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Byerly PA, Kearns AM, Welch A, Ochirbat ME, Marra PP, Wilson A, Campana MG, Fleischer RC. Museum genomics provide insight into the extinction of a specialist North American warbler species. Sci Rep 2024; 14:17047. [PMID: 39048633 PMCID: PMC11269716 DOI: 10.1038/s41598-024-67595-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 07/12/2024] [Indexed: 07/27/2024] Open
Abstract
Museum genomics provide an opportunity to investigate population demographics of extinct species, especially valuable when research prior to extinction was minimal. The Bachman's warbler (Vermivora bachmanii) is hypothesized to have gone extinct due to loss of its specialized habitat. However, little is known about other potential contributing factors such as natural rarity or changes to connectivity following habitat fragmentation. We examined mitochondrial DNA (mtDNA) and genome-wide SNPs using specimens collected from breeding and migration sites across the range of the Bachman's warbler. We found no signals of strong population structuring across the breeding range of Bachman's warblers in both mtDNA and genome-wide SNPs. Thus, long-term population isolation did not appear to be a significant contributor to the extinction of the Bachman's warbler. Instead, our findings support the theory that Bachman's warblers underwent a rapid decline likely driven by habitat destruction, which may have been exacerbated by the natural rarity, habitat specificity and low genetic diversity of the species.
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Affiliation(s)
- Paige A Byerly
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA.
| | - Anna M Kearns
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Australian National Wildlife Collection, CSIRO National Research Collections Australia, Canberra, Australia
| | - Andreanna Welch
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Department of Biosciences, Durham University, South Road, Durham, UK
| | - Margad-Erdene Ochirbat
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Peter P Marra
- Department of Biology and McCourt School of Public Policy, Georgetown University, 37th and O Streets NW, Washington, DC, 20057, USA
| | - Amy Wilson
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Michael G Campana
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
| | - Robert C Fleischer
- Center for Conservation Genomics, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20008, USA
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2
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Gyllenhaal EF, Brady SS, DeCicco LH, Naikatini A, Hime PM, Manthey JD, Kelly J, Moyle RG, Andersen MJ. Waves of Colonization and Gene Flow in a Great Speciator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.18.603796. [PMID: 39091784 PMCID: PMC11291091 DOI: 10.1101/2024.07.18.603796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Secondary contact between previously allopatric lineages offers a test of reproductive isolating mechanisms that may have accrued in isolation. Such instances of contact can produce stable hybrid zones-where reproductive isolation can further develop via reinforcement or phenotypic displacement-or result in the lineages merging. Ongoing secondary contact is most visible in continental systems, where steady input from parental taxa can occur readily. In oceanic island systems, however, secondary contact between closely related species of birds is relatively rare. When observed on sufficiently small islands, relative to population size, secondary contact likely represents a recent phenomenon. Here, we examine the dynamics of a group of birds whose apparent widespread hybridization influenced Ernst Mayr's foundational work on allopatric speciation: the whistlers of Fiji (Aves: Pachycephala). We demonstrate two clear instances of secondary contact within the Fijian archipelago, one resulting in a hybrid zone on a larger island, and the other resulting in a wholly admixed population on a smaller, adjacent island. We leveraged low genome-wide divergence in the hybrid zone to pinpoint a single genomic region associated with observed phenotypic differences. We use genomic data to present a new hypothesis that emphasizes rapid plumage evolution and post-divergence gene flow.
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Affiliation(s)
- Ethan F. Gyllenhaal
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - Serina S. Brady
- Carnegie Museum of Natural History, Pittsburgh, Pennsylvania, USA
| | - Lucas H. DeCicco
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | | | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Present Address: McDonnell Genome Institute and Department of Genetics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Joseph D. Manthey
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, USA
| | - John Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Robert G. Moyle
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, USA
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
| | - Michael J. Andersen
- Department of Biology and Museum of Southwestern Biology, University of New Mexico, Albuquerque, New Mexico, USA
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3
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Cumer T, Machado AP, San-Jose LM, Ducrest AL, Simon C, Roulin A, Goudet J. The genomic architecture of continuous plumage colour variation in the European barn owl ( Tyto alba). Proc Biol Sci 2024; 291:20231995. [PMID: 38196365 PMCID: PMC10777144 DOI: 10.1098/rspb.2023.1995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/30/2023] [Indexed: 01/11/2024] Open
Abstract
The maintenance of colour variation in wild populations has long fascinated evolutionary biologists, although most studies have focused on discrete traits exhibiting rather simple inheritance patterns and genetic architectures. However, the study of continuous colour traits and their potentially oligo- or polygenic genetic bases remains rare in wild populations. We studied the genetics of the continuously varying white-to-rufous plumage coloration of the European barn owl (Tyto alba) using a genome-wide association approach on the whole-genome data of 75 individuals. We confirmed a mutation at the melanocortin-1-receptor gene (MC1R) is involved in the coloration and identified two new regions, located in super-scaffolds 9 and 42. The combination of the three regions explains most of the colour variation (80.37%, 95% credible interval 58.45-100%). One discovered region, located in the sex chromosome, differs between the most extreme colorations in owls sharing a specific MC1R genotype. This region may play a role in the colour sex dimorphism of this species, possibly in interaction with the autosomal MC1R. We thus provide insights into the genetic architecture of continuous colour variation, pointing to an oligogenic basis with potential epistatic effects among loci that should aid future studies understanding how continuous colour variation is maintained in nature.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Luis M. San-Jose
- Laboratoire Évolution and Diversité Biologique, UMR 5174, CNRS, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Anne-Lyse Ducrest
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Céline Simon
