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Laurentino TG, Boileau N, Ronco F, Berner D. The ectodysplasin-A receptor is a candidate gene for lateral plate number variation in stickleback fish. G3 GENES|GENOMES|GENETICS 2022; 12:6563190. [PMID: 35377433 PMCID: PMC9157104 DOI: 10.1093/g3journal/jkac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 02/04/2023]
Abstract
Variation in lateral plating in stickleback fish represents a classical example of rapid and parallel adaptation in morphology. The underlying genetic architecture involves polymorphism at the ectodysplasin-A gene (EDA). However, lateral plate number is influenced by additional loci that remain poorly characterized. Here, we search for such loci by performing genome-wide differentiation mapping based on pooled whole-genome sequence data from a European stickleback population variable in the extent of lateral plating, while tightly controlling for the phenotypic effect of EDA. This suggests a new candidate locus, the EDA receptor gene (EDAR), for which additional support is obtained by individual-level targeted Sanger sequencing and by comparing allele frequencies among natural populations. Overall, our study illustrates the power of pooled whole-genome sequencing for searching phenotypically relevant loci and opens opportunities for exploring the population genetics and ecological significance of a new candidate locus for stickleback armor evolution.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Nicolas Boileau
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
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2
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Li J, Kültz D. Proteomics of Osmoregulatory Responses in Threespine Stickleback Gills. Integr Comp Biol 2020; 60:304-317. [PMID: 32458981 DOI: 10.1093/icb/icaa042] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by Liquid chromatography/Tandem mass spectrometry data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. Non-directional stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a non-directional response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine, and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. Non-directional stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient non-directional stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.
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Affiliation(s)
- Johnathon Li
- Department of Animal Sciences, University of California, Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
| | - Dietmar Kültz
- Department of Animal Sciences, University of California, Davis, Meyer Hall, One Shields Avenue, Davis, CA 95616, USA
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3
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Fish TNF and TNF receptors. SCIENCE CHINA-LIFE SCIENCES 2020; 64:196-220. [DOI: 10.1007/s11427-020-1712-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/12/2020] [Indexed: 12/29/2022]
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4
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Hubert JN, Allal F, Hervet C, Ravakarivelo M, Jeney Z, Vergnet A, Guyomard R, Vandeputte M. How could fully scaled carps appear in natural waters in Madagascar? Proc Biol Sci 2016; 283:rspb.2016.0945. [PMID: 27559059 DOI: 10.1098/rspb.2016.0945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 01/02/2023] Open
Abstract
The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the 'mirror' reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.
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Affiliation(s)
- Jean-Noël Hubert
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - François Allal
- Ifremer, UMR 9190 MARBEC, 34250 Palavas-les-Flots, France
| | - Caroline Hervet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | | | - René Guyomard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France Ifremer, 34250 Palavas-les-Flots, France
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5
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Cheng J, Sedlazek F, Altmüller J, Nolte AW. Ectodysplasin signalling genes and phenotypic evolution in sculpins (Cottus). Proc Biol Sci 2016; 282:rspb.2015.0746. [PMID: 26354934 DOI: 10.1098/rspb.2015.0746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Despite their deeply conserved function among vertebrates, ectodysplasin (Eda) signalling genes are involved in microevolutionary change in humans and sticklebacks. If such a dual role is common, Eda signalling genes constitute hotspots for morphological evolution. Variation in sculpin (Cottus) skin prickling and body shape resembles patterns caused by variation in Eda signalling in sticklebacks. We mapped Eda signalling genes and performed quantitative trait locus mapping in crosses between Cottus rhenanus and Cottus perifretum. A genomic region containing the Eda receptor (Edar) was strongly associated with prickling and contributed to shape. The expression of Edar in developing prickles and skeletal elements in Cottus was confirmed by in situ hybridization. Coding sequence changes between Edar alleles in C. rhenanus and C. perifretum exceeded sequence differentiation in other vertebrates. However, it is likely that additional genetic elements besides coding changes affect the phenotypic variation. Although the phenotype in a natural hybrid lineage between C. rhenanus and C. perifretum resembles C. perifretum, the respective coding Edar alleles are not fully fixed (88.6%). Hence, our results support an involvement of Eda signalling in microevolutionary changes, but imply that the Edar gene is affected by multiple evolutionary processes that vary among freshwater sculpins.
