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Evolution by Gene Loss

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Evolution by Gene Loss REVIEWS Evolution by gene loss Ricard Albalat and Cristian Cañestro Abstract | The recent increase in genomic data is revealing an unexpected perspective of gene loss as a pervasive source of genetic variation that can cause adaptive phenotypic diversity. This novel perspective of gene loss is raising new fundamental questions. How relevant has gene loss been in the divergence of phyla? How do genes change from being essential to dispensable and finally to being lost? Is gene loss mostly neutral, or can it be an effective way of adaptation? These questions are addressed, and insights are discussed from genomic studies of gene loss in populations and their relevance in evolutionary biology and biomedicine. Pseudogenization Loss is nothing else but change, and change is Here, we address some of the fundamental questions An evolutionary phenomenon Nature’s delight — Marcus Aurelius, AD 121–180 in evolutionary biology that have emerged from this novel whereby a gene loses its perspective of evolution by gene loss. Examples from all function, accumulates Great attention has in the past been paid to the mechan­ life kingdoms are covered, from bacteria to fungi and mutations and becomes a pseudogene. isms of evolution by gene duplication (that is, neofunc­ from plants to animals, including key examples of gene tionalization and subfunctionalization)1,2. By contrast, loss in humans. We review how gene loss has affected the Eumetazoan gene loss has often been associated with the loss of evolution of different phyla and address key questions, Clade that classically includes redundant gene duplicates without apparent functional including how genes can become dispensable, how many all animals (metazoan) except consequences, and therefore this process has mostly of our current genes are actually dispensable, how pat­ sponges and Placozoa, although recent analyses of been neglected as an evolutionary force. However, terns of gene loss are biased, and whether the effects of ctenophores have challenged genomic data, which is accumulating as a result of gene loss are mostly neutral or whether gene loss can the monophyly of this group. recent technological and methodological advances, actually be an effective way of adaptation. Finally, prom­ such as next­ generation sequencing, is revealing a ising future perspectives on the study of gene loss are dis­ new perspective of gene loss as a pervasive source of cussed. These include the development of computational genetic change that has great potential to cause adaptive pipelines to identify the complete catalogue of gene losses phenotypic diversity. that have occurred during the evolution of a given species, Two main molecular mechanisms can lead to the the effect that anticipated findings have on the fields of loss of a gene from a given genome. First, the loss of evolutionary biology and biomedicine, and the means by a gene can be the consequence of an abrupt muta­ which comparative population genomics approaches and tional event, such as an unequal crossing over during the measure of ‘population gene dispensability’ can help meiosis or the mobilization of a transposable or viral to discover new genes that are relevant for human health. element that leads to the sudden physical removal of the gene from an organism’s genome. Second, the loss Phylogenetic pervasiveness of gene loss of a gene can be the consequence of a slow process of The field of comparative genomics, and especially our accumulation of mutations during the pseudogenization perspective on animal evolution, changed after the that follows an initial loss­of­function mutation. This sequencing of the genome of various cnidarian species. initial mutation can be caused by nonsense mutations These studies revealed that the ancestral eumetazoan that generate truncated proteins, insertions or dele­ genome was much more complex than expected and 3–6 Departament de Genètica, tions that cause a frameshift, missense mutations that that gene loss was pervasive in many animal phyla Microbiologia i Estadística affect crucial amino acid positions, changes involving (FIG. 1). This new perspective superseded the traditional and Institut de Recerca de la splice sites that lead to aberrant transcripts or muta­ notion that had influenced the analyses of the first known Biodiversitat (IRBio), Facultat tions in regulatory regions that abolish gene expression. genomes (Caenorhabditis elegans, Drosophila melano- de Biologia, Universitat de In this Review, the term ‘gene loss’ is used in a broad gaster, Arabidopsis thaliana and human), the scala naturae, Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain. sense, not only referring to the absence of a gene that in which attempts were made to