51
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Láruson ÁJ, Yeaman S, Lotterhos KE. The Importance of Genetic Redundancy in Evolution. Trends Ecol Evol 2020; 35:809-822. [DOI: 10.1016/j.tree.2020.04.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022]
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52
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Kuriyama T, Murakami A, Brandley M, Hasegawa M. Blue, Black, and Stripes: Evolution and Development of Color Production and Pattern Formation in Lizards and Snakes. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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53
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Aardema ML, Stiassny MLJ, Alter SE. Genomic Analysis of the Only Blind Cichlid Reveals Extensive Inactivation in Eye and Pigment Formation Genes. Genome Biol Evol 2020; 12:1392-1406. [PMID: 32653909 PMCID: PMC7502198 DOI: 10.1093/gbe/evaa144] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2020] [Indexed: 12/21/2022] Open
Abstract
Trait loss represents an intriguing evolutionary problem, particularly when it occurs across independent lineages. Fishes in light-poor environments often evolve “troglomorphic” traits, including reduction or loss of both pigment and eyes. Here, we investigate the genomic basis of trait loss in a blind and depigmented African cichlid, Lamprologus lethops, and explore evolutionary forces (selection and drift) that may have contributed to these losses. This species, the only known blind cichlid, is endemic to the lower Congo River. Available evidence suggests that it inhabits deep, low-light habitats. Using genome sequencing, we show that genes related to eye formation and pigmentation, as well as other traits associated with troglomorphism, accumulated inactivating mutations rapidly after speciation. A number of the genes affected in L. lethops are also implicated in troglomorphic phenotypes in Mexican cavefish (Astyanax mexicanus) and other species. Analysis of heterozygosity patterns across the genome indicates that L. lethops underwent a significant population bottleneck roughly 1 Ma, after which effective population sizes remained low. Branch-length tests on a subset of genes with inactivating mutations show little evidence of directional selection; however, low overall heterozygosity may reduce statistical power to detect such signals. Overall, genome-wide patterns suggest that accelerated genetic drift from a severe bottleneck, perhaps aided by directional selection for the loss of physiologically expensive traits, caused inactivating mutations to fix rapidly in this species.
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Affiliation(s)
- Matthew L Aardema
- Department of Biology, Montclair State University.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York
| | - Melanie L J Stiassny
- Department of Ichthyology, American Museum of Natural History, New York, New York
| | - S Elizabeth Alter
- Department of Ichthyology, American Museum of Natural History, New York, New York.,The Graduate Center, City University of New York.,Department of Biology, York College/The City University of New York
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54
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Bruders R, Van Hollebeke H, Osborne EJ, Kronenberg Z, Maclary E, Yandell M, Shapiro MD. A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia). PLoS Genet 2020; 16:e1008274. [PMID: 32433666 PMCID: PMC7239393 DOI: 10.1371/journal.pgen.1008274] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 04/09/2020] [Indexed: 12/15/2022] Open
Abstract
Rock pigeons (Columba livia) display an extraordinary array of pigment pattern variation. One such pattern, Almond, is characterized by a variegated patchwork of plumage colors that are distributed in an apparently random manner. Almond is a sex-linked, semi-dominant trait controlled by the classical Stipper (St) locus. Heterozygous males (ZStZ+ sex chromosomes) and hemizygous Almond females (ZStW) are favored by breeders for their attractive plumage. In contrast, homozygous Almond males (ZStZSt) develop severe eye defects and often lack plumage pigmentation, suggesting that higher dosage of the mutant allele is deleterious. To determine the molecular basis of Almond, we compared the genomes of Almond pigeons to non-Almond pigeons and identified a candidate St locus on the Z chromosome. We found a copy number variant (CNV) within the differentiated region that captures complete or partial coding sequences of four genes, including the melanosome maturation gene Mlana. We did not find fixed coding changes in genes within the CNV, but all genes are misexpressed in regenerating feather bud collar cells of Almond birds. Notably, six other alleles at the St locus are associated with depigmentation phenotypes, and all exhibit expansion of the same CNV. Structural variation at St is linked to diversity in plumage pigmentation and gene expression, and thus provides a potential mode of rapid phenotypic evolution in pigeons. The genetic changes responsible for different animal color patterns are poorly understood, due in part to a paucity of research organisms that are both genetically tractable and phenotypically diverse. Domestic pigeons (Columba livia) have been artificially selected for many traits, including an enormous variety of color patterns that are variable both within and among different breeds of this single species. We investigated the genetic basis of a sex-linked color pattern in pigeons called Almond that is characterized by a sprinkled pattern of plumage pigmentation. Pigeons with one copy of the Almond allele have desirable color pattern; however, male pigeons with two copies of the Almond mutation have severely depleted pigmentation and congenital eye defects. By comparing the genomes of Almond and non-Almond pigeons, we discovered that Almond pigeons have extra copies of a chromosome region that contains a gene that is critical for the formation of pigment granules. We also found that different numbers of copies of this region are associated with varying degrees of pigment reduction. The Almond phenotype in pigeons bears a remarkable resemblance to Merle coat color mutants in dogs, and our new results from pigeons suggest that similar genetic mechanisms underlie these traits in both species. Our work highlights the role of gene copy number variation as a potential driver of rapid phenotypic evolution.
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Affiliation(s)
- Rebecca Bruders
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Hannah Van Hollebeke
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward J. Osborne
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Zev Kronenberg
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Emily Maclary
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
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55
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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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56
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Laurentino TG, Moser D, Roesti M, Ammann M, Frey A, Ronco F, Kueng B, Berner D. Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish. Nat Commun 2020; 11:1928. [PMID: 32317640 PMCID: PMC7174299 DOI: 10.1038/s41467-020-15657-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/19/2020] [Indexed: 11/29/2022] Open
Abstract
How rapidly natural selection sorts genome-wide standing genetic variation during adaptation remains largely unstudied experimentally. Here, we present a genomic release-recapture experiment using paired threespine stickleback fish populations adapted to selectively different lake and stream habitats. First, we use pooled whole-genome sequence data from the original populations to identify hundreds of candidate genome regions likely under divergent selection between these habitats. Next, we generate F2 hybrids from the same lake-stream population pair in the laboratory and release thousands of juveniles into a natural stream habitat. Comparing the individuals surviving one year of stream selection to a reference sample of F2 hybrids allows us to detect frequency shifts across the candidate regions toward the genetic variants typical of the stream population-an experimental outcome consistent with polygenic directional selection. Our study reveals that adaptation in nature can be detected as a genome-wide signal over just a single generation.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
| | - Dario Moser
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Matthias Ammann
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Anja Frey
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Benjamin Kueng
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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57
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Yusuf L, Heatley MC, Palmer JPG, Barton HJ, Cooney CR, Gossmann TI. Noncoding regions underpin avian bill shape diversification at macroevolutionary scales. Genome Res 2020; 30:553-565. [PMID: 32269134 PMCID: PMC7197477 DOI: 10.1101/gr.255752.119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022]
Abstract
Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence, and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein-coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1434 protein-coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein-coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cell pathways, including BMP and Wnt signaling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome-wide scale over macroevolutionary time is feasible. Although the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times.
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Affiliation(s)
- Leeban Yusuf
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Centre for Biological Diversity, School of Biology, University of St. Andrews, Fife, KY16 9TF, United Kingdom
| | - Matthew C Heatley
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Joseph P G Palmer
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, United Kingdom
| | - Henry J Barton
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Organismal and Evolutionary Biology Research Programme, Viikinkaari 9 (PL 56), University of Helsinki, Helsinki, FI-00014, Finland
| | - Christopher R Cooney
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Toni I Gossmann
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.,Department of Animal Behaviour, Bielefeld University, Bielefeld, DE-33501, Germany
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58
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Effects of predation risk on egg steroid profiles across multiple populations of threespine stickleback. Sci Rep 2020; 10:5239. [PMID: 32251316 PMCID: PMC7090078 DOI: 10.1038/s41598-020-61412-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/24/2020] [Indexed: 11/16/2022] Open
Abstract
Predation often has consistent effects on prey behavior and morphology, but whether the physiological mechanisms underlying these effects show similarly consistent patterns across different populations remains an open question. In vertebrates, predation risk activates the hypothalamic-pituitary-adrenal (HPA) axis, and there is growing evidence that activation of the maternal HPA axis can have intergenerational consequences via, for example, maternally-derived steroids in eggs. Here, we investigated how predation risk affects a suite of maternally-derived steroids in threespine stickleback eggs across nine Alaskan lakes that vary in whether predatory trout are absent, native, or have been stocked within the last 25 years. Using liquid chromatography coupled with mass spectroscopy (LC-MS/MS), we detected 20 steroids within unfertilized eggs. Factor analysis suggests that steroids covary within and across steroid classes (i.e. glucocorticoids, progestogens, sex steroids), emphasizing the modularity and interconnectedness of the endocrine response. Surprisingly, egg steroid profiles were not significantly associated with predator regime, although they were more variable when predators were absent compared to when predators were present, with either native or stocked trout. Despite being the most abundant steroid, cortisol was not consistently associated with predation regime. Thus, while predators can affect steroids in adults, including mothers, the link between maternal stress and embryonic development is more complex than a simple one-to-one relationship between the population-level predation risk experienced by mothers and the steroids mothers transfer to their eggs.