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, Lausanne CH-1015, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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4
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Valette T, Leitwein M, Lascaux JM, Desmarais E, Berrebi P, Guinand B. Redundancy analysis, genome-wide association studies and the pigmentation of brown trout (Salmo trutta L.). JOURNAL OF FISH BIOLOGY 2023; 102:96-118. [PMID: 36218076 DOI: 10.1111/jfb.15243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The association of molecular variants with phenotypic variation is a main issue in biology, often tackled with genome-wide association studies (GWAS). GWAS are challenging, with increasing, but still limited, use in evolutionary biology. We used redundancy analysis (RDA) as a complimentary ordination approach to single- and multitrait GWAS to explore the molecular basis of pigmentation variation in brown trout (Salmo trutta) belonging to wild populations impacted by hatchery fish. Based on 75,684 single nucleotide polymorphic (SNP) markers, RDA, single- and multitrait GWAS allowed the extraction of 337 independent colour patterning loci (CPLs) associated with trout pigmentation traits, such as the number of red and black spots on flanks. Collectively, these CPLs (i) mapped onto 35 out of 40 brown trout linkage groups indicating a polygenic genomic architecture of pigmentation, (ii) were found to be associated with 218 candidate genes, including 197 genes formerly mentioned in the literature associated to skin pigmentation, skin patterning, differentiation or structure notably in a close relative, the rainbow trout (Onchorhynchus mykiss), and (iii) related to functions relevant to pigmentation variation (e.g., calcium- and ion-binding, cell adhesion). Annotated CPLs include genes with well-known pigmentation effects (e.g., PMEL, SLC45A2, SOX10), but also markers associated with genes formerly found expressed in rainbow or brown trout skins. RDA was also shown to be useful to investigate management issues, especially the dynamics of trout pigmentation submitted to several generations of hatchery introgression.
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5
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Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00568-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Abstract
Zones of secondary contact provide a good opportunity to investigate the origin and dynamics of reproductive isolation between related populations. We analyzed genetic and phenotypic patterns and gene flow between two subspecies of the Eurasian magpie Pica pica s.l. which recently came into contact after presumably long periods of isolation. We describe the distribution of subspecies in a young contact zone at Argun’ river basin in southern Siberia where populations occur in parapatry and an older hybrid population in eastern Mongolia. Based on genome-wide SNP data, we analyzed patterns and strength of gene flow between the subspecies. Our results indicate occasional hybridization with backcrossing and asymmetric introgression along a wide range in Transbaikalia and locally in eastern Mongolia. Males of P. p. jankowskii apparently exhibit higher dispersal ability towards the west compared to P. p. leucoptera (towards the east). The former occasionally migrates to eastern Mongolia and Transbaikalia where introgression of nuclear, but not mitochondrial DNA was evident. Bioacoustic investigations showed differences between the subspecies in speed and structure of vocalization. We discovered intermediate calls of hybrid magpies and bilingual birds alternating calls that are typical for the two taxa. Furthermore, we found dramatically decreased reproductive success in hybridogeneous populations. By complementing our results with established phylogeographic patterns of P. pica s.l. based on a mitochondrial marker sequence, and considering indications of sterility of hybrids in the contact zone, we propose to elevate the two corresponding subspecies to species level: P. pica for the western form and P. serica for the eastern form.
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6
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Wolfgramm H, Martens J, Töpfer T, Vamberger M, Pathak A, Stuckas H, Päckert M. Asymmetric allelic introgression across a hybrid zone of the coal tit ( Periparus ater) in the central Himalayas. Ecol Evol 2021; 11:17332-17351. [PMID: 34938512 PMCID: PMC8668783 DOI: 10.1002/ece3.8369] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/26/2021] [Accepted: 11/02/2021] [Indexed: 11/07/2022] Open
Abstract
In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (Periparus ater) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western "spot-winged tit" (P. a. melanolophus) and Eastern Himalayan coal tits (P. a. aemodius) occur across a narrow range of <100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern P. a. aemodius into far western populations of phenotypic P. a. melanolophus but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.
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Affiliation(s)
- Hannes Wolfgramm
- Senckenberg Natural History Collections DresdenDresdenGermany
- Present address:
Department of Functional GenomicsInterfaculty Institute of Genetics and Functional GenomicsUniversity Medicine GreifswaldGreifswaldGermany
| | - Jochen Martens
- Institute of Organismic and Molecular Evolution (iomE)Johannes Gutenberg UniversityMainzGermany
| | - Till Töpfer
- Leibniz Institute for the Analysis of Biodiversity ChangeZoological Research Museum Alexander KoenigBonnGermany
| | | | - Abhinaya Pathak
- Department of National Parks and Wildlife ConservationKathmanduNepal
| | - Heiko Stuckas
- Senckenberg Natural History Collections DresdenDresdenGermany
| | - Martin Päckert
- Senckenberg Natural History Collections DresdenDresdenGermany
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7
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Funk ER, Mason NA, Pálsson S, Albrecht T, Johnson JA, Taylor SA. A supergene underlies linked variation in color and morphology in a Holarctic songbird. Nat Commun 2021; 12:6833. [PMID: 34824228 PMCID: PMC8616904 DOI: 10.1038/s41467-021-27173-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 11/08/2021] [Indexed: 01/01/2023] Open
Abstract
The genetic architecture of a phenotype can have considerable effects on the evolution of a trait or species. Characterizing genetic architecture provides insight into the complexity of a given phenotype and, potentially, the role of the phenotype in evolutionary processes like speciation. We use genome sequences to investigate the genetic basis of phenotypic variation in redpoll finches (Acanthis spp.). We demonstrate that variation in redpoll phenotype is broadly controlled by a ~55-Mb chromosomal inversion. Within this inversion, we find multiple candidate genes related to melanogenesis, carotenoid coloration, and bill shape, suggesting the inversion acts as a supergene controlling multiple linked traits. A latitudinal gradient in ecotype distribution suggests supergene driven variation in color and bill morphology are likely under environmental selection, maintaining supergene haplotypes as a balanced polymorphism. Our results provide a mechanism for the maintenance of ecotype variation in redpolls despite a genome largely homogenized by gene flow.
