Contrasting genetic paths to morphological and physiological evolution

Liao, Ben-Yang; Weng, Meng Pin; Zhang, Jianzhi

doi:10.1073/pnas.0910339107

Cited by 49 publications

(55 citation statements)

References 37 publications

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“…To some extent, this has been one of the most controversial issues in the research field of evolutionary developmental biology and has gained increasing interest in recent years (1)(2)(3)(25)(26)(27)(28)(29)(30). In particular, several recent studies have shown that genes affecting physiological traits (i.e., physiogenes) tend to evolve through changes in coding regions, whereas those controlling morphological traits (i.e., morphogenes) tend to accumulate more changes in regulatory regions (27,31,32). However, we argue that, although this is an interesting point of view, the real situation may be much more complex than we can imagine, for three reasons.…”

Section: Discussionmentioning

confidence: 99%

Divergence of duplicate genes in exon–intron structure

Guo

Shan

et al. 2012

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

695

505

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Gene duplication plays key roles in organismal evolution. Duplicate genes, if they survive, tend to diverge in regulatory and coding regions. Divergences in coding regions, especially those that can change the function of the gene, can be caused by amino acidaltering substitutions and/or alterations in exon-intron structure. Much has been learned about the mode, tempo, and consequences of nucleotide substitutions, yet relatively little is known about structural divergences. In this study, by analyzing 612 pairs of sibling paralogs from seven representative gene families and 300 pairs of one-to-one orthologs from different species, we investigated the occurrence and relative importance of structural divergences during the evolution of duplicate and nonduplicate genes. We found that structural divergences have been very prevalent in duplicate genes and, in many cases, have led to the generation of functionally distinct paralogs. Comparisons of the genomic sequences of these genes further indicated that the differences in exon-intron structure were actually accomplished by three main types of mechanisms (exon/intron gain/loss, exonization/pseudoexonization, and insertion/deletion), each of which contributed differently to structural divergence. Like nucleotide substitutions, insertion/deletion and exonization/pseudoexonization occurred more or less randomly, with the number of observable mutational events per gene pair being largely proportional to evolutionary time. Notably, however, compared with paralogs with similar evolutionary times, orthologs have accumulated significantly fewer structural changes, whereas the amounts of amino acid replacements accumulated did not show clear differences. This finding suggests that structural divergences have played a more important role during the evolution of duplicate than nonduplicate genes.alternative splicing | coding-sequence evolution | exon shuffling | frame-shift mutation | regulatory divergence G ene duplication plays important roles in organismal evolution. Paralogous genes, the products of gene duplication, initially have identical sequences and functions but tend to diverge in regulatory and coding regions. Divergence in regulatory regions can result in shifts in expression pattern, whereas changes in coding regions may lead to the acquisition of new functions. In the past few decades, owing to the availability of nucleotide, protein, and genomic sequences, as well as the accumulation of expressional and functional data, much has been learned about the mode, tempo, and consequences of duplicate gene evolution in coding and regulatory regions (1-15). However, there are still important issues that remain largely unexplored. For example, several recent studies have suggested that, although point mutation and insertion/deletion were generally believed to play overwhelming roles in coding-sequence evolution, the contributions of other mechanisms, such as exonization (a process in which an intronic or intergenic sequence becomes exonic) and pseudoexonization (the oppo...

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Section: Discussionmentioning

confidence: 99%

Divergence of duplicate genes in exon–intron structure

Guo

Shan

et al. 2012

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

695

505

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“…Morphological traits are more enriched with transcriptional regulators than physiological traits, more likely to be pleiotropic and evolve faster in expression profile (Liao et al 2010).…”

Section: Divergence By Integrationmentioning

confidence: 99%

Revision of Drusinae subfamily (Trichoptera, Limnephilidae): divergence by paraproct and paramere: speciation in isolation by integration