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59
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Zhang M, Suren H, Holliday JA. Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa. Genome Biol Evol 2020; 11:2256-2272. [PMID: 31298685 PMCID: PMC6735766 DOI: 10.1093/gbe/evz151] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2019] [Indexed: 12/14/2022] Open
Abstract
Local adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype- and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.
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Affiliation(s)
- Man Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia.,National Engineering Research Center for Floriculture, School of Landscape Architecture, Beijing Forestry University, China
| | - Haktan Suren
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia
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60
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VanKuren NW, Massardo D, Nallu S, Kronforst MR. Butterfly Mimicry Polymorphisms Highlight Phylogenetic Limits of Gene Reuse in the Evolution of Diverse Adaptations. Mol Biol Evol 2020; 36:2842-2853. [PMID: 31504750 DOI: 10.1093/molbev/msz194] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Some genes have repeatedly been found to control diverse adaptations in a wide variety of organisms. Such gene reuse reveals not only the diversity of phenotypes these unique genes control but also the composition of developmental gene networks and the genetic routes available to and taken by organisms during adaptation. However, the causes of gene reuse remain unclear. A small number of large-effect Mendelian loci control a huge diversity of mimetic butterfly wing color patterns, but reasons for their reuse are difficult to identify because the genetic basis of mimicry has primarily been studied in two systems with correlated factors: female-limited Batesian mimicry in Papilio swallowtails (Papilionidae) and non-sex-limited Müllerian mimicry in Heliconius longwings (Nymphalidae). Here, we break the correlation between phylogenetic relationship and sex-limited mimicry by identifying loci controlling female-limited mimicry polymorphism Hypolimnas misippus (Nymphalidae) and non-sex-limited mimicry polymorphism in Papilio clytia (Papilionidae). The Papilio clytia polymorphism is controlled by the genome region containing the gene cortex, the classic P supergene in Heliconius numata, and loci controlling color pattern variation across Lepidoptera. In contrast, female-limited mimicry polymorphism in Hypolimnas misippus is associated with a locus not previously implicated in color patterning. Thus, although many species repeatedly converged on cortex and its neighboring genes over 120 My of evolution of diverse color patterns, female-limited mimicry polymorphisms each evolved using a different gene. Our results support conclusions that gene reuse occurs mainly within ∼10 My and highlight the puzzling diversity of genes controlling seemingly complex female-limited mimicry polymorphisms.
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Affiliation(s)
| | - Darli Massardo
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Sumitha Nallu
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
| | - Marcus R Kronforst
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL
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61
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Kowalko J. Utilizing the blind cavefish Astyanax mexicanus to understand the genetic basis of behavioral evolution. J Exp Biol 2020; 223:223/Suppl_1/jeb208835. [DOI: 10.1242/jeb.208835] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
ABSTRACT
Colonization of novel habitats often results in the evolution of diverse behaviors. Comparisons between individuals from closely related populations that have evolved divergent behaviors in different environments can be used to investigate behavioral evolution. However, until recently, functionally connecting genotypes to behavioral phenotypes in these evolutionarily relevant organisms has been difficult. The development of gene editing tools will facilitate functional genetic analysis of genotype–phenotype connections in virtually any organism, and has the potential to significantly transform the field of behavioral genetics when applied to ecologically and evolutionarily relevant organisms. The blind cavefish Astyanax mexicanus provides a remarkable example of evolution associated with colonization of a novel habitat. These fish consist of a single species that includes sighted surface fish that inhabit the rivers of Mexico and southern Texas and at least 29 populations of blind cavefish from the Sierra Del Abra and Sierra de Guatemala regions of Northeast Mexico. Although eye loss and albinism have been studied extensively in A. mexicanus, derived behavioral traits including sleep loss, alterations in foraging and reduction in social behaviors are now also being investigated in this species to understand the genetic and neural basis of behavioral evolution. Astyanax mexicanus has emerged as a powerful model system for genotype–phenotype mapping because surface and cavefish are interfertile. Further, the molecular basis of repeated trait evolution can be examined in this species, as multiple cave populations have independently evolved the same traits. A sequenced genome and the implementation of gene editing in A. mexicanus provides a platform for gene discovery and identification of the contributions of naturally occurring variation to behaviors. This review describes the current knowledge of behavioral evolution in A. mexicanus with an emphasis on the molecular and genetic underpinnings of evolved behaviors. Multiple avenues of new research that can be pursued using gene editing tools are identified, and how these will enhance our understanding of behavioral evolution is discussed.
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Affiliation(s)
- Johanna Kowalko
- Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
- Program of Neurogenetics, Florida Atlantic University, Jupiter, FL 33458, USA
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62
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Ferreira MS, Alves PC, Callahan CM, Giska I, Farelo L, Jenny H, Mills LS, Hackländer K, Good JM, Melo‐Ferreira J. Transcriptomic regulation of seasonal coat color change in hares. Ecol Evol 2020; 10:1180-1192. [PMID: 32076506 PMCID: PMC7029059 DOI: 10.1002/ece3.5956] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/26/2019] [Accepted: 12/09/2019] [Indexed: 12/27/2022] Open
Abstract
Color molts from summer brown to winter white coats have evolved in several species to maintain camouflage year-round in environments with seasonal snow. Despite the eco-evolutionary relevance of this key phenological adaptation, its molecular regulation has only recently begun to be addressed. Here, we analyze skin transcription changes during the autumn molt of the mountain hare (Lepus timidus) and integrate the results with an established model of gene regulation across the spring molt of the closely related snowshoe hare (L. americanus). We quantified differences in gene expression among three stages of molt progression-"brown" (early molt), "intermediate," and "white" (late molt). We found 632 differentially expressed genes, with a major pulse of expression early in the molt, followed by a milder one in late molt. The functional makeup of differentially expressed genes anchored the sampled molt stages to the developmental timeline of the hair growth cycle, associating anagen to early molt and the transition to catagen to late molt. The progression of color change was characterized by differential expression of genes involved in pigmentation, circadian, and behavioral regulation. We found significant overlap between differentially expressed genes across the seasonal molts of mountain and snowshoe hares, particularly at molt onset, suggesting conservatism of gene regulation across species and seasons. However, some discrepancies suggest seasonal differences in melanocyte differentiation and the integration of nutritional cues. Our established regulatory model of seasonal coat color molt provides an important mechanistic context to study the functional architecture and evolution of this crucial seasonal adaptation.
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Affiliation(s)
- Mafalda S. Ferreira
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
| | - Paulo C. Alves
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
- Wildlife Biology ProgramUniversity of MontanaMissoulaMTUSA
| | | | - Iwona Giska
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
| | - Liliana Farelo
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
| | - Hannes Jenny
- Amt für Jagd und Fischerei GraubündenChurSwitzerland
| | - L. Scott Mills
- Wildlife Biology ProgramUniversity of MontanaMissoulaMTUSA
- Office of Research and Creative ScholarshipUniversity of MontanaMissoulaMTUSA
| | - Klaus Hackländer
- Institute of Wildlife Biology and Game ManagementBOKU—University of Natural Resources and Life SciencesViennaAustria
| | - Jeffrey M. Good
- Wildlife Biology ProgramUniversity of MontanaMissoulaMTUSA
- Division of Biological SciencesUniversity of MontanaMissoulaMTUSA
| | - José Melo‐Ferreira
- CIBIOCentro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de Ciências da Universidade do PortoPortoPortugal
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63
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Schneider K, Adams CE, Elmer KR. Parallel selection on ecologically relevant gene functions in the transcriptomes of highly diversifying salmonids. BMC Genomics 2019; 20:1010. [PMID: 31870285 PMCID: PMC6929470 DOI: 10.1186/s12864-019-6361-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/01/2019] [Indexed: 12/11/2022] Open
Abstract
Background Salmonid fishes are characterised by a very high level of variation in trophic, ecological, physiological, and life history adaptations. Some salmonid taxa show exceptional potential for fast, within-lake diversification into morphologically and ecologically distinct variants, often in parallel; these are the lake-resident charr and whitefish (several species in the genera Salvelinus and Coregonus). To identify selection on genes and gene categories associated with such predictable diversifications, we analysed 2702 orthogroups (4.82 Mbp total; average 4.77 genes/orthogroup; average 1783 bp/orthogroup). We did so in two charr and two whitefish species and compared to five other salmonid lineages, which do not evolve in such ecologically predictable ways, and one non-salmonid outgroup. Results All selection analyses are based on Coregonus and Salvelinus compared to non-diversifying taxa. We found more orthogroups were affected by relaxed selection than intensified selection. Of those, 122 were under significant relaxed selection, with trends of an overrepresentation of serine family amino acid metabolism and transcriptional regulation, and significant enrichment of behaviour-associated gene functions. Seventy-eight orthogroups were under significant intensified selection and were enriched for signalling process and transcriptional regulation gene ontology terms and actin filament and lipid metabolism gene sets. Ninety-two orthogroups were under diversifying/positive selection. These were enriched for signal transduction, transmembrane transport, and pyruvate metabolism gene ontology terms and often contained genes involved in transcriptional regulation and development. Several orthogroups showed signs of multiple types of selection. For example, orthogroups under relaxed and diversifying selection contained genes such as ap1m2, involved in immunity and development, and slc6a8, playing an important role in muscle and brain creatine uptake. Orthogroups under intensified and diversifying selection were also found, such as genes syn3, with a role in neural processes, and ctsk, involved in bone remodelling. Conclusions Our approach pinpointed relevant genomic targets by distinguishing among different kinds of selection. We found that relaxed, intensified, and diversifying selection affect orthogroups and gene functions of ecological relevance in salmonids. Because they were found consistently and robustly across charr and whitefish and not other salmonid lineages, we propose these genes have a potential role in the replicated ecological diversifications.