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Affiliation(s)
- Erik R Funk
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA.
| | - Nicholas A Mason
- Museum of Natural Science and Department of Biological Science, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Snæbjörn Pálsson
- Department of Life and Environmental Sciences, University of Iceland, Askja, Sturlugata 7, 101, Reykjavik, Iceland
| | - Tomáš Albrecht
- Department of Zoology, Charles University, Vinicna 7, CZ-12844, Prague, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, CZ-60365, Brno, Czech Republic
| | | | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, 80309, USA
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8
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Bravo GA, Schmitt CJ, Edwards SV. What Have We Learned from the First 500 Avian Genomes? ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021. [DOI: 10.1146/annurev-ecolsys-012121-085928] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels and rare genomic changes, are further resolving the avian tree of life. The accumulation of bird genomes, increasingly with long-read sequence data, greatly improves the resolution of genomic features such as germline-restricted chromosomes and the W chromosome, and is facilitating the comparative integration of genotypes and phenotypes. Community-based initiatives such as the Bird 10,000 Genomes Project and Vertebrate Genome Project are playing a fundamental role in amplifying and coalescing a vibrant international program in avian comparative genomics.
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Affiliation(s)
- Gustavo A. Bravo
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - C. Jonathan Schmitt
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
| | - Scott V. Edwards
- Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138, USA;, ,
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9
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McFarlane SE, Pemberton JM. Admixture mapping reveals loci for carcass mass in red deer x sika hybrids in Kintyre, Scotland. G3 (BETHESDA, MD.) 2021; 11:jkab274. [PMID: 34568926 PMCID: PMC8473967 DOI: 10.1093/g3journal/jkab274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/16/2021] [Indexed: 12/21/2022]
Abstract
We deployed admixture mapping on a sample of 386 deer from a hybrid swarm between native red deer (Cervus elaphus) and introduced Japanese sika (Cervus nippon) sampled in Kintyre, Scotland to search for quantitative trait loci (QTLs) underpinning phenotypic differences between the species. These two species are highly diverged genetically [Fst between pure species, based on 50K single nucleotide polymorphism (SNPs) = 0.532] and phenotypically: pure red have on average twice the carcass mass of pure sika in our sample (38.7 kg vs 19.1 kg). After controlling for sex, age, and population genetic structure, we found 10 autosomal genomic locations with QTL for carcass mass. Effect sizes ranged from 0.191 to 1.839 kg and as expected, in all cases the allele derived from sika conferred lower carcass mass. The sika population was fixed for all small carcass mass alleles, whereas the red deer population was typically polymorphic. GO term analysis of genes lying in the QTL regions are associated with oxygen transport. Although body mass is a likely target of selection, none of the SNPs marking QTL are introgressing faster or slower than expected in either direction.
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Affiliation(s)
- S Eryn McFarlane
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Department of Biology, Lund University, 22100 Lund, Sweden
| | - Josephine M Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
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10
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E Luzuriaga-Aveiga V, Ugarte M, Weir JT. Distinguishing genomic homogenization from parapatric speciation in an elevationally replacing pair of Ramphocelus tanagers. Mol Ecol 2021; 30:5517-5529. [PMID: 34403554 DOI: 10.1111/mec.16128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/14/2022]
Abstract
Geographically connected species pairs with weakly differentiated genomes could either represent cases of genomic homogenization in progress or of incipient parapatric speciation. Discriminating between these processes is difficult because intermediate stages of either may produce weakly differentiated genomes that diverge at few locations. We used coalescent modelling applied to a genome-wide sample of SNPs to discriminate between speciation with gene flow and genomic homogenization in two phenotypically distinct but genomically weakly diverged species of elevationally replacing Ramphocelus tanagers, forming a hybrid zone in the Andean foothills. We found overwhelming support for a model of genomic homogenization following secondary contact. Simulating under this model suggested that our species pair was differentiated (FST = 0.30) at secondary contact but that most of the genome has rapidly homogenized during 254 Ky of high gene flow towards the present (FST = 0.02). Despite extensive genome-wide homogenization, plumage remains distinctive with a narrower than expected geographic cline width, indicating divergent selection on colour. We found two SNPs significantly associated with plumage colour, which retain moderately high FST . We conclude that the majority of the genome has fused, but that divergent selection on select loci probably maintains the geographically structured colour differences between these incipient species.
