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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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Lu B, Qiu X, Yang W, Yao Z, Ma X, Deng S, Zhang Q, Fu J, Qi Y. Genetic Basis and Evolutionary Forces of Sexually Dimorphic Color Variation in a Toad-Headed Agamid Lizard. Mol Biol Evol 2024; 41:msae054. [PMID: 38466135 PMCID: PMC10963123 DOI: 10.1093/molbev/msae054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/17/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024] Open
Abstract
In the animal kingdom, sexually dimorphic color variation is a widespread phenomenon that significantly influences survival and reproductive success. However, the genetic underpinnings of this variation remain inadequately understood. Our investigation into sexually dimorphic color variation in the desert-dwelling Guinan population of the toad-headed agamid lizard (Phrynocephalus putjatai) utilized a multidisciplinary approach, encompassing phenotypic, ultrastructural, biochemical, genomic analyses, and behavioral experiments. Our findings unveil the association between distinct skin colorations and varying levels of carotenoid and pteridine pigments. The red coloration in males is determined by a genomic region on chromosome 14, housing four pigmentation genes: BCO2 and three 6-pyruvoyltetrahydropterin synthases. A Guinan population-specific nonsynonymous single nucleotide polymorphism in BCO2 is predicted to alter the electrostatic potential within the binding domain of the BCO2-β-carotene complex, influencing their interaction. Additionally, the gene MAP7 on chromosome 2 emerges as a potential contributor to the blue coloration in subadults and adult females. Sex-specific expression patterns point to steroid hormone-associated genes (SULT2B1 and SRD5A2) as potential upstream regulators influencing sexually dimorphic coloration. Visual modeling and field experiments support the potential selective advantages of vibrant coloration in desert environments. This implies that natural selection, potentially coupled with assortative mating, might have played a role in fixing color alleles, contributing to prevalence in the local desert habitat. This study provides novel insights into the genetic basis of carotenoid and pteridine-based color variation, shedding light on the evolution of sexually dimorphic coloration in animals. Moreover, it advances our understanding of the driving forces behind such intricate coloration patterns.
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Affiliation(s)
- Bin Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Xia Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
- College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Weizhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Zhongyi Yao
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Xiaofeng Ma
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Shunyan Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Qi Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
| | - Jinzhong Fu
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
- Department of Integrative Biology, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Yin Qi
- Chengdu Institute of Biology, Chinese Academy of Sciences, 610041 Chengdu, Sichuan, China
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3
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Sun X, Guo J, Li R, Zhang H, Zhang Y, Liu GE, Emu Q, Zhang H. Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep. Animals (Basel) 2024; 14:444. [PMID: 38338087 PMCID: PMC10854784 DOI: 10.3390/ani14030444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 01/12/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2-an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10-16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS.
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Affiliation(s)
- Xueliang Sun
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiazhong Guo
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Huanhuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yifei Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Quzhe Emu
- Animal Genetics and Breeding Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, No. 7, Niusha Road, Chengdu 610066, China
| | - Hongping Zhang
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (X.S.); (J.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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4
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Elkin J, Martin A, Courtier-Orgogozo V, Santos ME. Analysis of the genetic loci of pigment pattern evolution in vertebrates. Biol Rev Camb Philos Soc 2023; 98:1250-1277. [PMID: 37017088 DOI: 10.1111/brv.12952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.
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Affiliation(s)
- Joel Elkin
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, 800 22nd St. NW, Suite 6000, Washington, DC, 20052, USA
| | | | - M Emília Santos
- Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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5
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Machkour-M’Rabet S, Santamaría-Rivero W, Dzib-Chay A, Torres Cristiani L, MacKinnon-Haskins B. Multi-character approach reveals a new mangrove population of the Yellow Warbler complex, Setophaga petechia, on Cozumel Island, Mexico. PLoS One 2023; 18:e0287425. [PMID: 37347741 PMCID: PMC10287016 DOI: 10.1371/journal.pone.0287425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
The Setophaga petechia complex includes 43 subspecies distributed within the new world, of which some are migratory and others are resident, with only two resident subspecies in the Mexican Caribbean: Setophaga petechia bryanti a mangrove subspecies belonging to the erithachorides group resident on the mainland of the Yucatan Peninsula and Setophaga petechia rufivertex endemic to Cozumel Island and belonging to the petechia group. Recently, a new population of individuals presenting intermediate phenotypic traits and living in mangrove ecosystems was discovered and reported for Cozumel Island. In this study, we used a multi-character approach including genetic (five ISSR genetic markers), morphometric (eight traits), phenotypic (four characteristics of males), and acoustic dataset (11 parameters) to understand the process of differentiation and the status of these new island individuals in relation to the two well-established subspecies using a total of 60 individuals (20 for each group). Through multivariate analyses based on different dataset used in our study, we show how the new population is related to the endemic island subspecies, S. p. rufivertex and to the mainland subspecies, S. p. bryanti while demonstrating finite differences. We conclude that the new population of S. petechia on Cozumel Island is a well-established population with high level of differentiation.