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Affiliation(s)
- Kevin Schneider
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Colin E Adams
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.,Scottish Centre for Ecology and the Natural Environment, University of Glasgow, Rowardennan, G63 0AW, UK
| | - Kathryn R Elmer
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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64
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics. Genome Biol Evol 2019; 11:1552-1572. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz101] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2019] [Indexed: 12/13/2022] Open
Abstract
High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University.,Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University.,Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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65
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Coetzer WG, Grobler JP. Genetic variation among different springbok (Antidorcas marsupialis) colour variants. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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66
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Levsh O, Pluskal T, Carballo V, Mitchell AJ, Weng JK. Independent evolution of rosmarinic acid biosynthesis in two sister families under the Lamiids clade of flowering plants. J Biol Chem 2019; 294:15193-15205. [PMID: 31481469 PMCID: PMC6802498 DOI: 10.1074/jbc.ra119.010454] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 08/24/2019] [Indexed: 11/06/2022] Open
Abstract
As a means to maintain their sessile lifestyle amid challenging environments, plants produce an enormous diversity of compounds as chemical defenses against biotic and abiotic insults. The underpinning metabolic pathways that support the biosynthesis of these specialized chemicals in divergent plant species provide a rich arena for understanding the molecular evolution of complex metabolic traits. Rosmarinic acid (RA) is a phenolic natural product first discovered in plants of the mint family (Lamiaceae) and is recognized for its wide range of medicinal properties and potential applications in human dietary and medical interventions. Interestingly, the RA chemotype is present sporadically in multiple taxa of flowering plants as well as some hornworts and ferns, prompting the question whether its biosynthesis arose independently across different lineages. Here we report the elucidation of the RA biosynthetic pathway in Phacelia campanularia (desert bells). This species represents the borage family (Boraginaceae), an RA-producing family closely related to the Lamiaceae within the Lamiids clade. Using a multi-omics approach in combination with functional characterization of candidate genes both in vitro and in vivo, we found that RA biosynthesis in P. campanularia involves specific activities of a BAHD acyltransferase and two cytochrome P450 hydroxylases. Further phylogenetic and comparative structure-function analyses of the P. campanularia RA biosynthetic enzymes clearly indicate that RA biosynthesis has evolved independently at least twice in the Lamiids, an exemplary case of chemotypic convergence through disparate evolutionary trajectories.
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Affiliation(s)
- Olesya Levsh
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Tomáš Pluskal
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Valentina Carballo
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Andrew J Mitchell
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Jing-Ke Weng
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
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67
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Blankers T, Oh KP, Shaw KL. Parallel genomic architecture underlies repeated sexual signal divergence in Hawaiian Laupala crickets. Proc Biol Sci 2019; 286:20191479. [PMID: 31594503 PMCID: PMC6790767 DOI: 10.1098/rspb.2019.1479] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 09/13/2019] [Indexed: 12/13/2022] Open
Abstract
When the same phenotype evolves repeatedly, we can explore the predictability of genetic changes underlying phenotypic evolution. Theory suggests that genetic parallelism is less likely when phenotypic changes are governed by many small-effect loci compared to few of major effect, because different combinations of genetic changes can result in the same quantitative outcome. However, some genetic trajectories might be favoured over others, making a shared genetic basis to repeated polygenic evolution more likely. To examine this, we studied the genetics of parallel male mating song evolution in the Hawaiian cricket Laupala. We compared quantitative trait loci (QTL) underlying song divergence in three species pairs varying in phenotypic distance. We tested whether replicated song divergence between species involves the same QTL and whether the likelihood of QTL sharing is related to QTL effect size. Contrary to theoretical predictions, we find substantial parallelism in polygenic genetic architectures underlying repeated song divergence. QTL overlapped more frequently than expected based on simulated QTL analyses. Interestingly, QTL effect size did not predict QTL sharing, but did correlate with magnitude of phenotypic divergence. We highlight potential mechanisms driving these constraints on cricket song evolution and discuss a scenario that consolidates empirical quantitative genetic observations with micro-mutational theory.
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68
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Rougeux C, Gagnaire P, Praebel K, Seehausen O, Bernatchez L. Polygenic selection drives the evolution of convergent transcriptomic landscapes across continents within a Nearctic sister species complex. Mol Ecol 2019; 28:4388-4403. [DOI: 10.1111/mec.15226] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Clément Rougeux
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
| | | | - Kim Praebel
- Norwegian College of Fishery Science UiT The Arctic University of Norway Tromsø Norway
| | - Ole Seehausen
- Aquatic Ecology and Evolution Institute of Ecology & Evolution University of Bern Bern Switzerland
| | - Louis Bernatchez
- Département de biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec City QC Canada
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69
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Conith MR, Conith AJ, Albertson RC. Evolution of a soft-tissue foraging adaptation in African cichlids: Roles for novelty, convergence, and constraint. Evolution 2019; 73:2072-2084. [PMID: 31418824 DOI: 10.1111/evo.13824] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 06/25/2019] [Accepted: 07/05/2019] [Indexed: 12/12/2022]
Abstract
Understanding the origins of biodiversity demands consideration of both extrinsic (e.g., ecological opportunity) and intrinsic (e.g., developmental constraint) factors. Here, we use a combination of phylogenetic and genetic tools to address the origin of novelty in African cichlids. In particular, we focus on an extreme hypertrophied snout that is structurally integrated with the upper jaw. We show that this bizarre trait has evolved independently in at least two distinct and ecologically successful cichlid clades. We find that snout dimensions are decoupled both phenotypically and genetically, which has enabled it to evolve independently in multiple directions. Further, patterns of variation among species and within a genetic mapping pedigree suggest that relative to snout length, depth is under greater genetic and/or developmental constraint. Models of evolution suggest that snout shape is under selection for feeding behavior, with snout depth being important for algae scraping and snout length for sand sifting. Indeed, the deep snout of some algivores is achieved via an expansion of the intermaxillary ligament, which is important for jaw stability and may increase feeding performance. Overall, our data imply that the evolution of exaggerated snout depth required overcoming a genetic/developmental constraint, which led to expanded ecological opportunity via foraging adaptation.