correlate the apparent [email protected]; is identi fied when different species are compared, but increase of biological complexity in the evolutionary [email protected] also to any allelic variant carrying a loss­of­function ladder that leads up to humans with an increase in the 7 doi:10.1038/nrg.2016.39 (that is, non­functionalization) mutation that is found number of genes . The ancestral eumetazoan genome had Published online 18 Apr 2016 within a population. a gene repertoire made up of at least 7,766 gene families NATURE REVIEWS | GENETICS VOLUME 17 | JULY 2016 | 379 ©2016 Mac millan Publishers Li mited. All ri ghts reserved. REVIEWS Wnt10Wnt11Wnt16 Wnt1 Wnt2 Wnt3 Wnt4 Wnt5 Wnt6 Wnt7 Wnt8 Wnt9 WntA Homo sapiens Gallus gallus Xenopus tropicales Chordates Danio rerio A Ciona intestinalis Deuterostomes Branchiostoma floridae Saccoglossus kowalevskii Echinoderms 2 11 Strongylocentrotus purpuratus Paracentrotus lividus Drosophila melanogaster Anopheles gambiae Tribolium castaneum 4 Apis mellifera Ecdysozoa Bilateria 16 Protostomes 2 Acyrthosiphon pisum Daphnia pulex Arthropoda Glomeris marginata Achaearanea tepidariorum 10 Cupiennius salei Ixodes scapularis Nematoda Caenorhabditis elegans Annelida Platynereis dumerilii 3 Capitella teleta Helobdella robusta Mollusca Patella vulgata 8 Lottia gigantea Schmidtea mediterranea Lophotrochozoa 6–10 16 A Schistosoma mansoni Platyhelminthes Hymenolepis microstoma Echinococcus spp. Hydra magnipapillata Clytia hemisphaerica Cnidaria Acropora millepora Nematostella vectensis Trichoplax adhaerens nd Placozoa Amphimedon queenslandica Porifera Oscarella spp. Mnemiopsis leidyi nd Ctenophora Pleurobrachia pileus nd Figure 1 | The wingless (Wnt) family: a paradigmatic example of the pervasiveness of gene loss during metazoan evolution. In the past decade, the accumulation of fully sequenced genome data from various species has revealed great Nature Reviews | Genetics heterogeneity in the dynamics of gene loss within different animal groups. In ecdysoazoans, for instance, not all insects show Homologous the same rate of gene loss, and European honeybees (Apis mellifera) seem to have retained more genes than other insects 206 Genes that share sequence (for example, species of fly and mosquito in the Diptera order) . The finding, for instance, of an active DNA CpG methylation similarity because they have toolkit (that is, Dnmt1, Dnm3a, Dnmt3b and Mdb) in honeybees was particularly remarkable, as it has been lost in most other evolved from a common insects207,208. To date, the red flour beetle (Tribolium casteneum) has preserved the largest number of patchy orthologues that ancestral gene. are also present in humans but that were lost in all other sequenced insects209. The genomes of crustaceans and myriapods showed less gene loss, and these groups conserved more universal bilaterian genes than insects151,210. In lophotrocozoans, Bilaterian gene loss propensity is also heterogeneous among species. Mollusc gastropods, such as Lottia gigantea or annelids, such as An animal clade that Capitella teleta or Helobdella robusta, seem to have rates of gene retention similar to those in deuterostomes8, whereas other includes protostomes and deuterostomes. Members of lophotrocozoans, such as the flatworm Schmidtea mediterranea, have lost approximately 40% of the ancestral gene 8,171 this clade are characterized by families . Extensive gene loss (red boxes) has affected all Wnt gene subfamilies (1 to 11; 16 and A) throughout all metazoan a stage during their life cycle in taxa. Some gene losses seem to be ancestral (red circles) and thereby probably relevant for the evolution of entire groups (for which they have right–left example, ancestral loss of Wnt3 in the stem protostome). Other gene losses seem to occur recurrently in diverse lineages and symmetry (unlike the show a patchy distribution (for example, Wnt11 loss in some chordates, echinoderms, arthropods, nematodes, molluscs and radial symmetry present in sponges). Controversial animal phylogenies (dashed tree branches)211,212 or uncertain gene orthologies (nd) hinder the ability most cnidarians and sponges). to determine whether the absence of Wnt families in most basal metazoans (grey boxes) is due to gene losses or to gene gains. References for the list of Wnt genes in each species are supplied in Supplementary information S3 (box). Deuterostomes A superphylum that includes animals in which the first opening, the blastopore, that were putatively homologous with a gene in the sea protostomes had collectively lost 1,292 gene families (17%), becomes the anus. This anemone and at least one other gene in any bilaterian which suggests a different propensity for gene loss between superphylum includes analysed at the time (that is, D. melanogaster, C. elegans, the two groups. The increased availability
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