Oláh¹,

Beshkov²,

Chvojka³

et al. 2017

Opusc Zool

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Abstract.In the last few years we have described over 70 new incipient sibling limnephild species applying the discovered Trichoptera speciation traits of the paraproct and paramere for species recognition and delimitation. In this revision on Drusinae subfamily, comprising 177 species, we have applied these subtle, but rapid and stable speciation traits and described 49 new sibling species from the "well studied" European mountain ranges. Discussing the theoretical background we have elaborated and adapted a new character state ranking system of phenomics to revise the long-neglected taxonomy of the Drusinae subfamily and synonymised the Cryptothrix, Monocentra, Metanoea, Leptodrusus, Anomalopterygella, Hadimina genera with the Drusus genus. These old genera of artificial constructs were established exclusively by divergences of secondary sexual traits known already to have only species level ranking value. According to our new character ranking system in the Drusinae subfamily, beside the Drusus genus, only the Ecclisopteryx genus has been retained having robust generic level divegences of paraproct loss and ancestral duplication of spine organising centre on the paramere pattern. Speciation trait function of the peg-packed surface on the paraproct head in Drusus genus moved to the gonopod apices and integrated into variously shaped stimulatory organ in the Ecclisopteryx genus. In the Drusus genus the ancestral divergence of the single spine organising centre has integrated 11 species groups with remarkably stable paramere spine pattern. Based upon ancestral divergences in the paraproct architecture we have differenciated 28 species complexes inside the 11 species groups. The delineation of the 163 mostly incipient siblings species, inside the 28 species complexes with 44 new Drusus species, was based primarily on the divergences of speciation trait, that is in the stimulatory head shape of the apical arms on the dorsal branches of the paraproct. In the Ecclisopteryx genus with 14 species we have established two independent lineages both with a single species, as well as two species complexes with five new species applying the speciation trait of the genus, that is the shape divergence of the stimulatory organ on the dorsoapical surface of the gonopods.Based on the Darwinian natural selection, we do not understand how the discovered 70+49 new European incipient phylogenetic species of limnephilid caddisflies have been evolved in the isolated sky island habitats of high mountain ranges. This isolation induced speciation represents a challenge to the mechanistic reductionist concept of the natural selection. Our first trial to extract information from various disciplines to answer this question is presented in a brief theoretical discourse: (1) rethinking the status of natural selection towards postdarwinism; (2) teleology or teleonomy; (3) limits and potentials in understanding reality; (4) organisation of universe by integration; (5) what are and how the organising forces are powered to work in the emerging en...

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“…We examine whether ligand-coding genes are preferential targets for the generation of morphological evolution. In addition, we confront existing data to predictions that the corresponding allelic variation should be (1) potentially adaptive (Barrett and Hoekstra 2011;Pardo-Diaz et al 2015), (2) replicated over various phylogenetic levels (Gompel and Prud'homme 2009;Kopp 2009;Martin and Orgogozo 2013), and (3) cis-regulatory rather than coding (Prud'homme et al 2007;Carroll 2008;Stern and Orgogozo 2008;Liao et al 2010). …”

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confidence: 99%

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

Martin

Courtier‐Orgogozo

2017

Diversity and Evolution of Butterfly Wing Patterns

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What types of genetic changes underlie evolution? Secreted signaling molecules (syn. ligands) can induce cells to switch states and thus largely contribute to the emergence of complex forms in multicellular organisms. It has been proposed that morphological evolution should preferentially involve changes in developmental toolkit genes such as signaling pathway components or transcription factors. However, this hypothesis has never been formally confronted to the bulk of accumulated experimental evidence. Here we examine the importance of ligandcoding genes for morphological evolution in animals. We use Gephebase (http:// www.gephebase.org), a database of genotype-phenotype relationships for evolutionary changes, and survey the genetic studies that mapped signaling genes as causative loci of morphological variation. To date, 19 signaling genes represent 20% of the cases where an animal morphological change has been mapped to a gene (80/391). This includes the signaling gene Agouti, which harbors multiple cis-regulatory alleles linked to color variation in vertebrates, contrasting with the effects of coding variation in its target, the melanocortin receptor MC1R. In sticklebacks, genetic mapping approaches have identified 4 signaling genes out of 14 loci associated with lake adaptations. Finally, in butterflies, a total of 18 allelic variants of the WntA Wnt-family ligand cause color pattern adaptations related to wing mimicry, both within and between species. We discuss possible hypotheses explaining these cases of natural replication (genetic parallelism) and conclude that signaling ligand loci are an important source of sequence variation underlying morphological change in nature.

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Contrasting genetic paths to morphological and physiological evolution

Cited by 49 publications

References 37 publications

Divergence of duplicate genes in exon–intron structure

Divergence of duplicate genes in exon–intron structure

Revision of Drusinae subfamily (Trichoptera, Limnephilidae): divergence by paraproct and paramere: speciation in isolation by integration

Morphological Evolution Repeatedly Caused by Mutations in Signaling Ligand Genes

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