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Affiliation(s)
- Vanessa E Luzuriaga-Aveiga
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Mauricio Ugarte
- Área de Ornitología, Universidad Nacional de San Agustín de Arequipa, Museo de Historia Natural Arequipa, Peru
| | - Jason T Weir
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada.,Department of Ornithology, Royal Ontario Museum, Toronto, Ontario, Canada
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11
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Bennett KFP, Lim HC, Braun MJ. Sexual selection and introgression in avian hybrid zones: Spotlight on Manacus. Integr Comp Biol 2021; 61:1291-1309. [PMID: 34128981 DOI: 10.1093/icb/icab135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Hybrid zones offer a window into the processes and outcomes of evolution, from species formation or fusion to genomic underpinnings of specific traits and isolating mechanisms. Sexual selection is believed to be an important factor in speciation processes, and hybrid zones present special opportunities to probe its impact. The manakins (Aves, Pipridae) are a promising group in which to study the interplay of sexual selection and natural hybridization: they show substantial variation across the family in the strength of sexual selection they experience, they readily hybridize within and between genera, and they appear to have formed hybrid species, a rare event in birds. A hybrid zone between two manakins in the genus Manacus is unusual in that plumage and behavioral traits of one species have introgressed asymmetrically into populations of the second species through positive sexual selection, then apparently stalled at a river barrier. This is one of a handful of documented examples of asymmetric sexual trait introgression with a known selective mechanism. It offers opportunities to examine reproductive isolation, introgression, plumage color evolution, and natural factors enhancing or constraining the effects of sexual selection in real time. Here, we review previous work in this system, propose new hypotheses for observed patterns, and recommend approaches to test them.
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Affiliation(s)
- Kevin F P Bennett
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Haw Chuan Lim
- Department of Biology, George Mason University, Manassas, VA, USA.,Center for Conservation Genomics, Smithsonian Conservation Biology Institute, Washington, DC, USA
| | - Michael J Braun
- Behavior, Ecology, Evolution, and Systematics Program, University of Maryland, College Park, MD, USA.,Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
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12
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Love J, Goller F. Processes underlying complex patterns of song trait evolution in a Setophaga hybrid zone. Ecol Evol 2021; 11:7264-7277. [PMID: 34188811 PMCID: PMC8216987 DOI: 10.1002/ece3.7559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 11/12/2022] Open
Abstract
During secondary contact between two species when hybrids are less fit than parents, mating signals are expected to diverge, while aggressive signals are expected to converge. If a single signal trait is used in both mating and aggression, then the dynamics between these two forces could influence the evolutionary trajectory of that trait. We studied such a situation in an avian hybrid zone between two Setophaga species, where birdsong is used in both mate attraction and territory defense. We hypothesized that song modules of the two species will show separate and distinct geographic patterns due to the influence of selective pressures for effective territorial aggression and for effective mate attraction. We conducted geographic cline analyses and playback experiments across this hybrid zone. We found an unexpected geographic pattern of asymmetric introgression of song rhythm, which may be explained by results of the playback experiments that suggest that differences in song rhythm serve a greater role in mate attraction than in territory defense. In contrast, differences in syllable morphology show little evidence of importance in mate attraction or territorial defense. Song features converge in the hybrid zone, yet patterns of trait change suggest that the song production modules may vary in their modes of development and inheritance. Syringeal motor gesturing, which gives rise to syllable morphology, shows a nonclinal mosaic pattern, suggesting that this trait may be predominantly learned. In contrast, respiratory patterning, which forms song rhythm, shows a clinal geographic transition, suggesting that this trait could be more innate. The results indicate that opposing forces act independently on song via distinct modules of the song production mechanism, driving complex patterns of song trait evolution.
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Affiliation(s)
- Jay Love
- University of UtahSalt Lake CityUTUSA
| | - Franz Goller
- University of UtahSalt Lake CityUTUSA
- University of MünsterMünsterGermany
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13
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Aguillon SM, Walsh J, Lovette IJ. Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype. Proc Biol Sci 2021; 288:20201805. [PMID: 33468000 DOI: 10.1098/rspb.2020.1805] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers-yellow-shafted and red-shafted flickers-to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across approximately 7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean FST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wing and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.
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Affiliation(s)
- Stepfanie M Aguillon
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Jennifer Walsh
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Irby J Lovette
- Department of Ecology and Evolutionary Biology, Cornell University, 215 Tower Road, Ithaca, NY 14853, USA.,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
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14
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Wang S, Rohwer S, de Zwaan DR, Toews DPL, Lovette IJ, Mackenzie J, Irwin D. Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species. Evol Lett 2020; 4:502-515. [PMID: 33312686 PMCID: PMC7719548 DOI: 10.1002/evl3.198] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 09/20/2020] [Accepted: 09/30/2020] [Indexed: 11/18/2022] Open
Abstract
Speciation is one of the most important processes in biology, yet the study of the genomic changes underlying this process is in its infancy. North American warbler species Setophaga townsendi and Setophaga occidentalis hybridize in a stable hybrid zone, following a period of geographic separation. Genomic differentiation accumulated during geographic isolation can be homogenized by introgression at secondary contact, whereas genetic regions that cause low hybrid fitness can be shielded from such introgression. Here, we examined the genomic underpinning of speciation by investigating (1) the genetic basis of divergent pigmentation traits between species, (2) variation in differentiation across the genome, and (3) the evidence for selection maintaining differentiation in the pigmentation genes. Using tens of thousands of single nucleotide polymorphisms (SNPs) genotyped in hundreds of individuals within and near the hybrid zone, genome-wide association mapping revealed a single SNP associated with cheek, crown, breast coloration, and flank streaking, reflecting pleiotropy (one gene affecting multiple traits) or close physical linkage of different genes affecting different traits. This SNP is within an intron of the RALY gene, hence we refer to it as the RALY SNP. We then examined between-species genomic differentiation, using both genotyping-by-sequencing and whole genome sequencing. We found that the RALY SNP is within one of the highest peaks of differentiation, which contains three genes known to influence pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). Heterozygotes at this gene block are likely of reduced fitness, as the geographic cline of the RALY SNP has been narrow over two decades. Together, these results reflect at least one barrier to gene flow within this narrow (∼200 kb) genomic region that modulates plumage difference between species. Despite extensive gene flow between species across the genome, this study provides evidence that selection on a phenotype-associated genomic region maintains a stable species boundary.