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Affiliation(s)
- Jie Cheng
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann Strasse 2, 24306 Plön, Germany Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Fritz Sedlazek
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, 1030 Vienna, Austria Cold Spring Harbor Laboratory, Simons Center for Quantitative Biology, Cold Spring Harbor, New York, NY, USA
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Arne W Nolte
- Department for Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, August-Thienemann Strasse 2, 24306 Plön, Germany
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6
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Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins. Cell 2016; 164:45-56. [PMID: 26774823 DOI: 10.1016/j.cell.2015.12.007] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 09/03/2015] [Accepted: 11/24/2015] [Indexed: 02/01/2023]
Abstract
Changes in bone size and shape are defining features of many vertebrates. Here we use genetic crosses and comparative genomics to identify specific regulatory DNA alterations controlling skeletal evolution. Armor bone-size differences in sticklebacks map to a major effect locus overlapping BMP family member GDF6. Freshwater fish express more GDF6 due in part to a transposon insertion, and transgenic overexpression of GDF6 phenocopies evolutionary changes in armor-plate size. The human GDF6 locus also has undergone distinctive regulatory evolution, including complete loss of an enhancer that is otherwise highly conserved between chimps and other mammals. Functional tests show that the ancestral enhancer drives expression in hindlimbs but not forelimbs, in locations that have been specifically modified during the human transition to bipedalism. Both gain and loss of regulatory elements can localize BMP changes to specific anatomical locations, providing a flexible regulatory basis for evolving species-specific changes in skeletal form.
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7
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Reno PL. Genetic and developmental basis for parallel evolution and its significance for hominoid evolution. Evol Anthropol 2015; 23:188-200. [PMID: 25347977 DOI: 10.1002/evan.21417] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Greater understanding of ape comparative anatomy and evolutionary history has brought a general appreciation that the hominoid radiation is characterized by substantial homoplasy.(1-4) However, little consensus has been reached regarding which features result from repeated evolution. This has important implications for reconstructing ancestral states throughout hominoid evolution, including the nature of the Pan-Homo last common ancestor (LCA). Advances from evolutionary developmental biology (evo-devo) have expanded the diversity of model organisms available for uncovering the morphogenetic mechanisms underlying instances of repeated phenotypic change. Of particular relevance to hominoids are data from adaptive radiations of birds, fish, and even flies demonstrating that parallel phenotypic changes often use similar genetic and developmental mechanisms. The frequent reuse of a limited set of genes and pathways underlying phenotypic homoplasy suggests that the conserved nature of the genetic and developmental architecture of animals can influence evolutionary outcomes. Such biases are particularly likely to be shared by closely related taxa that reside in similar ecological niches and face common selective pressures. Consideration of these developmental and ecological factors provides a strong theoretical justification for the substantial homoplasy observed in the evolution of complex characters and the remarkable parallel similarities that can occur in closely related taxa. Thus, as in other branches of the hominoid radiation, repeated phenotypic evolution within African apes is also a distinct possibility. If so, the availability of complete genomes for each of the hominoid genera makes them another model to explore the genetic basis of repeated evolution.
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Affiliation(s)
- Philip L Reno
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802
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8
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Roux J, Rosikiewicz M, Robinson-Rechavi M. What to compare and how: Comparative transcriptomics for Evo-Devo. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2015; 324:372-82. [PMID: 25864439 PMCID: PMC4949521 DOI: 10.1002/jez.b.22618] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 02/19/2015] [Indexed: 12/30/2022]
Abstract
Evolutionary developmental biology has grown historically from the capacity to relate patterns of evolution in anatomy to patterns of evolution of expression of specific genes, whether between very distantly related species, or very closely related species or populations. Scaling up such studies by taking advantage of modern transcriptomics brings promising improvements, allowing us to estimate the overall impact and molecular mechanisms of convergence, constraint or innovation in anatomy and development. But it also presents major challenges, including the computational definitions of anatomical homology and of organ function, the criteria for the comparison of developmental stages, the annotation of transcriptomics data to proper anatomical and developmental terms, and the statistical methods to compare transcriptomic data between species to highlight significant conservation or changes. In this article, we review these challenges, and the ongoing efforts to address them, which are emerging from bioinformatics work on ontologies, evolutionary statistics, and data curation, with a focus on their implementation in the context of the development of our database Bgee (http://bgee.org). J. Exp. Zool. (Mol. Dev. Evol.) 324B: 372–382, 2015. © 2015 The Authors. J. Exp. Zool. (Mol. Dev. Evol.) published by Wiley Periodicals, Inc.
