Functional Effects of a Retained Ancestral Polymorphism in<i>Prestin</i>

Li, Yuanyuan; Liu, Zhen; Qi, Fei-Yan; Zhou, Xin; Shi, Peng

doi:10.1093/molbev/msw222

Cited by 14 publications

(12 citation statements)

References 27 publications

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“…The phenomenon of hemiplasy likely explains the distribution of multiple ecologically important traits (e.g., refs. 39 and 40), but can mislead standard methods for inferring the number of times a trait has involved and the timing of these transitions (25–27). The goal of the work presented here is to quantify the risk of incorrectly inferring homoplasy when hemiplasy is occurring.…”

Section: Discussionmentioning

confidence: 99%

Quantifying the risk of hemiplasy in phylogenetic inference

Guerrero

Hahn

2018

Proc. Natl. Acad. Sci. U.S.A.

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SignificanceConvergent evolution provides key evidence for the action of natural selection. The process of convergence is often inferred because the same trait appears in multiple species that are not closely related. However, different parts of the genome can reveal different relationships among species, with some genes or regions uniting lineages that appear unrelated in the species tree. If changes in traits occur in these discordant regions, a false pattern of convergence can be produced (known as “hemiplasy”). Here, we provide a way to quantify the probability that hemiplasy occurs and contrast it with the probability of convergence. We find that hemiplasy is likely to explain many apparent cases of convergent evolution, even when the fraction of discordant regions is low.

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Section: Discussionmentioning

confidence: 99%

Quantifying the risk of hemiplasy in phylogenetic inference

Guerrero

Hahn

2018

Proc. Natl. Acad. Sci. U.S.A.

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“…Prestin orthologs from non-echolocating bats and whales engineered to have the single convergent substitution N7T showed significant functional differences, all in the same direction of effect, and indeed became more functionally similar to the wild-type protein found in their echolocating relatives (4). Analogous interrogation of N308S yielded similar results (7).…”

Section: Molecular Convergence Test Flags Lung-weight Genes In High-amentioning

confidence: 74%

A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales

Marcovitz

Turakhia

Chen

et al. 2019

Proc. Natl. Acad. Sci. U.S.A.

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Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.

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“…A further manual examination of the six aforementioned hearing-related proteins (prestin, Dfnb59, Slitrk6, Strc, Tecta, Cabp2) also shows that none of the parallel substitutions occur specifically in these echolocating mammals, with the exception of Strc H320Q that our screen uncovered ( Figure S4). Notably, the N7T and P26L substitutions that were experimentally shown to affect prestin function also occur in the non-echolocating elephant shrew and Felidae (big cats) / minke whale, respectively ( Figure S4A) [37]. This suggests that the observation of a derived substitution in a background species does not necessarily preclude a functional effect on the protein, and that pure patterns of convergence rarely exists when taxonomic sampling depth increases [38].…”

Section: Resultsmentioning

confidence: 93%

Molecular parallelism in fast-twitch muscle proteins in echolocating mammals

Lee

Lewis

Moural

et al. 2018

Preprint

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Detecting associations between genomic changes and phenotypic differences is fundamental to understanding how phenotypes evolved. By developing a method to systematically screen for parallel amino acid substitutions, we discovered that echolocating bats and dolphins exhibit more parallel substitutions than expected in fast-twitch but in not slow-twitch muscle fiber proteins. Both bats and dolphins rely on specialized superfast muscles to produce an extremely rapid call rate when homing in on their prey. We show that these genes with parallel substitutions are expressed in the superfast call-producing muscle of bats and demonstrate that the calcium storage protein calsequestrin 1 of bats and dolphins form calcium-sequestering polymers at lower calcium concentrations, consistent with adaptations to rapid calcium transients required for superfast muscle physiology. Our results provide molecular insights into the convergent evolution of vocalization in echolocating mammals and demonstrate the potential of systematic screens to uncover associations between genomic changes and phenotypic differences.

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Functional Effects of a Retained Ancestral Polymorphism inPrestin

Cited by 14 publications

References 27 publications

Quantifying the risk of hemiplasy in phylogenetic inference

Quantifying the risk of hemiplasy in phylogenetic inference

A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales

Molecular parallelism in fast-twitch muscle proteins in echolocating mammals

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