1
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Kenyon HL, Martin PR. Color as an Interspecific Badge of Status: A Comparative Test. Am Nat 2023; 202:433-447. [PMID: 37792917 DOI: 10.1086/725916] [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] [Indexed: 10/06/2023]
Abstract
AbstractAnimals as diverse as cephalopods, insects, fish, and mammals signal social dominance to conspecifics to avoid costly fights. Even though between-species fights may be equally costly, the extent to which dominance signals are used between species is unknown. Here, we test the hypothesis that differences in color are associated with dominance between closely related species that aggressively interact over resources, examining between-species variation in colors that are used in within-species badges of status (black, white, and carotenoid coloration) in a comparative analysis of diverse species of birds. We found that dominant species have more black, on average, than subordinate species, particularly in regions important for aggressive signaling (face, throat, and bill). Furthermore, dominant species were more likely to have more black in comparisons in which the dominant species was similar in size or smaller than the subordinate, suggesting that black may be a more important signal when other signals of dominance (size) are missing. Carotenoid colors (i.e., red, pink, orange, and yellow) were not generally associated with dominance but may signal dominance in some taxonomic groups. White may have opposing functions: white was associated with dominance in species in which black was also associated with dominance but was associated with subordinance in species in which carotenoid-based dominance signals may be used. Overall, these results provide new evidence that colors may function broadly as signals of dominance among competing species. Such signals could help to mediate aggressive interactions among species, thereby reducing some costs of co-occurrence and facilitating coexistence in nature.
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2
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Wood AW, Szpiech ZA, Lovette IJ, Smith BT, Toews DPL. Genomes of the extinct Bachman's warbler show high divergence and no evidence of admixture with other extant Vermivora warblers. Curr Biol 2023:S0960-9822(23)00690-5. [PMID: 37329885 DOI: 10.1016/j.cub.2023.05.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 06/19/2023]
Abstract
Bachman's warbler1 (Vermivora bachmanii)-last sighted in 1988-is one of the only North American passerines to recently go extinct.2,3,4 Given extensive ongoing hybridization of its two extant congeners-the blue-winged warbler (V. cyanoptera) and golden-winged warbler (V. chrysoptera)5,6,7,8-and shared patterns of plumage variation between Bachman's warbler and hybrids between those extant species, it has been suggested that Bachman's warbler might have also had a component of hybrid ancestry. Here, we use historic DNA (hDNA) and whole genomes of Bachman's warblers collected at the turn of the 20th century to address this. We combine these data with the two extant Vermivora species to examine patterns of population differentiation, inbreeding, and gene flow. In contrast to the admixture hypothesis, the genomic evidence is consistent with V. bachmanii having been a highly divergent, reproductively isolated species, with no evidence of introgression. We show that these three species have similar levels of runs of homozygosity (ROH), consistent with effects of a small long-term effective population size or population bottlenecks, with one V. bachmanii outlier showing numerous long ROH and a FROH greater than 5%. We also found-using population branch statistic estimates-previously undocumented evidence of lineage-specific evolution in V. chrysoptera near a pigmentation gene candidate, CORIN, which is a known modifier of ASIP, which is in turn involved in melanic throat and mask coloration in this family of birds. Together, these genomic results also highlight how natural history collections are such invaluable repositories of information about extant and extinct species.
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Affiliation(s)
- Andrew W Wood
- Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA; Institute for Computational and Data Sciences, Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, 619 Mueller Laboratory, University Park, State College, PA 16802, USA.