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Affiliation(s)
- Julien Roux
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Human Genetics, University of Chicago, Chicago, Illinois
| | - Marta Rosikiewicz
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Marc Robinson-Rechavi
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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9
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Harris RM, Dijkstra PD, Hofmann HA. Complex structural and regulatory evolution of the pro-opiomelanocortin gene family. Gen Comp Endocrinol 2014; 195:107-15. [PMID: 24188887 DOI: 10.1016/j.ygcen.2013.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 11/25/2022]
Abstract
The melanocortin system is a neuroendocrine machinery that has been associated with phenotypic diversification in a number of vertebrate lineages. Central to the highly pleiotropic melanocortin system is the pro-opiomelanocortin (pomc) gene family, a family of pre-prohormones that each give rise to melanocyte stimulating hormone (MSH), adrenocorticotropic releasing hormone (ACTH), β-lipotropin hormone, and β-endorphin. Here we examine the structure, tissue expression profile, and pattern of cis transcriptional regulation of the three pomc paralogs (α1, α2, and β) in the model cichlid fish Astatotilapia burtoni and other cichlids, teleosts, and mammals. We found that the hormone-encoding regions of pomc α1, pomc α2 and pomc β are highly conserved, with a few notable exceptions. Surprisingly, the pomc β gene of cichlids and pomacentrids (damselfish) encodes a novel melanocortin peptide, ε-MSH, as a result of a tandem duplication of the segment encoding ACTH. All three genes are expressed in the brain and peripheral tissues, but pomc α1 and α2 show a more spatially restricted expression profile than pomc β. In addition, the promoters of each pomc gene have diverged in nucleotide sequence, which may have facilitated the diverse tissue-specific expression profiles of these paralogs across species. Increased understanding of the mechanisms regulating pomc gene expression will be invaluable to the study of pomc in the context of phenotypic evolution.
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Affiliation(s)
- Rayna M Harris
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Peter D Dijkstra
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, United States
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, United States; Institute for Neuroscience, The University of Texas at Austin, Austin, TX 78712, United States.
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10
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11
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The ectodysplasin pathway: from diseases to adaptations. Trends Genet 2013; 30:24-31. [PMID: 24070496 DOI: 10.1016/j.tig.2013.08.006] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 08/06/2013] [Accepted: 08/20/2013] [Indexed: 01/08/2023]
Abstract
The ectodysplasin (EDA) pathway, which is active during the development of ectodermal organs, including teeth, hairs, feathers, and mammary glands, and which is crucial for fine-tuning the developmental network controlling the number, size, and density of these structures, was discovered by studying human patients affected by anhidrotic/hypohidrotic ectodermal dysplasia. It comprises three main gene products: EDA, a ligand that belongs to the tumor necrosis factor (TNF)-α family, EDAR, a receptor related to the TNFα receptors, and EDARADD, a specific adaptor. This core pathway relies on downstream NF-κB pathway activation to regulate target genes. The pathway has recently been found to be associated with specific adaptations in natural populations: the magnitude of armor plates in sticklebacks and the hair structure in Asian human populations. Thus, despite its role in human disease, the EDA pathway is a 'hopeful pathway' that could allow adaptive changes in ectodermal appendages which, as specialized interfaces with the environment, are considered hot-spots of morphological evolution.
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12
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13
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Catchen J, Bassham S, Wilson T, Currey M, O’Brien C, Yeates Q, Cresko WA. The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing. Mol Ecol 2013; 22:2864-83. [PMID: 23718143 PMCID: PMC3712868 DOI: 10.1111/mec.12330] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2012] [Revised: 02/11/2013] [Accepted: 02/27/2013] [Indexed: 12/16/2022]
Abstract
Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history.
