Processed pseudogenes: A substrate for evolutionary innovation

Troskie, Robin-Lee; Faulkner, Geoffrey J.; Cheetham, Seth W.

doi:10.1002/bies.202100186

Cited by 28 publications

(16 citation statements)

References 102 publications

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“…3 a, b). Although most pseudogenes are thought to be nonfunctional, a few transcribed pseudogenes have been reported to obtain the defined functions through rapid evolution 44 . Our results reveal that most RPLP2 processed pseudogenes in P. glacialis harbor faster evolutionary rate (Ka/Ks) than that of complete RPLP2 genes among eight butterflies (Fig.…”

Section: Discussionmentioning

confidence: 99%

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zhao,

Su,

et al. 2023

Nat Commun

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Parnassius glacialis is a typical “Out of the QTP” alpine butterfly that originated on the Qinghai-Tibet Plateau (QTP) and dispersed into relatively low-altitude mountainous. Here we assemble a chromosome-level genome of P. glacialis and resequence 9 populations in order to explore the genome evolution and local adaptation of this species. These results indicated that the rapid accumulation and slow unequal recombination of transposable elements (TEs) contributed to the formation of its large genome. Several ribosomal gene families showed extensive expansion and selective evolution through transposon-mediated processed pseudogenes. Additionally, massive structural variations (SVs) of TEs affected the genetic differentiation of low-altitude populations. These low-altitude populations might have experienced a genetic bottleneck in the past and harbor genes with selective signatures which may be responsible for the potential adaptation to low-altitude environments. These results provide a foundation for understanding genome evolution and local adaptation for “Out of the QTP” of P. glacialis.

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Section: Discussionmentioning

confidence: 99%

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Zhao,

Su,

et al. 2023

Nat Commun

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“…S1). This phenomenon results from the fact that each of these genes belongs to a large gene family whose members share some conserved domains with each other, and these functional paralogs (family members) underwent further duplication likely through retrotransposition that gave rise to hundreds of thousands of truncated pseudogenes (Troskie, et al 2021). Meanwhile, high duplication levels of a few genes in certain species (e.g.…”

Section: Longevity-associated Genes Underwent a Higher Rate Of Expans...mentioning

confidence: 99%

“…Typically, pseudogenes derived from retrotransposition lack the upstream of the promoters of their parental genes. To obtain transcriptional activity, pseudogenes must be located downstream of a pre-existing promoter in close proximity, or a novel promoter must evolve (Troskie, et al 2021). By analysing the loci of PIK3R1 duplications in the genomes of H. glaber and M. myotis, we noticed that most of them are located either in introns or intergenic regions adjacent to protein-coding genes.…”

Section: Pik3r1 May Have Experienced Convergent Duplications In the L...mentioning

confidence: 99%

Duplications of human longevity-associated genes across placental mammals

Huang

Jiang

et al. 2023

Preprint

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Natural selection has shaped a wide range of lifespans across mammals, with a few long-lived species showing negligible signs of ageing. Approaches used to elucidate the genetic mechanisms underlying mammalian longevity usually involve phylogenetic selection tests on candidate genes, analyses of differential gene expression between age cohorts or species, and measuring age-related epigenetic changes. However, the link between gene duplication and evolution of mammalian longevity has not been widely investigated. Here, we explored the association between gene duplication and mammalian lifespan by analysing 287 human longevity-associated genes across 37 placental mammals. We estimated that the expansion rate of these genes is eight times higher than their contraction rate across these 37 species. Using phylogenetic approaches, we identified 43 genes whose duplication levels are significantly correlated with longevity quotients (FDR < 0.05). In particular, strong correlation observed for four genes (CREBBP, PIK3R1, HELLS, FOXM1) appears to be driven mainly by their high duplication levels in two ageing extremists, the naked mole rat (Heterocephalus glaber) and the greater mouse-eared bat (Myotis myotis). Further sequence and expression analyses suggest that the gene PIK3R1 may have undergone a convergent duplication event, whereby the similar region of its coding sequence was independently duplicated multiple times in both of these long-lived species. Collectively, this study identified several candidate genes whose duplications may underlie the extreme longevity in mammals, and highlighted the potential role of gene duplication in the evolution of mammalian long lifespans.