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Affiliation(s)
- Moira R Conith
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - Andrew J Conith
- Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
| | - R Craig Albertson
- Graduate Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, 01003.,Department of Biology, University of Massachusetts, Amherst, Massachusetts, 01003
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70
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Walsh J, Benham PM, Deane‐Coe PE, Arcese P, Butcher BG, Chan YL, Cheviron ZA, Elphick CS, Kovach AI, Olsen BJ, Shriver WG, Winder VL, Lovette IJ. Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows. Evol Lett 2019; 3:324-338. [PMID: 31388443 PMCID: PMC6675146 DOI: 10.1002/evl3.126] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022] Open
Abstract
Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection of 12 candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection of loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNew York14850
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew York14853
| | - Phred M. Benham
- Division of Biological SciencesUniversity of MontanaMissoulaMontana59812
| | - Petra E. Deane‐Coe
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNew York14850
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew York14853
| | - Peter Arcese
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBritish ColumbiaT6T1Z4Canada
| | - Bronwyn G. Butcher
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNew York14850
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew York14853
| | | | | | - Chris S. Elphick
- Ecology and Evolutionary BiologyUniversity of ConnecticutStorrsConnecticut06269
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire03824
| | - Brian J. Olsen
- School of Biology and EcologyUniversity of MaineOronoMaine04469
| | - W. Gregory Shriver
- Department of Entomology and Wildlife EcologyUniversity of DelawareNewarkDelaware19716
| | | | - Irby J. Lovette
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNew York14850
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNew York14853
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71
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Lamichhaney S, Card DC, Grayson P, Tonini JFR, Bravo GA, Näpflin K, Termignoni-Garcia F, Torres C, Burbrink F, Clarke JA, Sackton TB, Edwards SV. Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180248. [PMID: 31154982 PMCID: PMC6560268 DOI: 10.1098/rstb.2018.0248] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
Evolutionary convergence has been long considered primary evidence of adaptation driven by natural selection and provides opportunities to explore evolutionary repeatability and predictability. In recent years, there has been increased interest in exploring the genetic mechanisms underlying convergent evolution, in part, owing to the advent of genomic techniques. However, the current 'genomics gold rush' in studies of convergence has overshadowed the reality that most trait classifications are quite broadly defined, resulting in incomplete or potentially biased interpretations of results. Genomic studies of convergence would be greatly improved by integrating deep 'vertical', natural history knowledge with 'horizontal' knowledge focusing on the breadth of taxonomic diversity. Natural history collections have and continue to be best positioned for increasing our comprehensive understanding of phenotypic diversity, with modern practices of digitization and databasing of morphological traits providing exciting improvements in our ability to evaluate the degree of morphological convergence. Combining more detailed phenotypic data with the well-established field of genomics will enable scientists to make progress on an important goal in biology: to understand the degree to which genetic or molecular convergence is associated with phenotypic convergence. Although the fields of comparative biology or comparative genomics alone can separately reveal important insights into convergent evolution, here we suggest that the synergistic and complementary roles of natural history collection-derived phenomic data and comparative genomics methods can be particularly powerful in together elucidating the genomic basis of convergent evolution among higher taxa. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Sangeet Lamichhaney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Daren C. Card
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
- Department of Biology, University of Texas Arlington, Arlington, TX 76019, USA
| | - Phil Grayson
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - João F. R. Tonini
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Kathrin Näpflin
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Flavia Termignoni-Garcia
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Torres
- Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
- Department of Geological Sciences, The University of Texas at Austin, Austin, MA 78712, USA
| | - Frank Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY 10024, USA
| | - Julia A. Clarke
- Department of Biology, The University of Texas at Austin, Austin, MA 78712, USA
- Department of Geological Sciences, The University of Texas at Austin, Austin, MA 78712, USA
| | | | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA 02138, USA
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72
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Stern DB, Crandall KA. The Evolution of Gene Expression Underlying Vision Loss in Cave Animals. Mol Biol Evol 2019; 35:2005-2014. [PMID: 29788330 PMCID: PMC6063295 DOI: 10.1093/molbev/msy106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms. Here, we analyze gene expression variation in adult eye tissue across the freshwater crayfish, representing four independent vision-loss events in caves. Species and individual expression patterns cluster by eye function rather than phylogeny, suggesting convergence in transcriptome evolution in independently blind animals. However, this clustering is not greater than what is observed in surface species with conserved eye function after accounting for phylogenetic expectations. Modeling expression evolution suggests that there is a common increase in evolutionary rates in the blind lineages, consistent with a relaxation of selective constraint maintaining optimal expression levels. This is evidence for a repeated loss of expression constraint in the transcriptomes of blind animals and that convergence occurs via a similar trajectory through genetic drift.
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Affiliation(s)
- David B Stern
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
| | - Keith A Crandall
- Department of Epidemiology and Biostatistics, Milken Institute School of Public Health, Computational Biology Institute, The George Washington University, Washington, DC
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73
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Tian L, Rahman SR, Ezray BD, Franzini L, Strange JP, Lhomme P, Hines HM. A homeotic shift late in development drives mimetic color variation in a bumble bee. Proc Natl Acad Sci U S A 2019; 116:11857-11865. [PMID: 31043564 PMCID: PMC6575597 DOI: 10.1073/pnas.1900365116] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Natural phenotypic radiations, with their high diversity and convergence, are well-suited for informing how genomic changes translate to natural phenotypic variation. New genomic tools enable discovery in such traditionally nonmodel systems. Here, we characterize the genomic basis of color pattern variation in bumble bees (Hymenoptera, Apidae, Bombus), a group that has undergone extensive convergence of setal color patterns as a result of Müllerian mimicry. In western North America, multiple species converge on local mimicry patterns through parallel shifts of midabdominal segments from red to black. Using genome-wide association, we establish that a cis-regulatory locus between the abdominal fate-determining Hox genes, abd-A and Abd-B, controls the red-black color switch in a western species, Bombus melanopygus Gene expression analysis reveals distinct shifts in Abd-B aligned with the duration of setal pigmentation at the pupal-adult transition. This results in atypical anterior Abd-B expression, a late developmental homeotic shift. Changing expression of Hox genes can have widespread effects, given their important role across segmental phenotypes; however, the late timing reduces this pleiotropy, making Hox genes suitable targets. Analysis of this locus across mimics and relatives reveals that other species follow independent genetic routes to obtain the same phenotypes.
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Affiliation(s)
- Li Tian
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | | | - Briana D Ezray
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - Luca Franzini
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
| | - James P Strange
- United States Department of Agriculture-Agricultural Research Service Pollinating Insects Research Unit, Utah State University, Logan, UT 84322
| | - Patrick Lhomme
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Biodiversity and Crop Improvement Program, International Center of Agricultural Research in the Dry Areas, 10112 Rabat, Morocco
| | - Heather M Hines
- Department of Biology, The Pennsylvania State University, University Park, PA 16802;
- Department of Entomology, The Pennsylvania State University, University Park, PA 16802
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74
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Fischer EK, Nowicki JP, O'Connell LA. Evolution of affiliation: patterns of convergence from genomes to behaviour. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180242. [PMID: 31154971 DOI: 10.1098/rstb.2018.0242] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Affiliative behaviours have evolved many times across animals. Research on the mechanisms underlying affiliative behaviour demonstrates remarkable convergence across species spanning wide evolutionary distances. Shared mechanisms have been identified with genomic approaches analysing genetic variants and gene expression differences as well as neuroendocrine and molecular approaches exploring the role of hormones and signalling molecules. We review the genomic and neural basis of pair bonding and parental care across diverse taxa to shed light on mechanistic patterns that underpin the convergent evolution of affiliative behaviour. We emphasize that mechanisms underlying convergence in complex phenotypes like affiliation should be evaluated on a continuum, where signatures of convergence may vary across levels of biological organization. In particular, additional comparative studies within and across major vertebrate lineages will be essential in resolving when and why shared neural substrates are repeatedly targeted in the independent evolution of affiliation, and how similar mechanisms are evolutionarily tuned to give rise to species-specific variations in behaviour. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Eva K Fischer
- Department of Biology, Stanford University , Stanford, CA 95305 , USA
| | - Jessica P Nowicki
- Department of Biology, Stanford University , Stanford, CA 95305 , USA
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75
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Mendes FK, Livera AP, Hahn MW. The perils of intralocus recombination for inferences of molecular convergence. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180244. [PMID: 31154973 DOI: 10.1098/rstb.2018.0244] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence ('hemiplasy') can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and Drosophila, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of Drosophila protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and Drosophila, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Fábio K Mendes
- 1 Department of Computer Science, The University of Auckland , Auckland 1010 , New Zealand.,2 Department of Biology, Indiana University , Bloomington, IN 47405 , USA
| | - Andrew P Livera
- 2 Department of Biology, Indiana University , Bloomington, IN 47405 , USA
| | - Matthew W Hahn
- 2 Department of Biology, Indiana University , Bloomington, IN 47405 , USA.,3 Department of Computer Science, Indiana University , Bloomington, IN 47405 , USA
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76
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Lim MCW, Witt CC, Graham CH, Dávalos LM. Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. Genome Biol Evol 2019; 11:1573-1585. [PMID: 31028697 PMCID: PMC6553502 DOI: 10.1093/gbe/evz090] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination is a highly conserved process that has profound effects on genome evolution. At a fine-scale, recombination rates can vary drastically across genomes, often localized into small recombination "hotspots" with highly elevated rates, surrounded by regions with little recombination. In most species studied, the location of hotspots within genomes is highly conserved across broad evolutionary timescales. The main exception to this pattern is in mammals, where hotspot location can evolve rapidly among closely related species and even among populations within a species. Hotspot position in mammals is controlled by the gene, Prdm9, whereas in species with conserved hotspots, a functional Prdm9 is typically absent. Due to a limited number of species where recombination rates have been estimated at a fine-scale, it remains unclear whether hotspot conservation is always associated with the absence of a functional Prdm9. Threespine stickleback fish (Gasterosteus aculeatus) are an excellent model to examine the evolution of recombination over short evolutionary timescales. Using a linkage disequilibrium-based approach, we found recombination rates indeed varied at a fine-scale across the genome, with many regions organized into narrow hotspots. Hotspots had highly divergent landscapes between stickleback populations, where only ∼15% of these hotspots were shared. Our results indicate that fine-scale recombination rates may be diverging between closely related populations of threespine stickleback fish. Interestingly, we found only a weak association of a PRDM9 binding motif within hotspots, which suggests that threespine stickleback fish may possess a novel mechanism for targeting recombination hotspots at a fine-scale.