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Affiliation(s)
- Julian Catchen
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Susan Bassham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Taylor Wilson
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Mark Currey
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Conor O’Brien
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - Quick Yeates
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
| | - William A. Cresko
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA 97403
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14
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Martin A, Orgogozo V. The Loci of repeated evolution: a catalog of genetic hotspots of phenotypic variation. Evolution 2013; 67:1235-50. [PMID: 23617905 DOI: 10.1111/evo.12081] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/26/2013] [Indexed: 12/11/2022]
Abstract
What is the nature of the genetic changes underlying phenotypic evolution? We have catalogued 1008 alleles described in the literature that cause phenotypic differences among animals, plants, and yeasts. Surprisingly, evolution of similar traits in distinct lineages often involves mutations in the same gene ("gene reuse"). This compilation yields three important qualitative implications about repeated evolution. First, the apparent evolution of similar traits by gene reuse can be traced back to two alternatives, either several independent causative mutations or a single original mutational event followed by sorting processes. Second, hotspots of evolution-defined as the repeated occurrence of de novo mutations at orthologous loci and causing similar phenotypic variation-are omnipresent in the literature with more than 100 examples covering various levels of analysis, including numerous gain-of-function events. Finally, several alleles of large effect have been shown to result from the aggregation of multiple small-effect mutations at the same hotspot locus, thus reconciling micromutationist theories of adaptation with the empirical observation of large-effect variants. Although data heterogeneity and experimental biases prevented us from extracting quantitative trends, our synthesis highlights the existence of genetic paths of least resistance leading to viable evolutionary change.
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Affiliation(s)
- Arnaud Martin
- Department of Ecology and Evolutionary Biology, Cornell University, Corson Hall, 215 Tower Road, Ithaca, New York, 14853, USA.
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15
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Conte GL, Arnegard ME, Peichel CL, Schluter D. The probability of genetic parallelism and convergence in natural populations. Proc Biol Sci 2012; 279:5039-47. [PMID: 23075840 PMCID: PMC3497250 DOI: 10.1098/rspb.2012.2146] [Citation(s) in RCA: 268] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Genomic and genetic methods allow investigation of how frequently the same genes are used by different populations during adaptive evolution, yielding insights into the predictability of evolution at the genetic level. We estimated the probability of gene reuse in parallel and convergent phenotypic evolution in nature using data from published studies. The estimates are surprisingly high, with mean probabilities of 0.32 for genetic mapping studies and 0.55 for candidate gene studies. The probability declines with increasing age of the common ancestor of compared taxa, from about 0.8 for young nodes to 0.1–0.4 for the oldest nodes in our study. Probability of gene reuse is higher when populations begin from the same ancestor (genetic parallelism) than when they begin from divergent ancestors (genetic convergence). Our estimates are broadly consistent with genomic estimates of gene reuse during repeated adaptation to similar environments, but most genomic studies lack data on phenotypic traits affected. Frequent reuse of the same genes during repeated phenotypic evolution suggests that strong biases and constraints affect adaptive evolution, resulting in changes at a relatively small subset of available genes. Declines in the probability of gene reuse with increasing age suggest that these biases diverge with time.
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Affiliation(s)
- Gina L Conte
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, British Columbia, Canada.
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16
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Leaver SD, Reimchen TE. Abrupt changes in defence and trophic morphology of the giant threespine stickleback (Gasterosteussp.) following colonization of a vacant habitat. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01969.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stephen D. Leaver
- Department of Biology; University of Victoria; PO Box 3020 Victoria BC V8W 3N5 Canada
| | - Thomas E. Reimchen
- Department of Biology; University of Victoria; PO Box 3020 Victoria BC V8W 3N5 Canada
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17
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The genomic basis of adaptive evolution in threespine sticklebacks. Nature 2012; 484:55-61. [PMID: 22481358 PMCID: PMC3322419 DOI: 10.1038/nature10944] [Citation(s) in RCA: 1222] [Impact Index Per Article: 101.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2011] [Accepted: 02/08/2012] [Indexed: 12/18/2022]
Abstract
Marine stickleback fish have colonized and adapted to innumerable streams and lakes formed since the last ice age, providing an exceptional opportunity to characterize genomic mechanisms underlying repeated ecological adaptation in nature. Here we develop a high quality reference genome assembly for threespine sticklebacks. By sequencing the genomes of 20 additional individuals from a global set of marine and freshwater populations, we identify a genome-wide set of loci that are consistently associated with marine-freshwater divergence. Our results suggest that reuse of globally-shared standing genetic variation, including chromosomal inversions, plays an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation. Both coding and regulatory changes occur in the set of loci underlying marine-freshwater evolution, with regulatory changes likely predominating in this classic example of repeated adaptive evolution in nature.