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3
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Walsh J, Billerman SM, Butcher BG, Rohwer VG, Toews DPL, Vila-Coury V, Lovette IJ. A complex genomic architecture underlies reproductive isolation in a North American oriole hybrid zone. Commun Biol 2023; 6:154. [PMID: 36747071 PMCID: PMC9902562 DOI: 10.1038/s42003-023-04532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 01/26/2023] [Indexed: 02/08/2023] Open
Abstract
Natural hybrid zones provide powerful opportunities for identifying the mechanisms that facilitate and inhibit speciation. Documenting the extent of genomic admixture allows us to discern the architecture of reproductive isolation through the identification of isolating barriers. This approach is particularly powerful for characterizing the accumulation of isolating barriers in systems exhibiting varying levels of genomic divergence. Here, we use a hybrid zone between two species-the Baltimore (Icterus galbula) and Bullock's (I. bullockii) orioles-to investigate this architecture of reproductive isolation. We combine whole genome re-sequencing with data from an additional 313 individuals amplityped at ancestry-informative markers to characterize fine-scale patterns of admixture, and to quantify links between genes and the plumage traits. On a genome-wide scale, we document several putative barriers to reproduction, including elevated peaks of divergence above a generally high genomic baseline, a large putative inversion on the Z chromosome, and complex interactions between melanogenesis-pathway candidate genes. Concordant and coincident clines for these different genomic regions further suggest the coupling of pre- and post-mating barriers. Our findings of complex and coupled interactions between pre- and post-mating barriers suggest a relatively rapid accumulation of barriers between these species, and they demonstrate the complexities of the speciation process.
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Affiliation(s)
- Jennifer Walsh
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA.
| | - Shawn M Billerman
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Bronwyn G Butcher
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Vanya G Rohwer
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - David P L Toews
- Department of Biology, Penn State University, University Park, Pennsylvania, USA
| | - Vicens Vila-Coury
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
| | - Irby J Lovette
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, NY, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
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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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Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, Christmas MJ, Huang Y, Maldonado-Linares A, Puigcerver M, Jiménez-Blasco I, Andrade P, Gonçalves D, Friis G, Roig I, Webster MT, Leonard JA, Vilà C. Massive genome inversion drives coexistence of divergent morphs in common quails. Curr Biol 2021; 32:462-469.e6. [PMID: 34847353 DOI: 10.1016/j.cub.2021.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats,1,2 and whose females may lay successive clutches at different locations while migrating.3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jiménez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.
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Affiliation(s)
- Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain.
| | - Sara Ravagni
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - J Domingo Rodríguez-Teijeiro
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Andros Maldonado-Linares
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manel Puigcerver
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Jiménez-Blasco
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - David Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Guillermo Friis
- Center for Genomics and Systems Biology, New York University-Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain.
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6
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Kulikova IV. Molecular Mechanisms and Gene Regulation of Melanic Plumage Coloration in Birds. RUSS J GENET+ 2021. [DOI: 10.1134/s102279542108007x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Shi X, Wu J, Lang X, Wang C, Bai Y, Riley DG, Liu L, Ma X. Comparative transcriptome and histological analyses provide insights into the skin pigmentation in Minxian black fur sheep (Ovis aries). PeerJ 2021; 9:e11122. [PMID: 33986980 PMCID: PMC8086576 DOI: 10.7717/peerj.11122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/25/2021] [Indexed: 12/30/2022] Open
Abstract
Background Minxian black fur (MBF) sheep are found in the northwestern parts of China. These sheep have developed several special traits. Skin color is a phenotype subject to strong natural selection and diverse skin colors are likely a consequence of differences in gene regulation. Methods Skin structure, color differences, and gene expression (determined by RNA sequencing) were evaluated the Minxian black fur and Small-tail Han sheep (n = 3 each group), which are both native Chinese sheep breeds. Results Small-tail Han sheep have a thicker skin and dermis than the Minxian black fur sheep (P < 0.01); however, the quantity of melanin granules is greater (P < 0.01) in Minxian black fur sheep with a more extensive distribution in skin tissue and hair follicles. One hundred thirty-three differentially expressed genes were significantly associated with 37 ontological terms and two critical KEGG pathways for pigmentation (“tyrosine metabolism” and “melanogenesis” pathways). Important genes from those pathways with known involvement in pigmentation included OCA2 melanosomal transmembrane protein (OCA2), dopachrome tautomerase (DCT), tyrosinase (TYR) and tyrosinase related protein (TYRP1), melanocortin 1 receptor (MC1R), and premelanosome protein (PMEL). The results from our histological and transcriptome analyses will form a foundation for additional investigation into the genetic basis and regulation of pigmentation in these sheep breeds.