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Affiliation(s)
- Silu Wang
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| | - Sievert Rohwer
- Department of Biology and Burke MuseumUniversity of WashingtonSeattleWashington98195
| | - Devin R. de Zwaan
- Department of Forest and Conservation SciencesUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| | - David P. L. Toews
- Department of Biology619 Mueller LaboratoryPennsylvania State UniversityUniversity ParkPennsylvania16802
| | - Irby J. Lovette
- Fuller Evolutionary Biology ProgramCornell Lab of OrnithologyIthacaNew York14850
| | - Jacqueline Mackenzie
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T1Z4Canada
| | - Darren Irwin
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBCV6T1Z4Canada
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15
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Kirschel ANG, Nwankwo EC, Pierce DK, Lukhele SM, Moysi M, Ogolowa BO, Hayes SC, Monadjem A, Brelsford A. CYP2J19 mediates carotenoid colour introgression across a natural avian hybrid zone. Mol Ecol 2020; 29:4970-4984. [PMID: 33058329 DOI: 10.1111/mec.15691] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 02/06/2023]
Abstract
It has long been of interest to identify the phenotypic traits that mediate reproductive isolation between related species, and more recently, the genes that underpin them. Much work has focused on identifying genes associated with animal colour, with the candidate gene CYP2J19 identified in laboratory studies as the ketolase converting yellow dietary carotenoids to red ketocarotenoids in birds with red pigments. However, evidence that CYP2J19 explains variation between red and yellow feather coloration in wild populations of birds is lacking. Hybrid zones provide the opportunity to identify genes associated with specific traits. Here we investigate genomic regions associated with colour in red-fronted and yellow-fronted tinkerbirds across a hybrid zone in southern Africa. We sampled 85 individuals, measuring spectral reflectance of forecrown feathers and scoring colours from photographs, while testing for carotenoid presence with Raman spectroscopy. We performed a genome-wide association study to identify associations with carotenoid-based coloration, using double-digest RAD sequencing aligned to a short-read whole genome of a Pogoniulus tinkerbird. Admixture mapping using 104,933 single nucleotide polymorphisms (SNPs) identified a region of chromosome 8 that includes CYP2J19 as the only locus with more than two SNPs significantly associated with both crown hue and crown score, while Raman spectra provided evidence of ketocarotenoids in red feathers. Asymmetric backcrossing in the hybrid zone suggests that yellow-fronted females mate more often with red-fronted males than vice versa. Female red-fronted tinkerbirds mating assortatively with red-crowned males is consistent with the hypothesis that converted carotenoids are an honest signal of quality.
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Affiliation(s)
| | - Emmanuel C Nwankwo
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Daniel K Pierce
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | - Sifiso M Lukhele
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Michaella Moysi
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Bridget O Ogolowa
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Sophia C Hayes
- Department of Chemistry, University of Cyprus, Nicosia, Cyprus
| | - Ara Monadjem
- Department of Biological Sciences, University of Eswatini, Kwaluseni, Eswatini.,Department of Zoology & Entomology, Mammal Research Institute, University of Pretoria, Hatfield, South Africa
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
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16
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Khalil S, Welklin JF, McGraw KJ, Boersma J, Schwabl H, Webster MS, Karubian J. Testosterone regulates CYP2J19-linked carotenoid signal expression in male red-backed fairywrens ( Malurus melanocephalus). Proc Biol Sci 2020; 287:20201687. [PMID: 32933448 PMCID: PMC7542802 DOI: 10.1098/rspb.2020.1687] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022] Open
Abstract
Carotenoid pigments produce most red, orange and yellow colours in vertebrates. This coloration can serve as an honest signal of quality that mediates social and mating interactions, but our understanding of the underlying mechanisms that control carotenoid signal production, including how different physiological pathways interact to shape and maintain these signals, remains incomplete. We investigated the role of testosterone in mediating gene expression associated with a red plumage sexual signal in red-backed fairywrens (Malurus melanocephalus). In this species, males within a single population can flexibly produce either red/black nuptial plumage or female-like brown plumage. Combining correlational analyses with a field-based testosterone implant experiment and quantitative polymerase chain reaction, we show that testosterone mediates expression of carotenoid-based plumage in part by regulating expression of CYP2J19, a ketolase gene associated with ketocarotenoid metabolism and pigmentation in birds. This is, to our knowledge, the first time that hormonal regulation of a specific genetic locus has been linked to carotenoid production in a natural context, revealing how endocrine mechanisms produce sexual signals that shape reproductive success.
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Affiliation(s)
- Sarah Khalil
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
| | - Joseph F. Welklin
- Macaulay Library, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Kevin J. McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Jordan Boersma
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Hubert Schwabl
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michael S. Webster
- Macaulay Library, Cornell Laboratory of Ornithology, Ithaca, NY, USA
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY, USA
| | - Jordan Karubian
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, USA
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17
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Toews DPL, Kramer GR, Jones AW, Brennan CL, Cloud BE, Andersen DE, Lovette IJ, Streby H. Genomic identification of intergeneric hybrids in New World wood-warblers (Aves: Parulidae). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa085] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
AbstractThe documentation of hybrids between distantly related taxa can illustrate an initial step to explain how genes might move between species that do not exhibit complete reproductive isolation. In birds, some of the most phylogenetically distant hybrid combinations occur between genera. Traditionally, morphological and plumage characters have been used to assign the identity of the parental species of a putative hybrid, although recently, nuclear introns also have been used. Here, we demonstrate how high-throughput short-read DNA sequence data can be used to identify the parentage of a putative intergeneric hybrid, in this case between a blue-winged warbler (Vermivora cyanoptera) and a cerulean warbler (Setophaga cerulea). This hybrid had mitochondrial DNA of a cerulean warbler, indicating the maternal parent. For hundreds of single nucleotide polymorphisms within six regions of the nuclear genome that differentiate blue-winged warblers and golden-winged warblers (Vermivora chrysoptera), the hybrid had roughly equal ancestry assignment to blue-winged and cerulean warblers, suggesting a blue-winged warbler as the paternal parent species and demonstrating that this was a first generation (F1) hybrid between these species. Unlike other recently characterized intergeneric warbler hybrids, this individual hybrid learned to song match its maternal parent species, suggesting that it might have been the result of an extra-pair mating and raised in a cerulean warbler nest.