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Affiliation(s)
- Marisa C W Lim
- Department of Ecology and Evolution, Stony Brook University
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico
| | - Catherine H Graham
- Department of Ecology and Evolution, Stony Brook University
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University
- Consortium for Inter-Disciplinary Environmental Research, Stony Brook University
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77
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Nelson TC, Jones MR, Velotta JP, Dhawanjewar AS, Schweizer RM. UNVEILing connections between genotype, phenotype, and fitness in natural populations. Mol Ecol 2019; 28:1866-1876. [PMID: 30830713 PMCID: PMC6525050 DOI: 10.1111/mec.15067] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/12/2019] [Accepted: 02/27/2019] [Indexed: 12/29/2022]
Abstract
Understanding the links between genetic variation and fitness in natural populations is a central goal of evolutionary genetics. This monumental task spans the fields of classical and molecular genetics, population genetics, biochemistry, physiology, developmental biology, and ecology. Advances to our molecular and developmental toolkits are facilitating integrative approaches across these traditionally separate fields, providing a more complete picture of the genotype-phenotype map in natural and non-model systems. Here, we summarize research presented at the first annual symposium of the UNVEIL Network, an NSF-funded collaboration between the University of Montana and the University of Nebraska, Lincoln, which took place from the 1st to the 3rd of June, 2018. We discuss how this body of work advances basic evolutionary science, what it implies for our ability to predict evolutionary change, and how it might inform novel conservation strategies.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | - Matthew R Jones
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | - Jonathan P Velotta
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
| | | | - Rena M Schweizer
- Division of Biological Sciences, University of Montana, 32 Campus Dr HS 104, Missoula, MT, 59812
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78
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Schweizer RM, Durvasula A, Smith J, Vohr SH, Stahler DR, Galaverni M, Thalmann O, Smith DW, Randi E, Ostrander EA, Green RE, Lohmueller KE, Novembre J, Wayne RK. Natural Selection and Origin of a Melanistic Allele in North American Gray Wolves. Mol Biol Evol 2019; 35:1190-1209. [PMID: 29688543 DOI: 10.1093/molbev/msy031] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pigmentation is often used to understand how natural selection affects genetic variation in wild populations since it can have a simple genetic basis, and can affect a variety of fitness-related traits (e.g., camouflage, thermoregulation, and sexual display). In gray wolves, the K locus, a β-defensin gene, causes black coat color via a dominantly inherited KB allele. The allele is derived from dog-wolf hybridization and is at high frequency in North American wolf populations. We designed a DNA capture array to probe the geographic origin, age, and number of introgression events of the KB allele in a panel of 331 wolves and 20 dogs. We found low diversity in KB, but not ancestral ky, wolf haplotypes consistent with a selective sweep of the black haplotype across North America. Further, North American wolf KB haplotypes are monophyletic, suggesting that a single adaptive introgression from dogs to wolves most likely occurred in the Northwest Territories or Yukon. We use a new analytical approach to date the origin of the KB allele in Yukon wolves to between 1,598 and 7,248 years ago, suggesting that introgression with early Native American dogs was the source. Using population genetic simulations, we show that the K locus is undergoing natural selection in four wolf populations. We find evidence for balancing selection, specifically in Yellowstone wolves, which could be a result of selection for enhanced immunity in response to distemper. With these data, we demonstrate how the spread of an adaptive variant may have occurred across a species' geographic range.
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Affiliation(s)
- Rena M Schweizer
- Division of Biological Sciences, University of Montana, Missoula, MT.,Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
| | - Arun Durvasula
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - Joel Smith
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | | | - Olaf Thalmann
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | - Douglas W Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY
| | - Ettore Randi
- Department of Biology, University of Bologna, Bologna, Italy.,Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA
| | - John Novembre
- Department of Ecology and Evolution, University of Chicago, Chicago, IL.,Department of Human Genetics, University of Chicago, IL
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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79
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Wu CC, Klaesson A, Buskas J, Ranefall P, Mirzazadeh R, Söderberg O, Wolf JBW. In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation. J Exp Biol 2019; 222:jeb194431. [PMID: 30718374 PMCID: PMC6650291 DOI: 10.1242/jeb.194431] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 01/31/2019] [Indexed: 01/12/2023]
Abstract
Functional validation of candidate genes involved in adaptation and speciation remains challenging. Here, we exemplify the utility of a method quantifying individual mRNA transcripts in revealing the molecular basis of divergence in feather pigment synthesis during early-stage speciation in crows. Using a padlock probe assay combined with rolling circle amplification, we quantified cell-type-specific gene expression in the histological context of growing feather follicles. Expression of Tyrosinase Related Protein 1 (TYRP1), Solute Carrier Family 45 member 2 (SLC45A2) and Hematopoietic Prostaglandin D Synthase (HPGDS) was melanocyte-limited and significantly reduced in follicles from hooded crow, explaining the substantially lower eumelanin content in grey versus black feathers. The central upstream Melanocyte Inducing Transcription Factor (MITF) only showed differential expression specific to melanocytes - a feature not captured by bulk RNA-seq. Overall, this study provides insight into the molecular basis of an evolutionary young transition in pigment synthesis, and demonstrates the power of histologically explicit, statistically substantiated single-cell gene expression quantification for functional genetic inference in natural populations.
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Affiliation(s)
- Chi-Chih Wu
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Axel Klaesson
- Department of Pharmaceutical Biosciences, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Julia Buskas
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Petter Ranefall
- Science of Life Laboratories and Department of Information Technology, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Reza Mirzazadeh
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm SE-17165, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Jochen B W Wolf
- Science of Life Laboratories and Department of Evolutionary Biology, Uppsala University, SE-752 36 Uppsala, Sweden
- Division of Evolutionary Biology, Faculty of Biology, LMU Munich, D-82152 Planegg-Martinsried, Germany
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80
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Pfeifer SP, Laurent S, Sousa VC, Linnen CR, Foll M, Excoffier L, Hoekstra HE, Jensen JD. The Evolutionary History of Nebraska Deer Mice: Local Adaptation in the Face of Strong Gene Flow. Mol Biol Evol 2019; 35:792-806. [PMID: 29346646 PMCID: PMC5905656 DOI: 10.1093/molbev/msy004] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight. Yet, connecting theoretical results with empirical data has proven challenging, owing to a lack of information on the relationship between genotype, phenotype, and fitness. Here, we examine the demographic and selective history of deer mice in and around the Nebraska Sand Hills, a system in which variation at the Agouti locus affects cryptic coloration that in turn affects the survival of mice in their local habitat. We first genotyped 250 individuals from 11 sites along a transect spanning the Sand Hills at 660,000 single nucleotide polymorphisms across the genome. Using these genomic data, we found that deer mice first colonized the Sand Hills following the last glacial period. Subsequent high rates of gene flow have served to homogenize the majority of the genome between populations on and off the Sand Hills, with the exception of the Agouti pigmentation locus. Furthermore, mutations at this locus are strongly associated with the pigment traits that are strongly correlated with local soil coloration and thus responsible for cryptic coloration.
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Affiliation(s)
- Susanne P Pfeifer
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ
| | - Stefan Laurent
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vitor C Sousa
- Institute of Ecology & Evolution, University of Berne, Berne, Switzerland.,Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | | | - Matthieu Foll
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Excoffier
- Institute of Ecology & Evolution, University of Berne, Berne, Switzerland
| | - Hopi E Hoekstra
- Department of Organismic & Evolutionary Biology and Molecular & Cellular Biology, Museum of Comparative Zoology, Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Jeffrey D Jensen
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University, Tempe, AZ
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81
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Barrett RDH, Laurent S, Mallarino R, Pfeifer SP, Xu CCY, Foll M, Wakamatsu K, Duke-Cohan JS, Jensen JD, Hoekstra HE. Linking a mutation to survival in wild mice. Science 2019; 363:499-504. [DOI: 10.1126/science.aav3824] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022]
Abstract
Adaptive evolution in new or changing environments can be difficult to predict because the functional connections between genotype, phenotype, and fitness are complex. Here, we make these explicit connections by combining field and laboratory experiments in wild mice. We first directly estimate natural selection on pigmentation traits and an underlying pigment locus, Agouti, by using experimental enclosures of mice on different soil colors. Next, we show how a mutation in Agouti associated with survival causes lighter coat color through changes in its protein binding properties. Together, our findings demonstrate how a sequence variant alters phenotype and then reveal the ensuing ecological consequences that drive changes in population allele frequency, thereby illuminating the process of evolution by natural selection.