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Affiliation(s)
- Xiaolei Shi
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Jianping Wu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - Xia Lang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Cailian Wang
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China.,Key Laboratory for Sheep, Goat, and Cattle Germplasm and Straw Feed in Gansu Province, Lanzhou, Gansu Province, China
| | - Yan Bai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
| | - David Greg Riley
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - Lishan Liu
- Animal Husbandry, Pasture, and Green Agriculture Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu Province, China
| | - Xiaoming Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu Province, China
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8
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Gwee CY, Lee QL, Mahood SP, Hung Le Manh, Tizard R, Eiamampai K, Round PD, Rheindt FE. The interplay of colour and bioacoustic traits in the differentiation of a Southeast Asian songbird complex. Mol Ecol 2020; 30:297-309. [PMID: 33135269 DOI: 10.1111/mec.15718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 12/26/2022]
Abstract
Morphological traits have served generations of biologists as a taxonomic indicator, and have been the main basis for defining and classifying species diversity for centuries. A quantitative integration of behavioural characters, such as vocalizations, in studies on biotic differentiation has arisen more recently, and the relative importance of these different traits in the diversification process remains poorly understood. To provide a framework within which to interpret the evolutionary interplay between morphological and behavioural traits, we generated a draft genome of a cryptic Southeast Asian songbird, the limestone wren-babbler Napothera crispifrons. We resequenced whole genomes of multiple individuals of all three traditional subspecies and of a distinct leucistic population. We demonstrate strong genomic and mitochondrial divergence among all three taxa, pointing to the existence of three species-level lineages. Despite its great phenotypic distinctness, the leucistic population was characterized by shallow genomic differentiation from its neighbour, with only a few localized regions emerging as highly diverged. Quantitative bioacoustic analysis across multiple traits revealed deep differences especially between the two taxa characterized by limited plumage differentiation. Our study demonstrates that differentiation in these furtive songbirds has resulted in a complex mosaic of colour-based and bioacoustic differences among populations. Extreme colour differences can be anchored in few genomic loci and may therefore arise and subside rapidly.
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Affiliation(s)
- Chyi Yin Gwee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Qiao Le Lee
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Simon P Mahood
- Wildlife Conservation Society Cambodia Program, Sangkat Tonle Bassac, Phnom Penh, Cambodia.,Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, NT, Australia
| | - Hung Le Manh
- Institute of Ecology and Biological Resources, Graduated University of Science and Technology, Vietnam Academy of Science and Technology (VAST), Caugiay, Hanoi, Vietnam
| | - Robert Tizard
- Global Conservation Program, Wildlife Conservation Society, Bronx, NY, USA
| | - Krairat Eiamampai
- Wildlife Research Division, Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, Thailand
| | - Philip D Round
- Department of Biology, Faculty of Science, Mahidol University, Rachadhavi, Bangkok, Thailand
| | - Frank E Rheindt
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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9
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Dai C, Dong F, Yang X. Morphotypes or distinct species? A multilocus assessment of two East Asian scimitar babblers (Aves, Timaliidae). ZOOL SCR 2020. [DOI: 10.1111/zsc.12411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University) Ministry of Education Guilin China
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
- Guangxi Key Laboratory of Rare and Endangered Animal Ecology Guangxi Normal University Guilin China
- School of Biological Sciences Guizhou Normal College Guiyang China
| | - Feng Dong
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China
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10
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Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
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Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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11
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Walsh J, Clucas GV, MacManes MD, Thomas WK, Kovach AI. Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone. Ecol Evol 2019; 9:13477-13494. [PMID: 31871659 PMCID: PMC6912898 DOI: 10.1002/ece3.5804] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022] Open
Abstract
The role of species divergence due to ecologically based divergent selection-or ecological speciation-in generating and maintaining biodiversity is a central question in evolutionary biology. Comparison of the genomes of phylogenetically related taxa spanning a selective habitat gradient enables discovery of divergent signatures of selection and thereby provides valuable insight into the role of divergent ecological selection in speciation. Tidal marsh ecosystems provide tractable opportunities for studying organisms' adaptations to selective pressures that underlie ecological divergence. Sharp environmental gradients across the saline-freshwater ecotone within tidal marshes present extreme adaptive challenges to terrestrial vertebrates. Here, we sequence 20 whole genomes of two avian sister species endemic to tidal marshes-the saltmarsh sparrow (Ammospiza caudacutus) and Nelson's sparrow (A. nelsoni)-to evaluate the influence of selective and demographic processes in shaping genome-wide patterns of divergence. Genome-wide divergence between these two recently diverged sister species was notably high (genome-wide F ST = 0.32). Against a background of high genome-wide divergence, regions of elevated divergence were widespread throughout the genome, as opposed to focused within islands of differentiation. These patterns may be the result of genetic drift resulting from past tidal march colonization events in conjunction with divergent selection to different environments. We identified several candidate genes that exhibited elevated divergence between saltmarsh and Nelson's sparrows, including genes linked to osmotic regulation, circadian rhythm, and plumage melanism-all putative candidates linked to adaptation to tidal marsh environments. These findings provide new insights into the roles of divergent selection and genetic drift in generating and maintaining biodiversity.