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Affiliation(s)
- David P L Toews
- Department of Biology, Pennsylvania State University, State College, PA, USA
| | - Gunnar R Kramer
- Department of Environmental Sciences, University of Toledo, Toledo, OH, USA
| | | | | | - Benjamin E Cloud
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - David E Andersen
- US Geological Survey, Minnesota Cooperative Fish and Wildlife Research Unit, University of Minnesota, St Paul, MN, USA
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Henry Streby
- Department of Environmental Sciences, University of Toledo, Toledo, OH, USA
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18
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Shang H, Hess J, Pickup M, Field DL, Ingvarsson PK, Liu J, Lexer C. Evolution of strong reproductive isolation in plants: broad-scale patterns and lessons from a perennial model group. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190544. [PMID: 32654641 DOI: 10.1098/rstb.2019.0544] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many recent studies have addressed the mechanisms operating during the early stages of speciation, but surprisingly few studies have tested theoretical predictions on the evolution of strong reproductive isolation (RI). To help address this gap, we first undertook a quantitative review of the hybrid zone literature for flowering plants in relation to reproductive barriers. Then, using Populus as an exemplary model group, we analysed genome-wide variation for phylogenetic tree topologies in both early- and late-stage speciation taxa to determine how these patterns may be related to the genomic architecture of RI. Our plant literature survey revealed variation in barrier complexity and an association between barrier number and introgressive gene flow. Focusing on Populus, our genome-wide analysis of tree topologies in speciating poplar taxa points to unusually complex genomic architectures of RI, consistent with earlier genome-wide association studies. These architectures appear to facilitate the 'escape' of introgressed genome segments from polygenic barriers even with strong RI, thus affecting their relationships with recombination rates. Placed within the context of the broader literature, our data illustrate how phylogenomic approaches hold great promise for addressing the evolution and temporary breakdown of RI during late stages of speciation. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.
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Affiliation(s)
- Huiying Shang
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria.,Helmholtz Centre for Environmental Research, Halle (Saale), Germany
| | - Melinda Pickup
- Institute of Science and Technology (IST), Klosterneuburg, Austria
| | - David L Field
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria.,Edith Cowan University, Perth, Australia
| | - Pär K Ingvarsson
- Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science, Sichuan University, Chengdu, People's Republic of China
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030 Vienna, Austria
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19
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Rivera-Colón AG, Westerman EL, Van Belleghem SM, Monteiro A, Papa R. Multiple Loci Control Eyespot Number Variation on the Hindwings of Bicyclus anynana Butterflies. Genetics 2020; 214:1059-1078. [PMID: 32019848 PMCID: PMC7153931 DOI: 10.1534/genetics.120.303059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 12/26/2020] [Indexed: 11/18/2022] Open
Abstract
The underlying genetic changes that regulate the appearance and disappearance of repeated traits, or serial homologs, remain poorly understood. One hypothesis is that variation in genomic regions flanking master regulatory genes, also known as input-output genes, controls variation in trait number, making the locus of evolution almost predictable. Another hypothesis implicates genetic variation in up- or downstream loci of master control genes. Here, we use the butterfly Bicyclus anynana, a species that exhibits natural variation in eyespot number on the dorsal hindwing, to test these two hypotheses. We first estimated the heritability of dorsal hindwing eyespot number by breeding multiple butterfly families differing in eyespot number and regressing eyespot numbers of offspring on midparent values. We then estimated the number and identity of independent genetic loci contributing to eyespot number variation by performing a genome-wide association study with restriction site-associated DNA sequencing from multiple individuals varying in number of eyespots sampled across a freely breeding laboratory population. We found that dorsal hindwing eyespot number has a moderately high heritability of ∼0.50 and is characterized by a polygenic architecture. Previously identified genomic regions involved in eyespot development, and novel ones, display high association with dorsal hindwing eyespot number, suggesting that homolog number variation is likely determined by regulatory changes at multiple loci that build the trait, and not by variation at single master regulators or input-output genes.