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Zheng W, Gianoulis TA, Karczewski KJ, Zhao H, Snyder M. Regulatory Variation Within and Between Species. Annu Rev Genomics Hum Genet 2011; 12:327-46. [DOI: 10.1146/annurev-genom-082908-150139] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Wei Zheng
- Department of Molecular, Cellular, and Developmental Biology, Biostatics Resources, Keck Laboratory, Yale University, New Haven, Connecticut 06520;
| | - Tara A. Gianoulis
- Department of Genetics and Wyss Institute for Biologically Inspired Engineering, Harvard Medical School, Boston, Massachusetts 02115;
| | - Konrad J. Karczewski
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305; ,
| | - Hongyu Zhao
- Biostatistics Division, Yale School of Public Health, New Haven, Connecticut 06520;
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305; ,
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19
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Barrett RDH. Adaptive evolution of lateral plates in three-spined stickleback Gasterosteus aculeatus: a case study in functional analysis of natural variation. JOURNAL OF FISH BIOLOGY 2010; 77:311-328. [PMID: 20646158 DOI: 10.1111/j.1095-8649.2010.02640.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The three-spined stickleback Gasterosteus aculeatus is a model species for studying questions in ecology and evolution. The rapid diversification of G. aculeatus in post-glacial freshwater environments, combined with recently developed molecular tools, provides a unique opportunity to study the functional basis of fitness variation in natural populations. In derived freshwater populations, a number of morphological traits have diverged in parallel from the marine ancestral state, including the number of lateral armour plates. Evolution of reduced armour in freshwater populations is due to positive selection from both abiotic and biotic mechanisms. The major effect gene (ectodysplasin-A or Eda), along with several minor effect genetic regions, has recently been shown to control lateral plate variation. Field experiments have further determined the fitness consequences of allelic variation at the major effect locus. This work helps elucidate the mechanisms connecting genetic variation with phenotypic variation and fitness in the wild, a synthesis that should be applicable to many other phenotypic traits and species of fishes.
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Affiliation(s)
- R D H Barrett
- Department of Zoology, University of British Columbia, 6270 University Blvd., Vancouver, British Columbia, V6T 1Z4 Canada.
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Papa R, Martin A, Reed RD. Genomic hotspots of adaptation in butterfly wing pattern evolution. Curr Opin Genet Dev 2008; 18:559-64. [DOI: 10.1016/j.gde.2008.11.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2008] [Revised: 11/18/2008] [Accepted: 11/18/2008] [Indexed: 01/24/2023]
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Analysis of the temporal requirement for eda in hair and sweat gland development. J Invest Dermatol 2008; 129:984-93. [PMID: 18923450 DOI: 10.1038/jid.2008.318] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
EDA signaling is important in skin appendage initiation. Its possible involvement in appendage subtype determination and postinduction stage appendage development, however, has not been studied systematically. To address these issues we manipulated Eda-A1 transgene expression in a tetracycline-regulated conditional mouse model, where the transgene is the only source of active ectodysplasin (Eda). We find that Eda-A1 restores sweat glands and all hair subtypes in Tabby, but each requires its action at an idiosyncratic time of development: by E17 for guard, by E19 for awl, and starting at E18 for zigzag/auchen hair. Guard and awl hairs were indistinguishable from their wild-type counterparts; but restored zigzag and auchen hairs, although recognizable, were somewhat smaller and lacked characteristic bends. Notably, secondary hair follicle formation of awl, auchen, and zigzag hairs required higher Eda-A1 expression level than did guard hair or sweat glands. Furthermore, Eda-A1 expression is required until the early dermal papilla stage for guard hair germs to make follicles, but is dispensable for their maturation. Similarly, sweat gland pegs require Eda-A1 at an early stage to form mature glands. Thus we infer that EDA signaling is needed for the determination and development of various skin appendages at spatiotemporally restricted intervals.