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Affiliation(s)
- Jennifer Walsh
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
- Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyCornell UniversityIthacaNYUSA
- Department of Ecology and Evolutionary BiologyCornell UniversityIthacaNYUSA
| | - Gemma V. Clucas
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
- Present address:
Cornell Lab of OrnithologyIthacaNYUSA
| | - Matthew D. MacManes
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Hubbard Center for Genome StudiesDurhamNHUSA
| | - W. Kelley Thomas
- Department of Molecular, Cellular and Biomedical SciencesUniversity of New HampshireDurhamNHUSA
- Hubbard Center for Genome StudiesDurhamNHUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
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12
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Bam S, Hart L, Willows-Munro S. Mc1r genotype and plumage colouration in highly polymorphic jackal buzzards, Buteo rufofuscus. AFRICAN ZOOLOGY 2019. [DOI: 10.1080/15627020.2019.1658539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sophia Bam
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Lorinda Hart
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Sandi Willows-Munro
- School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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13
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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: 1.0] [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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14
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Wang G, Yu S, Liao J. Identification and Characterisation of Alternative Splice Variants of Hoxb9 and Their Correlation with Melanogenesis in the Black-Boned Chicken. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2019. [DOI: 10.1590/1806-9061-2018-0904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- G Wang
- Leshan Normal University, China
| | - S Yu
- Leshan Normal University, China
| | - J Liao
- Leshan Normal University, China
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15
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Yu S, Wang G, Liao J, Tang M. Transcriptome profile analysis identifies candidate genes for the melanin pigmentation of breast muscle in Muchuan black-boned chicken. Poult Sci 2018; 97:3446-3455. [PMID: 29982752 DOI: 10.3382/ps/pey238] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 06/07/2018] [Indexed: 12/28/2022] Open
Abstract
Melanin-based coloration in the meat of black-boned chicken is a major economic issue in China. Variation in the pigmentation (hypopigmentation) of chicken muscle causes direct economic losses every year. To determine the molecular mechanisms involved in the melanogenesis of muscle tissue, this study used high-throughput sequencing to compare differences in the transcriptome between black (BM) and white (WM) chicken breast muscles. We constructed 6 cDNA libraries from BM and WM groups in Muchuan black-boned chickens. A comparison between the BM and WM groups revealed 264 differentially expressed genes, of which 152 were upregulated, whereas 112 were downregulated in black muscle. Gene ontology and a Kyoto Encyclopedia of Genes and Genomes pathway analysis identified several differentially enriched biological functions and processes of the 2 muscles. Seven promising candidate genes [PMEL, Ras-related protein RAB29, and 5 solute carrier superfamily genes: SLC6A9, SLC38A4, SLC22A5, SLC35F3, and SLC16A3] may play an important role in the melanogenesis of chicken muscle. Our data provide a valuable resource for identifying genes whose functions are critical for muscle melanogenesis, and will assist studies of the molecular mechanisms of melanogenesis regulation in chicken muscle.