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“…A 2021 review in Nature found that over 130,000 discrete genetic elements 'previously called junk DNA' have been already reported in the literature to have biological functions -and showed that functions for non-coding DNA are being discovered at a rapid pace (Gates et al 2021). Even pseudogenes, frequently cited as a form of genetic junk that demonstrates common ancestry, are no longer considered to necessarily be genetic 'junk' (Cheetham, Faulkner & Dinger 2020;Kovalenko & Patrushev 2018;Pink et al 2011;Poliseno 2012;Poliseno et al 2010;Troskie, Faulkner & Cheetham 2021). The assumption that non-coding DNA that we share with apes is merely functionless 'junk' reflecting our common ancestry is no longer sustainable.…”

Section: Human-chimp Genetic Similaritymentioning

confidence: 99%

Qualified agreement: How scientific discoveries support theistic belief

Meyer¹

2022

Reformed Theology in Africa Series

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Peer review declarationThe publisher (AOSIS) endorses the South African 'National Scholarly Book Publishers Forum Best Practice for Peer Review of Scholarly Books.' The manuscript underwent an evaluation to compare the level of originality with other published works and was subjected to rigorous two-step peer review before publication, with the identities of the reviewers not revealed to the editor(s) or author(s). The reviewers were independent of the publisher, editor(s), and author(s). The publisher shared feedback on the similarity report and the reviewers' inputs with the manuscript's editor(s) or author(s) to improve the manuscript. Where the reviewers recommended revision and improvements, the editor(s) or author(s) responded adequately to such recommendations. The reviewers commented positively on the scholarly merits of the manuscript and recommended that the book be published. v Research justificationScience and Faith in Dialogue presents a cogent, compelling case for concordance between science and theism. The term theism used in this book refers to the belief in God's existence. Within theology, the term theism is often used to convey a range of presuppositions about the nature and attributes of God. The topic of God's attributes does not fall within the scope of this study. Based on scientific and natural theological perspectives, two pillars of natural theology are revisited: the Cosmological Argument and the Argument from Design. The book argues that modern science provides undeniable evidence and a scientific basis for these classical arguments to infer a rationally justifiable endorsement of theism as being concordant with reason and science -nature is seen as operating orderly on comprehensible, rational, consistent laws, in line with the conviction that God is Creator. The expression 'undeniable evidence and scientific basis' is not understood as scientific proof but rather as inference, footprint, signature, deductive reasoning and rational justification for theism in world view. The premise that theism asserts a more causally adequate explanation of recent developments in modern natural science (than naturalism) is based upon: (1) Strong epistemological support: explanatory power and confirmation of hypothesis (rather than just deductive entailment); and (2) the contemporary cosmological consensus, building upon the rigour of the physical sciences and illuminating biological discoveries. The discovery that the universe had a beginning and the abundant scientific evidence for fine-tuning is best explained by theism. The phrase 'global fine-tuning' refers to fine-tuning of initial conditions, fundamental forces and other physical laws and constants for an expanding universe and the formation of galaxies, stars and planets. The phrase 'local fine-tuning' refers to the protection of the earth by the planetary giants, earth's life-sustaining capabilities, water and its miraculous properties for life, earth's rare habitability fine-tuned for life and scientific discovery. The phrase 'biological fin...

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Processed pseudogenes: A substrate for evolutionary innovation

Cited by 28 publications

References 102 publications

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Dispersal from the Qinghai-Tibet plateau by a high-altitude butterfly is associated with rapid expansion and reorganization of its genome

Duplications of human longevity-associated genes across placental mammals

Qualified agreement: How scientific discoveries support theistic belief

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