionary trajectories of this hitherto understudied phenomenon.

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Parallel Amino Acid Deletions of Prestin Protein in Two Dramatically Divergent Bat Lineages Suggest the Complexity of the Evolution of Echolocation in Bats

Cited by 3 publications

References 19 publications

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Non-Reversible Models for Mammals

Assessing Confidence in Root Placement on Phylogenies: An Empirical Study Using Nonreversible Models for Mammals

Recurrent Sequence Evolution After Independent Gene Duplication

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