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Affiliation(s)
- Shigang Yu
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Gang Wang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Juan Liao
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
| | - Mei Tang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan 614000, China
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16
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Abolins-Abols M, Kornobis E, Ribeca P, Wakamatsu K, Peterson MP, Ketterson ED, Milá B. Differential gene regulation underlies variation in melanic plumage coloration in the dark-eyed junco (Junco hyemalis
). Mol Ecol 2018; 27:4501-4515. [DOI: 10.1111/mec.14878] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/22/2018] [Accepted: 09/07/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Mikus Abolins-Abols
- Department of Animal Biology; University of Illinois; Urbana Illinois
- Department of Biology; Indiana University; Bloomington Indiana
| | - Etienne Kornobis
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | | | - Kazumasa Wakamatsu
- Department of Chemistry; Fujita Health University School of Health Sciences; Toyoake Aichi Japan
| | | | | | - Borja Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
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17
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Soulsbury CD, Lipponen A, Wood K, Mein CA, Hoffman JI, Lebigre C. Age- and quality-dependent DNA methylation correlate with melanin-based coloration in a wild bird. Ecol Evol 2018; 8:6547-6557. [PMID: 30038756 PMCID: PMC6053554 DOI: 10.1002/ece3.4132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 03/16/2018] [Accepted: 03/29/2018] [Indexed: 12/11/2022] Open
Abstract
Secondary sexual trait expression can be influenced by fixed individual factors (such as genetic quality) as well as by dynamic factors (such as age and environmentally induced gene expression) that may be associated with variation in condition or quality. In particular, melanin-based traits are known to relate to condition and there is a well-characterized genetic pathway underpinning their expression. However, the mechanisms linking variable trait expression to genetic quality remain unclear. One plausible mechanism is that genetic quality could influence trait expression via differential methylation and differential gene expression. We therefore conducted a pilot study examining DNA methylation at a candidate gene (agouti-related neuropeptide: AgRP) in the black grouse Lyrurus tetrix. We specifically tested whether CpG methylation covaries with age and multilocus heterozygosity (a proxy of genetic quality) and from there whether the expression of a melanin-based ornament (ultraviolet-blue chroma) correlates with DNA methylation. Consistent with expectations, we found clear evidence for age- and heterozygosity-specific patterns of DNA methylation, with two CpG sites showing the greatest DNA methylation in highly heterozygous males at their peak age of reproduction. Furthermore, DNA methylation at three CpG sites was significantly positively correlated with ultraviolet-blue chroma. Ours is the first study to our knowledge to document age- and quality-dependent variation in DNA methylation and to show that dynamic sexual trait expression across the lifespan of an organism is associated with patterns of DNA methylation. Although we cannot demonstrate causality, our work provides empirical support for a mechanism that could potentially link key individual factors to variation in sexual trait expression in a wild vertebrate.
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Affiliation(s)
| | - Anssi Lipponen
- Department of Biological and Environmental ScienceUniversity of JyväskyläFinland
- A. I. Virtanen Institute for Molecular SciencesUniversity of Eastern FinlandKuopioFinland
| | - Kristie Wood
- The Genome Centre, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Charles A. Mein
- The Genome Centre, Barts and The London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Joseph I. Hoffman
- Department of Animal BehaviourUniversity of BielefeldBielefeldGermany
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18
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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: 5.3] [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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19
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Yu S, Liao J, Tang M, Wang Y, Wei X, Mao L, Zeng C, Wang G. A functional single nucleotide polymorphism in the tyrosinase gene promoter affects skin color and transcription activity in the black-boned chicken. Poult Sci 2017; 96:4061-4067. [DOI: 10.3382/ps/pex217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 08/22/2017] [Indexed: 12/14/2022] Open
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20
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Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160805. [PMID: 28386436 PMCID: PMC5367300 DOI: 10.1098/rsos.160805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Mathieu Gautier
- INRA, UMR 1062 CBGP (INRA, IRD, Cirad, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France
| | - Emeline Lhuillier
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- INRA, UAR1209, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Pierre-Jean G. Malé
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake Aichi 470-1192, Japan
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Claire Mould
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Jade Bruxaux
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
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