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Affiliation(s)
- Angel G Rivera-Colón
- Department of Evolution, Ecology, and Behavior, University of Illinois, Urbana-Champaign, Illinois 61801
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, 00925, Puerto Rico
| | - Erica L Westerman
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas 72701
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, 00925, Puerto Rico
| | - Antónia Monteiro
- Department of Biological Sciences, National University of Singapore, Singapore 117543
- Yale-NUS College, Singapore 138609
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, 00925, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, 00926, Puerto Rico
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20
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Bresadola L, Caseys C, Castiglione S, Buerkle CA, Wegmann D, Lexer C. Admixture mapping in interspecific Populus hybrids identifies classes of genomic architectures for phytochemical, morphological and growth traits. THE NEW PHYTOLOGIST 2019; 223:2076-2089. [PMID: 31104343 PMCID: PMC6771622 DOI: 10.1111/nph.15930] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 05/06/2019] [Indexed: 05/03/2023]
Abstract
The genomic architecture of functionally important traits is key to understanding the maintenance of reproductive barriers and trait differences when divergent populations or species hybridize. We conducted a genome-wide association study (GWAS) to study trait architecture in natural hybrids of two ecologically divergent Populus species. We genotyped 472 seedlings from a natural hybrid zone of Populus alba and Populus tremula for genome-wide markers from reduced representation sequencing, phenotyped the plants in common gardens for 46 phytochemical (phenylpropanoid), morphological and growth traits, and used a Bayesian polygenic model for mapping. We detected three classes of genomic architectures: traits with finite, detectable associations of genetic loci with phenotypic variation in addition to highly polygenic heritability; traits with indications for polygenic heritability only; and traits with no detectable heritability. For the first class, we identified genome regions with plausible candidate genes for phenylpropanoid biosynthesis or its regulation, including MYB transcription factors and glycosyl transferases. GWAS in natural, recombinant hybrids represent a promising step towards resolving the genomic architecture of phenotypic traits in long-lived species. This facilitates the fine-mapping and subsequent functional characterization of genes and networks causing differences in hybrid performance and fitness.
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Affiliation(s)
- Luisa Bresadola
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
| | - Céline Caseys
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Plant SciencesUniversity of California DavisOne Shields AvenueDavisCA95616USA
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’University of SalernoVia Giovanni Paolo II 13284084Fisciano, SalernoItaly
| | - C. Alex Buerkle
- Department of BotanyUniversity of Wyoming1000 E. University Ave.LaramieWY82071USA
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Swiss Institute of Bioinformatics1700FribourgSwitzerland
| | - Christian Lexer
- Department of BiologyUniversity of FribourgChemin du Musée 101700FribourgSwitzerland
- Department of Botany and Biodiversity ResearchFaculty of Life SciencesUniversity of ViennaRennweg 12A‐1030ViennaAustria
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21
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Makarova AV, Mitrofanova OV, Vakhrameev AB, Dementeva NV. Molecular-genetic bases of plumage coloring in chicken. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.499] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The color of plumage in birds is an important feature, often determining descent to a particular species or breed. It serves as a key factor in the interaction of birds with each other due to their well-developed visual perception of the surrounding world. In poultry including chickens, the color of the plumage can be treated as a genetic marker, useful for identifying breeds, populations and breeding groups with their specific traits. The origin of diverse color plumage is the result of two interrelated physical processes, chemical and optical, due to which pigment and structural colors in the color are formed. The pigment melanin, which is presented in two forms, eumelanin and pheomelanin, is widely spread in birds. The basis for the formation of melanin is the aromatic amino acid tyrosine. The process of melano-genesis involves many loci, part of the complex expression of plumage color genes. In birds, the solid black color locus encodes the melanocortin 1 receptor (MC1R), mutations in which lead to a change in receptor activation and form different variants of the E locus. Using the GWAS analysis, possible genes affecting the formation of color in chickens were detected. The biosynthesis and types of melanin are affected by the activity of the enzyme tyrosine, and mutations in the tyrosinase gene (TYR) cause albinism in different species. The formation mechanism of brown, silver, gold, lavender and a number of other shades is determined by the influence on the work of the MC1R genes and TYR specific modifier genes. Thus, locus I currently associated with the PMEL17 gene inhibits the expression of eumelanin, and the MLPH gene affects tyrosinase function. Research on the mechanisms of formation of the secondary coloring of plumage in chickens is being actively conducted nowadays. The formation of a marble feather pattern is associated with the mutation of the endothelin B2 receptor (EDNRB2), in the coding part of the gene of which a polymorphism is found associated with the mo locus. The molecular base that causes the feather banding (locus B and autosomal recessive banding) is identified. Today, only some genes that determine the color of the plumage of chickens are studied and described. Different genes can produce similar plumage patterns, and different phenotypes can be determined by the polymorphism of a single gene. Using molecular methods, you can more accurately identify these differences. This overview shows the nature of melanin coloration in birds using the example of chickens of various breeds and also attempts to systematize knowledge about the molecular-genetic mechanisms of the appearance of various types of coloration.
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Affiliation(s)
- A. V. Makarova
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
| | - O. V. Mitrofanova
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
| | - A. B. Vakhrameev
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
| | - N. V. Dementeva
- Russian Research Institute of Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry
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22
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Brennan RS, Healy TM, Bryant HJ, La MV, Schulte PM, Whitehead A. Integrative Population and Physiological Genomics Reveals Mechanisms of Adaptation in Killifish. Mol Biol Evol 2018; 35:2639-2653. [PMID: 30102365 PMCID: PMC11325861 DOI: 10.1093/molbev/msy154] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Adaptive divergence between marine and freshwater (FW) environments is important in generating phyletic diversity within fishes, but the genetic basis of this process remains poorly understood. Genome selection scans can identify adaptive loci, but incomplete knowledge of genotype-phenotype connections makes interpreting their significance difficult. In contrast, association mapping (genome-wide association mapping [GWAS], random forest [RF] analyses) links genotype to phenotype, but offer limited insight into the evolutionary forces shaping variation. Here, we combined GWAS, RF, and selection scans to identify loci important in adaptation to FW environments. We utilized FW-native and brackish water (BW)-native populations of Atlantic killifish (Fundulus heteroclitus) as well as a naturally admixed population between the two. We measured morphology and multiple physiological traits that differ between populations and may contribute to osmotic adaptation (salinity tolerance, hypoxia tolerance, metabolic rate, body shape) and used a reduced representation approach for genome-wide genotyping. Our results show patterns of population divergence in physiological capabilities that are consistent with local adaptation. Population genomic scans between BW-native and FW-native populations identified genomic regions evolving by natural selection, whereas association mapping revealed loci that contribute to variation for each trait. There was substantial overlap in the genomic regions putatively under selection and loci associated with phenotypic traits, particularly for salinity tolerance, suggesting that these regions and genes are important for adaptive divergence between BW and FW environments. Together, these data provide insight into the mechanisms that enable diversification of fishes across osmotic boundaries.