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82
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Abstract
Convergent 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. Convergent evolution—the appearance of the same character state in apparently unrelated organisms—is often inferred when a trait is incongruent with the species tree. However, trait incongruence can also arise from changes that occur on discordant gene trees, a process referred to as hemiplasy. Hemiplasy is rarely taken into account in studies of convergent evolution, despite the fact that phylogenomic studies have revealed rampant discordance. Here, we study the relative probabilities of homoplasy (including convergence and reversal) and hemiplasy for an incongruent trait. We derive expressions for the probabilities of the two events, showing that they depend on many of the same parameters. We find that hemiplasy is as likely—or more likely—than homoplasy for a wide range of conditions, even when levels of discordance are low. We also present a method to calculate the ratio of these two probabilities (the “hemiplasy risk factor”) along the branches of a phylogeny of arbitrary length. Such calculations can be applied to any tree to identify when and where incongruent traits may be due to hemiplasy.
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83
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Esfeld K, Berardi AE, Moser M, Bossolini E, Freitas L, Kuhlemeier C. Pseudogenization and Resurrection of a Speciation Gene. Curr Biol 2018; 28:3776-3786.e7. [PMID: 30472000 DOI: 10.1016/j.cub.2018.10.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/05/2018] [Accepted: 10/05/2018] [Indexed: 12/13/2022]
Abstract
A persistent question in evolutionary biology is how complex phenotypes evolve and whether phenotypic transitions are reversible. Multiple losses of floral pigmentation have been documented in the angiosperms, but color re-gain has not yet been described, supporting that re-gain is unlikely. Pollinator-mediated selection in Petunia has resulted in several color shifts comprised of both losses and gains of color. The R2R3-MYB transcription factor AN2 has been identified as a major locus responsible for shifts in pollinator preference. Whereas the loss of visible color has previously been attributed to repeated pseudogenization of AN2, here, we describe the mechanism of an independent re-gain of floral color via AN2 evolution. In P. secreta, purple color is restored through the improbable resurrection of AN2 gene function from a non-functional AN2-ancestor by a single reading-frame-restoring mutation. Thus, floral color evolution in Petunia is mechanistically dependent on AN2 functionality, highlighting its role as a hotspot in color transitions and a speciation gene for the genus.
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Affiliation(s)
- Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Andrea E Berardi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Eligio Bossolini
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Loreta Freitas
- Department of Genetics, University Fed Rio Grande do Sul, POB 15053, Porto Alegre, 91501970 Rio Grande do Sul, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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84
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Mandic M, Ramon ML, Gerstein AC, Gracey AY, Richards JG. Variable gene transcription underlies phenotypic convergence of hypoxia tolerance in sculpins. BMC Evol Biol 2018; 18:163. [PMID: 30390629 PMCID: PMC6215679 DOI: 10.1186/s12862-018-1275-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 10/18/2018] [Indexed: 01/03/2023] Open
Abstract
Background The degree by which mechanisms underlying phenotypic convergence are similar among taxa depends on the number of evolutionary paths available for selection to act upon. Likelihood of convergence will be influenced by an interplay of factors such as genetic architecture, phylogenetic history and population demography. To determine if there is convergence or divergence in mechanisms underlying phenotypic similarity, we assessed whether gene transcription patterns differed among species with similar levels of hypoxia tolerance. Results Three species of marine fish from the superfamily Cottoidea (smoothhead sculpin [Artedius lateralis], sailfin sculpin [Nautichthys oculofasciatus] and Pacific staghorn sculpin [Leptocottus armatus]), all of which have previously been shown to share the same level of hypoxia tolerance, were exposed to short-(8 h) and longer-term (72 h) hypoxia and mRNA transcripts were assessed using a custom microarray. We examined hypoxia-induced transcription patterns in metabolic and protein production pathways and found that a high proportion of genes associated with these biological processes showed significant differences among the species. Specifically, the data suggest that the smoothhead sculpin, unlike the sailfin sculpin and the Pacific staghorn sculpin, relied on amino acid degradation rather than glycolysis or fatty acid oxidation to generate ATP during hypoxia exposure. There was also variation across the species in the transcription of genes involved in protein production (e.g. mRNA processing and protein translation), such that it increased in the smoothhead sculpin, decreased in the sailfin sculpin and was variable in the Pacific staghorn sculpin. Conclusions Changes in metabolic and protein production pathways are part of the key responses of fishes to exposures to environmental hypoxia. Yet, species with similar overall hypoxia tolerance exhibited different transcriptional responses in these pathways, indicating flexibility and complexity of interactions in the evolution of the mechanisms underlying the hypoxia tolerance phenotype. The variation in the hypoxia-induced transcription of genes across species with similar hypoxia tolerance suggests that similar whole-animal phenotypes can emerge from divergent evolutionary paths that may affect metabolically important functions. Electronic supplementary material The online version of this article (10.1186/s12862-018-1275-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Milica Mandic
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada. .,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada.
| | - Marina L Ramon
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Aleeza C Gerstein
- Department of Genetics, Cell Biology and Development, University of Minnesota, 321 Church Street, Minneapolis, MN, 55455, USA
| | - Andrew Y Gracey
- Department of Biological Sciences, University of Southern California, 3616 Trousdale Parkway, Los Angeles, CA, 90089-0371, USA
| | - Jeffrey G Richards
- Department of Zoology, University of British Columbia, 6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada.,Bamfield Marine Sciences Centre, 100 Pachena Dr, Bamfield, BC, V0R 1B0, Canada
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85
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Rivas MJ, Saura M, Pérez-Figueroa A, Panova M, Johansson T, André C, Caballero A, Rolán-Alvarez E, Johannesson K, Quesada H. Population genomics of parallel evolution in gene expression and gene sequence during ecological adaptation. Sci Rep 2018; 8:16147. [PMID: 30385764 PMCID: PMC6212547 DOI: 10.1038/s41598-018-33897-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/08/2018] [Indexed: 11/17/2022] Open
Abstract
Natural selection often produces parallel phenotypic changes in response to a similar adaptive challenge. However, the extent to which parallel gene expression differences and genomic divergence underlie parallel phenotypic traits and whether they are decoupled or not remains largely unexplored. We performed a population genomic study of parallel ecological adaptation among replicate ecotype pairs of the rough periwinkle (Littorina saxatilis) at a regional geographical scale (NW Spain). We show that genomic changes underlying parallel phenotypic divergence followed a complex pattern of both repeatable differences and of differences unique to specific ecotype pairs, in which parallel changes in expression or sequence are restricted to a limited set of genes. Yet, the majority of divergent genes were divergent either for gene expression or coding sequence, but not for both simultaneously. Overall, our findings suggest that divergent selection significantly contributed to the process of parallel molecular differentiation among ecotype pairs, and that changes in expression and gene sequence underlying phenotypic divergence could, at least to a certain extent, be considered decoupled processes.
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Affiliation(s)
- María José Rivas
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - María Saura
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Andrés Pérez-Figueroa
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Marina Panova
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Tomas Johansson
- Department of Biology, University of Lund, SE-223 62, Lund, Sweden
| | - Carl André
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Armando Caballero
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Emilio Rolán-Alvarez
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain
| | - Kerstin Johannesson
- Department of Marine Sciences, Tjärnö, University of Gothenburg, SE-452 96, Strömstad, Sweden
| | - Humberto Quesada
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, 36310, Vigo, Spain.
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86
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Yeaman S, Gerstein AC, Hodgins KA, Whitlock MC. Quantifying how constraints limit the diversity of viable routes to adaptation. PLoS Genet 2018; 14:e1007717. [PMID: 30296265 PMCID: PMC6193742 DOI: 10.1371/journal.pgen.1007717] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 10/18/2018] [Accepted: 09/26/2018] [Indexed: 12/25/2022] Open
Abstract
Convergent adaptation occurs at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns of genetic repeatability provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel index to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This index is explicitly based on the probability of observing a given amount of repeatability by chance under a given null hypothesis and is readily compared among different species and types of trait. We also formulate an index to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these indices can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to stress in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution. How many ways can evolution solve the same adaptive problem? While convergent adaptation is evident in many organisms at the phenotypic level, we are only beginning to understand how commonly this convergence extends to the genome scale. Quantifying the repeatability of adaptation at the genome scale is therefore critical for assessing how constraints affect the diversity of viable genetic responses. Here, we develop probability-based indices to quantify the deviation between observed repeatability and expectations under a range of null hypotheses, and an estimator of the proportion of loci in the genome that can contribute to adaptation. We demonstrate the usage of these indices with individual-based simulations and example datasets from yeast and conifers and discuss how they differ from previously developed approaches to studying repeatability. Because these indices are unitless, they provide a general approach to quantifying and comparing how constraints drive convergence at the genome scale across a wide range of traits and taxa.