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Harris MP, Rohner N, Schwarz H, Perathoner S, Konstantinidis P, Nüsslein-Volhard C. Zebrafish eda and edar mutants reveal conserved and ancestral roles of ectodysplasin signaling in vertebrates. PLoS Genet 2008; 4:e1000206. [PMID: 18833299 PMCID: PMC2542418 DOI: 10.1371/journal.pgen.1000206] [Citation(s) in RCA: 151] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2007] [Accepted: 08/22/2008] [Indexed: 12/28/2022] Open
Abstract
The genetic basis of the development and variation of adult form of vertebrates is not well understood. To address this problem, we performed a mutant screen to identify genes essential for the formation of adult skeletal structures of the zebrafish. Here, we describe the phenotypic and molecular characterization of a set of mutants showing loss of adult structures of the dermal skeleton, such as the rays of the fins and the scales, as well as the pharyngeal teeth. The mutations represent adult-viable, loss of function alleles in the ectodysplasin (eda) and ectodysplasin receptor (edar) genes. These genes are frequently mutated in the human hereditary disease hypohidrotic ectodermal dysplasia (HED; OMIM 224900, 305100) that affects the development of integumentary appendages such as hair and teeth. We find mutations in zebrafish edar that affect similar residues as mutated in human cases of HED and show similar phenotypic consequences. eda and edar are not required for early zebrafish development, but are rather specific for the development of adult skeletal and dental structures. We find that the defects of the fins and scales are due to the role of Eda signaling in organizing epidermal cells into discrete signaling centers of the scale epidermal placode and fin fold. Our genetic analysis demonstrates dose-sensitive and organ-specific response to alteration in levels of Eda signaling. In addition, we show substantial buffering of the effect of loss of edar function in different genetic backgrounds, suggesting canalization of this developmental system. We uncover a previously unknown role of Eda signaling in teleosts and show conservation of the developmental mechanisms involved in the formation and variation of both integumentary appendages and limbs. Lastly, our findings point to the utility of adult genetic screens in the zebrafish in identifying essential developmental processes involved in human disease and in morphological evolution.
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Affiliation(s)
- Matthew P Harris
- Max Planck Institute for Developmental Biology, Tübingen, Germany.
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Pantalacci S, Chaumot A, Benoît G, Sadier A, Delsuc F, Douzery EJP, Laudet V. Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development. Mol Biol Evol 2008; 25:912-28. [PMID: 18304980 DOI: 10.1093/molbev/msn038] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap because it is involved in vertebrate skin appendage development such as scales, teeth, hair, and feathers that take an obvious part in the adaptation of species to their environment. We benefited from the large amount of genomic data now available to explore the evolution of the upstream genes of the EDA pathway. In mammals, these genes are eda (encoding 2 ligands, EDA-A1 and EDA-A2), edar (EDA-A1 receptor), edaradd (EDA receptor [EDAR] adapter), xedar (EDA-A2 receptor), and troy (a XEDAR-related receptor). We show that the evolution of EDA pathway genes combines both strongly conserved features and evolutionary shifts. These shifts are found at different signaling levels (from the ligand to intracellular signaling) and at different taxonomic levels (class, suborder, and genera). Although conserved features likely participate to the similarities found in the early development of vertebrate skin appendages, these shifts might account for innovations and specializations. Moreover, our study demonstrates that we can now benefit from the large number of sequenced vertebrate genomes to explore the evolution of specific signaling pathways and thereby to open new perspectives for developmental biology and evolutionary developmental biology.
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Affiliation(s)
- Sophie Pantalacci
- Molecular Zoology Team, Institut de Génomique Fonctionnelle de Lyon, Université de Lyon, Institut Fédératif Biosciences 128 Gerland Lyon Sud, CNRS, INRA, Université Claude Bernard Lyon 1, 69364 Lyon cedex 07, France
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