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Affiliation(s)
- Reid S Brennan
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
- Department of Biology, University of Vermont, Burlington, VT
| | - Timothy M Healy
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, CA
| | - Heather J Bryant
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Man Van La
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
| | - Patricia M Schulte
- Department of Zoology, The University of British Columbia, Vancouver, BC, Canada
| | - Andrew Whitehead
- Department of Environmental Toxicology, University of California-Davis, Davis, CA
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23
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Irwin DE, Milá B, Toews DPL, Brelsford A, Kenyon HL, Porter AN, Grossen C, Delmore KE, Alcaide M, Irwin JH. A comparison of genomic islands of differentiation across three young avian species pairs. Mol Ecol 2018; 27:4839-4855. [PMID: 30187980 DOI: 10.1111/mec.14858] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/10/2018] [Accepted: 07/14/2018] [Indexed: 02/06/2023]
Abstract
Detailed evaluations of genomic variation between sister species often reveal distinct chromosomal regions of high relative differentiation (i.e., "islands of differentiation" in FST ), but there is much debate regarding the causes of this pattern. We briefly review the prominent models of genomic islands of differentiation and compare patterns of genomic differentiation in three closely related pairs of New World warblers with the goal of evaluating support for the four models. Each pair (MacGillivray's/mourning warblers; Townsend's/black-throated green warblers; and Audubon's/myrtle warblers) consists of forms that were likely separated in western and eastern North American refugia during cycles of Pleistocene glaciations and have now come into contact in western Canada, where each forms a narrow hybrid zone. We show strong differences between pairs in their patterns of genomic heterogeneity in FST , suggesting differing selective forces and/or differing genomic responses to similar selective forces among the three pairs. Across most of the genome, levels of within-group nucleotide diversity (πWithin ) are almost as large as levels of between-group nucleotide distance (πBetween ) within each pair, suggesting recent common ancestry and/or gene flow. In two pairs, a pattern of the FST peaks having low πBetween suggests that selective sweeps spread between geographically differentiated groups, followed by local differentiation. This "sweep-before-differentiation" model is consistent with signatures of gene flow within the yellow-rumped warbler species complex. These findings add to our growing understanding of speciation as a complex process that can involve phases of adaptive introgression among partially differentiated populations.
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Affiliation(s)
- Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Cornell Lab of Ornithology & Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Alan Brelsford
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Evolution, Ecology and Organismal Biology, University of California, Riverside, California
| | - Haley L Kenyon
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biology, Queen's University, Biosciences Complex, Kingston, Ontario, Canada
| | - Alison N Porter
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christine Grossen
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Kira E Delmore
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Max Planck Institute for Evolutionary Biology, Behavioural Genomics, Plön, Germany
| | - Miguel Alcaide
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jessica H Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Dissection by genomic and plumage variation of a geographically complex hybrid zone between two Australian non-sister parrot species, Platycercus adscitus and Platycercus eximius. Heredity (Edinb) 2018; 122:402-416. [PMID: 30082918 PMCID: PMC6460760 DOI: 10.1038/s41437-018-0127-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 06/23/2018] [Accepted: 06/27/2018] [Indexed: 01/27/2023] Open
Abstract
The study of hybrid zones advances understanding of the speciation process, and approaches incorporating genomic data are increasingly used to draw significant conclusions about the impact of hybridisation. Despite the progress made, the complex interplay of factors that can lead to substantially variable hybridisation outcomes are still not well understood, and many systems and/or groups remain comparatively poorly studied. Our study aims to broaden the literature on avian hybrid zones, investigating a potentially geographically and temporally complex putative hybrid zone between two native Australian non-sister parrot species, the pale-headed and eastern rosellas (Platycercus adscitus and Platycercus eximius, respectively). We analysed six plumage traits and >1400 RADseq loci and detected hybrid individuals and an unexpectedly complex geographic structure. The hybrid zone is larger than previously described due to either observer bias or its movement over recent decades. It comprises different subregions where genetic and plumage signals of admixture vary markedly in their concordance. Evidence of contemporary hybridisation (later generation and backcrossed individuals) both within and beyond the previously defined zone, when coupled with a lack of F1 hybrids and differential patterns of introgression among potentially diagnostic loci, indicates a lack of post-zygotic barriers to gene flow between species. Despite ongoing gene flow, species boundaries are likely maintained largely by strong pre-mating barriers. These findings are discussed in detail and future avenues for research into this system are proposed, which would be of benefit to the speciation and hybrid zone literature.
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Brelsford A, Toews DPL, Irwin DE. Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration. Proc Biol Sci 2018; 284:rspb.2017.1106. [PMID: 29118129 DOI: 10.1098/rspb.2017.1106] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/10/2017] [Indexed: 12/30/2022] Open
Abstract
Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers (Setophaga coronata auduboni/S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple single-nucleotide polymorphisms (SNPs) across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that make up feathers. A carotenoid-based trait that differs between the taxa-throat colour-had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits-colours of the eye line and eye spot-show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.
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Affiliation(s)
- Alan Brelsford
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.,Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA, 92521, USA
| | - David P L Toews
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4 .,Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Darren E Irwin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, Canada V6T 1Z4
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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