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Affiliation(s)
- Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- * E-mail:
| | - Aleeza C. Gerstein
- Department of Microbiology & Immunology, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kathryn A. Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Michael C. Whitlock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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87
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Replicability of Introgression Under Linked, Polygenic Selection. Genetics 2018; 210:1411-1427. [PMID: 30274989 DOI: 10.1534/genetics.118.301429] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/28/2018] [Indexed: 11/18/2022] Open
Abstract
We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation.
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88
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Vickrey AI, Bruders R, Kronenberg Z, Mackey E, Bohlender RJ, Maclary ET, Maynez R, Osborne EJ, Johnson KP, Huff CD, Yandell M, Shapiro MD. Introgression of regulatory alleles and a missense coding mutation drive plumage pattern diversity in the rock pigeon. eLife 2018; 7:e34803. [PMID: 30014848 PMCID: PMC6050045 DOI: 10.7554/elife.34803] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 06/05/2018] [Indexed: 12/17/2022] Open
Abstract
Birds and other vertebrates display stunning variation in pigmentation patterning, yet the genes controlling this diversity remain largely unknown. Rock pigeons (Columba livia) are fundamentally one of four color pattern phenotypes, in decreasing order of melanism: T-check, checker, bar (ancestral), or barless. Using whole-genome scans, we identified NDP as a candidate gene for this variation. Allele-specific expression differences in NDP indicate cis-regulatory divergence between ancestral and melanistic alleles. Sequence comparisons suggest that derived alleles originated in the speckled pigeon (Columba guinea), providing a striking example of introgression. In contrast, barless rock pigeons have an increased incidence of vision defects and, like human families with hereditary blindness, carry start-codon mutations in NDP. In summary, we find that both coding and regulatory variation in the same gene drives wing pattern diversity, and post-domestication introgression supplied potentially advantageous melanistic alleles to feral populations of this ubiquitous urban bird.
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Affiliation(s)
- Anna I Vickrey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Rebecca Bruders
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Zev Kronenberg
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Emma Mackey
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Ryan J Bohlender
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Emily T Maclary
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Raquel Maynez
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
| | - Edward J Osborne
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois Urbana-ChampaignChampaignUnited States
| | - Chad D Huff
- Department of Epidemiology, MD Anderson Cancer CenterUniversity of TexasHoustonUnited States
| | - Mark Yandell
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Michael D Shapiro
- School of Biological SciencesUniversity of UtahSalt Lake CityUnited States
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89
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Re C, Fišer Ž, Perez J, Tacdol A, Trontelj P, Protas ME. Common Genetic Basis of Eye and Pigment Loss in Two Distinct Cave Populations of the Isopod Crustacean Asellus aquaticus. Integr Comp Biol 2018; 58:421-430. [DOI: 10.1093/icb/icy028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Cassandra Re
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
| | - Žiga Fišer
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Justin Perez
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
| | - Allyson Tacdol
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
| | - Peter Trontelj
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana SI-1000, Slovenia
| | - Meredith E Protas
- Dominican University of California, 50 Acacia Avenue, San Rafael, CA 94901, USA
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90
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Nigenda‐Morales SF, Hu Y, Beasley JC, Ruiz‐Piña HA, Valenzuela‐Galván D, Wayne RK. Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (
Didelphis virginiana
). Mol Ecol 2018; 27:2680-2697. [DOI: 10.1111/mec.14712] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Sergio F. Nigenda‐Morales
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
| | - Yibo Hu
- Key Lab of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Chaoyang, Beijing China
| | - James C. Beasley
- Savannah River Ecology Lab Warnell School of Forestry and Natural Resources University of Georgia Aiken South Carolina
| | - Hugo A. Ruiz‐Piña
- Centro de Investigaciones Regionales “Dr. Hideyo Noguchi” Universidad Autónoma de Yucatán Mérida Yucatán Mexico
| | - David Valenzuela‐Galván
- Departamento de Ecología Evolutiva Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Morelos Mexico
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
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91
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Amazonas DR, Portes-Junior JA, Nishiyama-Jr MY, Nicolau CA, Chalkidis HM, Mourão RH, Grazziotin FG, Rokyta DR, Gibbs HL, Valente RH, Junqueira-de-Azevedo IL, Moura-da-Silva AM. Molecular mechanisms underlying intraspecific variation in snake venom. J Proteomics 2018; 181:60-72. [DOI: 10.1016/j.jprot.2018.03.032] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/08/2018] [Accepted: 03/31/2018] [Indexed: 10/17/2022]
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92
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Ferraz T, Rossoni DM, Althoff SL, Pissinatti A, Paixão-Cortês VR, Bortolini MC, González-José R, Marroig G, Salzano FM, Gonçalves GL, Hünemeier T. Contrasting patterns of RUNX2 repeat variations are associated with palate shape in phyllostomid bats and New World primates. Sci Rep 2018; 8:7867. [PMID: 29777172 PMCID: PMC5959863 DOI: 10.1038/s41598-018-26225-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/02/2018] [Indexed: 12/21/2022] Open
Abstract
Establishing the genetic basis that underlies craniofacial variability in natural populations is one of the main topics of evolutionary and developmental studies. One of the genes associated with mammal craniofacial variability is RUNX2, and in the present study we investigated the association between craniofacial length and width and RUNX2 across New World bats (Phyllostomidae) and primates (Catarrhini and Platyrrhini). Our results showed contrasting patterns of association between the glutamate/alanine ratios (Q/A ratio) and palate shape in these highly diverse groups. In phyllostomid bats, we found an association between shorter/broader faces and increase of the Q/A ratio. In New World monkeys (NWM) there was a positive correlation of increasing Q/A ratios to more elongated faces. Our findings reinforced the role of the Q/A ratio as a flexible genetic mechanism that would rapidly change the time of skull ossification throughout development. However, we propose a scenario in which the influence of this genetic adjustment system is indirect. The Q/A ratio would not lead to a specific phenotype, but throughout the history of a lineage, would act along with evolutionary constraints, as well as other genes, as a facilitator for adaptive morphological changes.
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Affiliation(s)
- Tiago Ferraz
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.,Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Daniela M Rossoni
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | | | | | | | - Maria Cátira Bortolini
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Rolando González-José
- Patagonian Institute of Social and Human Sciences, National Council for Scientific and Technological Research-CONICET, U9120ACD, Puerto Madryn, Argentina
| | - Gabriel Marroig
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil
| | - Francisco M Salzano
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Gislene L Gonçalves
- Department of Genetics, Biosciences Institute, Federal University of Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil.,Department of Environmental Resources, Faculty of Agrarian Sciences, University of Tarapacá, Arica, Chile
| | - Tábita Hünemeier
- Department of Genetics and Evolutionary Biology, Biosciences Institute, University of São Paulo, 05508-900, São Paulo, SP, Brazil.
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93
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Schielzeth H, Rios Villamil A, Burri R. Success and failure in replication of genotype-phenotype associations: How does replication help in understanding the genetic basis of phenotypic variation in outbred populations? Mol Ecol Resour 2018; 18:739-754. [PMID: 29575806 DOI: 10.1111/1755-0998.12780] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 03/09/2018] [Accepted: 03/09/2018] [Indexed: 12/29/2022]
Abstract
Recent developments in sequencing technologies have facilitated genomewide mapping of phenotypic variation in natural populations. Such mapping efforts face a number of challenges potentially leading to low reproducibility. However, reproducible research forms the basis of scientific progress. We here discuss the options for replication and the reasons for potential nonreproducibility. We then review the evidence for reproducible quantitative trait loci (QTL) with a focus on natural animal populations. Existing case studies of replication fall into three categories: (i) traits that have been mapped to major effect loci (including chromosomal inversion and supergenes) by independent research teams; (ii) QTL fine-mapped in discovery populations; and (iii) attempts to replicate QTL across multiple populations. Major effect loci, in particular those associated with inversions, have been successfully replicated in several cases within and across populations. Beyond such major effect variants, replication has been more successful within than across populations, suggesting that QTL discovered in natural populations may often be population-specific. This suggests that biological causes (differences in linkage patterns, allele frequencies or context-dependencies of QTL) contribute to nonreproducibility. Evidence from other fields, notably animal breeding and QTL mapping in humans, suggests that a significant fraction of QTL is indeed reproducible in direction and magnitude at least within populations. However, there is also a large number of QTL that cannot be easily reproduced. We put forward that more studies should explicitly address the causes and context-dependencies of QTL signals, in particular to disentangle linkage differences, allele frequency differences and gene-by-environment interactions as biological causes of nonreproducibility of QTL, especially between populations.
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Affiliation(s)
- Holger Schielzeth
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Alejandro Rios Villamil
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
| | - Reto Burri
- Population Ecology Group, Institute of Ecology and Evolution, Friedrich Schiller University, Jena, Germany
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94
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McGirr JA, Martin CH. Parallel evolution of gene expression between trophic specialists despite divergent genotypes and morphologies. Evol Lett 2018; 2:62-75. [PMID: 30283665 PMCID: PMC6089502 DOI: 10.1002/evl3.41] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/22/2017] [Accepted: 01/03/2018] [Indexed: 12/20/2022] Open
Abstract
Parallel evolution of gene expression commonly underlies convergent niche specialization, but parallel changes in expression could also underlie divergent specialization. We investigated divergence in gene expression and whole-genome genetic variation across three sympatric Cyprinodon pupfishes endemic to San Salvador Island, Bahamas. This recent radiation consists of a generalist and two derived specialists adapted to novel niches: a scale-eating and a snail-eating pupfish. We sampled total mRNA from all three species at two early developmental stages and compared gene expression with whole-genome genetic differentiation among all three species in 42 resequenced genomes. Eighty percent of genes that were differentially expressed between snail-eaters and generalists were up or down regulated in the same direction between scale-eaters and generalists; however, there were no fixed variants shared between species underlying these parallel changes in expression. Genes showing parallel evolution of expression were enriched for effects on metabolic processes, whereas genes showing divergent expression were enriched for effects on cranial skeleton development and pigment biosynthesis, reflecting the most divergent phenotypes observed between specialist species. Our findings reveal that even divergent niche specialists may exhibit convergent adaptation to higher trophic levels through shared genetic pathways. This counterintuitive result suggests that parallel evolution in gene expression can accompany divergent ecological speciation during adaptive radiation.
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Affiliation(s)
- Joseph A. McGirr
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27514
| | - Christopher H. Martin
- Department of BiologyUniversity of North Carolina at Chapel HillChapel HillNorth Carolina27514
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95
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San-Jose LM, Roulin A. Genomics of coloration in natural animal populations. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0337. [PMID: 28533454 DOI: 10.1098/rstb.2016.0337] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2017] [Indexed: 12/28/2022] Open
Abstract
Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.
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Affiliation(s)
- Luis M San-Jose
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Building Le Biophore, 1015 Lausanne, Switzerland
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96
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Zimova M, Hackländer K, Good JM, Melo‐Ferreira J, Alves PC, Mills LS. Function and underlying mechanisms of seasonal colour moulting in mammals and birds: what keeps them changing in a warming world? Biol Rev Camb Philos Soc 2018; 93:1478-1498. [DOI: 10.1111/brv.12405] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Marketa Zimova
- Wildlife Biology Program University of Montana Missoula MT 59812 U.S.A
- Fisheries, Wildlife, and Conservation Biology Program, Department of Forestry and Environmental Resources North Carolina State University Raleigh NC 27695 U.S.A
| | - Klaus Hackländer
- Fisheries, Wildlife, and Conservation Biology Program, Department of Forestry and Environmental Resources North Carolina State University Raleigh NC 27695 U.S.A
- Institute of Wildlife Biology and Game Management BOKU ‐ University of Natural Resources and Life Sciences Vienna 1180 Austria
| | - Jeffrey M. Good
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
| | - José Melo‐Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Campus Agrário de Vairão, 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Rua do Campo Alegre, 4169‐007 Porto Portugal
| | - Paulo Célio Alves
- Wildlife Biology Program University of Montana Missoula MT 59812 U.S.A
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Campus Agrário de Vairão, 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Rua do Campo Alegre, 4169‐007 Porto Portugal
| | - L. Scott Mills
- Wildlife Biology Program and Office of Research and Creative Scholarship University of Montana Missoula MT 59812 USA
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97
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Genetic Basis of Body Color and Spotting Pattern in Redheaded Pine Sawfly Larvae ( Neodiprion lecontei). Genetics 2018; 209:291-305. [PMID: 29496749 DOI: 10.1534/genetics.118.300793] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/22/2018] [Indexed: 11/18/2022] Open
Abstract
Pigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand the existing sample of color loci, we performed QTL mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly (Neodiprion lecontei): carotenoid-based yellow body color and melanin-based spotting pattern. For both traits, our QTL models explained a substantial proportion of phenotypic variation and suggested a genetic architecture that is neither monogenic nor highly polygenic. Additionally, we used our linkage map to anchor the current N. lecontei genome assembly. With these data, we identified promising candidate genes underlying (1) a loss of yellow pigmentation in populations in the mid-Atlantic/northeastern United States [C locus-associated membrane protein homologous to a mammalian HDL receptor-2 gene (Cameo2) and lipid transfer particle apolipoproteins II and I gene (apoLTP-II/I)], and (2) a pronounced reduction in black spotting in Great Lakes populations [members of the yellow gene family, tyrosine hydroxylase gene (pale), and dopamine N-acetyltransferase gene (Dat)]. Several of these genes also contribute to color variation in other wild and domesticated taxa. Overall, our findings are consistent with the hypothesis that predictable genes of large effect contribute to color evolution in nature.
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98
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Pereira RJ, Sasaki MC, Burton RS. Adaptation to a latitudinal thermal gradient within a widespread copepod species: the contributions of genetic divergence and phenotypic plasticity. Proc Biol Sci 2018; 284:rspb.2017.0236. [PMID: 28446698 DOI: 10.1098/rspb.2017.0236] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/23/2017] [Indexed: 01/26/2023] Open
Abstract
Understanding how populations adapt to heterogeneous thermal regimes is essential for comprehending how latitudinal gradients in species diversification are formed, and how taxa will respond to ongoing climate change. Adaptation can occur by innate genetic factors, by phenotypic plasticity, or by a combination of both mechanisms. Yet, the relative contribution of such mechanisms to large-scale latitudinal gradients of thermal tolerance across conspecific populations remains unclear. We examine thermal performance in 11 populations of the intertidal copepod Tigriopus californicus, ranging from Baja California Sur (Mexico) to British Columbia (Canada). Common garden experiments show that survivorship to acute heat-stress differs between populations (by up to 3.8°C in LD50 values), reflecting a strong genetic thermal adaptation. Using a split-brood experiment with two rearing temperatures, we also show that developmental phenotypic plasticity is beneficial to thermal tolerance (by up to 1.3°C), and that this effect differs across populations. Although genetic divergence in heat tolerance strongly correlates with latitude and temperature, differences in the plastic response do not. In the context of climate warming, our results confirm the general prediction that low-latitude populations are most susceptible to local extinction because genetic adaptation has placed physiological limits closer to current environmental maxima, but our results also contradict the prediction that phenotypic plasticity is constrained at lower latitudes.
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Affiliation(s)
- Ricardo J Pereira
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA .,Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
| | - Matthew C Sasaki
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Marine Science Department, University of Connecticut, Groton, CT, USA
| | - Ronald S Burton
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA
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99
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Castiglione GM, Schott RK, Hauser FE, Chang BSW. Convergent selection pressures drive the evolution of rhodopsin kinetics at high altitudes via nonparallel mechanisms. Evolution 2018; 72:170-186. [DOI: 10.1111/evo.13396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/02/2017] [Indexed: 01/01/2023]
Affiliation(s)
- Gianni M. Castiglione
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Ryan K. Schott
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Frances E. Hauser
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
| | - Belinda S. W. Chang
- Department of Cell & Systems Biology; University of Toronto; Toronto Ontario M5S 3G5 Canada
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto Ontario M5S 3B2 Canada
- Centre for the Analysis of Genome Evolution and Function; University of Toronto; Toronto Ontario M5S 3B2 Canada
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100
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Dijkstra PD, Border SE. How does male-male competition generate negative frequency-dependent selection and disruptive selection during speciation? Curr Zool 2018; 64:89-99. [PMID: 29492042 PMCID: PMC5809039 DOI: 10.1093/cz/zox079] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Accepted: 12/16/2017] [Indexed: 11/14/2022] Open
Abstract
Natural selection has been shown to drive population differentiation and speciation. The role of sexual selection in this process is controversial; however, most of the work has centered on mate choice while the role of male-male competition in speciation is relatively understudied. Here, we outline how male-male competition can be a source of diversifying selection on male competitive phenotypes, and how this can contribute to the evolution of reproductive isolation. We highlight how negative frequency-dependent selection (advantage of rare phenotype arising from stronger male-male competition between similar male phenotypes compared with dissimilar male phenotypes) and disruptive selection (advantage of extreme phenotypes) drives the evolution of diversity in competitive traits such as weapon size, nuptial coloration, or aggressiveness. We underscore that male-male competition interacts with other life-history functions and that variable male competitive phenotypes may represent alternative adaptive options. In addition to competition for mates, aggressive interference competition for ecological resources can exert selection on competitor signals. We call for a better integration of male-male competition with ecological interference competition since both can influence the process of speciation via comparable but distinct mechanisms. Altogether, we present a more comprehensive framework for studying the role of male-male competition in speciation, and emphasize the need for better integration of insights gained from other fields studying the evolutionary, behavioral, and physiological consequences of agonistic interactions.
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Affiliation(s)
- Peter D Dijkstra
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
| | - Shana E Border
- Department of Biology, Central Michigan University, Mount Pleasant, MI 48859, USA
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