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Affiliation(s)
- Salima Machkour-M’Rabet
- Laboratorio de Ecología Molecular y Conservación, Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur (ECOSUR), Chetumal, Quintana Roo, México
| | | | | | - Leopoldo Torres Cristiani
- Laboratorio de Ecología Molecular y Conservación, Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur (ECOSUR), Chetumal, Quintana Roo, México
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6
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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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7
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Cheng H, Zhang Z, Wen J, Lenstra JA, Heller R, Cai Y, Guo Y, Li M, Li R, Li W, He S, Wang J, Shao J, Song Y, Zhang L, Billah M, Wang X, Liu M, Jiang Y. Long divergent haplotypes introgressed from wild sheep are associated with distinct morphological and adaptive characteristics in domestic sheep. PLoS Genet 2023; 19:e1010615. [PMID: 36821549 PMCID: PMC9949681 DOI: 10.1371/journal.pgen.1010615] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/13/2023] [Indexed: 02/24/2023] Open
Abstract
The worldwide sheep population comprises more than 1000 breeds. Together, these exhibit a considerable morphological diversity, which has not been extensively investigated at the molecular level. Here, we analyze whole-genome sequencing individuals of 1,098 domestic sheep from 154 breeds, and 69 wild sheep from seven Ovis species. On average, we detected 6.8%, 1.0% and 0.2% introgressed sequence in domestic sheep originating from Iranian mouflon, urial and argali, respectively, with rare introgressions from other wild species. Interestingly, several introgressed haplotypes contributed to the morphological differentiations across sheep breeds, such as a RXFP2 haplotype from Iranian mouflon conferring the spiral horn trait, a MSRB3 haplotype from argali strongly associated with ear morphology, and a VPS13B haplotype probably originating from urial and mouflon possibly associated with facial traits. Our results reveal that introgression events from wild Ovis species contributed to the high rate of morphological differentiation in sheep breeds, but also to individual variation within breeds. We propose that long divergent haplotypes are a ubiquitous source of phenotypic variation that allows adaptation to a variable environment, and that these remain intact in the receiving population probably due to reduced recombination.
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Affiliation(s)
- Hong Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiayue Wen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wenrong Li
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Sangang He
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
| | - Jintao Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Junjie Shao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yuxuan Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Masum Billah
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Mingjun Liu
- Key Laboratory of Ruminant Genetics, Breeding & Reproduction, Ministry of Agriculture, China
- Key Laboratory of Animal Biotechnology of Xinjiang, Institute of Biotechnology, Xinjiang Academy of Animal Science, Urumqi, Xinjiang, China
- * E-mail: (ML); (YJ)
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- * E-mail: (ML); (YJ)
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8
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Baiz MD, Benavides C A, Miller ET, Wood AW, Toews DPL. Gut microbiome composition better reflects host phylogeny than diet diversity in breeding wood-warblers. Mol Ecol 2023; 32:518-536. [PMID: 36325817 DOI: 10.1111/mec.16762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
Understanding the factors that shape microbiomes can provide insight into the importance of host-symbiont interactions and on co-evolutionary dynamics. Unlike for mammals, previous studies have found little or no support for an influence of host evolutionary history on avian gut microbiome diversity and instead have suggested a greater influence of the environment or diet due to fast gut turnover. Because effects of different factors may be conflated by captivity and sampling design, examining natural variation using large sample sizes is important. Our goal was to overcome these limitations by sampling wild birds to compare environmental, dietary and evolutionary influences on gut microbiome structure. We performed faecal metabarcoding to characterize both the gut microbiome and diet of 15 wood-warbler species across a 4-year period and from two geographical localities. We find host taxonomy generally explained ~10% of the variation between individuals, which is ~6-fold more variation of any other factor considered, including diet diversity. Further, gut microbiome similarity was more congruent with the host phylogeny than with host diet similarity and we found little association between diet diversity and microbiome diversity. Together, our results suggest evolutionary history is the strongest predictor of gut microbiome differentiation among wood-warblers. Although the phylogenetic signal of the warbler gut microbiome is not very strong, our data suggest that a stronger influence of diet (as measured by diet diversity) does not account for this pattern. The mechanism underlying this phylogenetic signal is not clear, but we argue host traits may filter colonization and maintenance of microbes.
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Affiliation(s)
- Marcella D Baiz
- Department of Biology, Pennylvania State University, University Park, Pennsylvania, USA
| | - Andrea Benavides C
- Department of Biology, Pennylvania State University, University Park, Pennsylvania, USA
| | | | - Andrew W Wood
- Department of Biology, Pennylvania State University, University Park, Pennsylvania, USA
| | - David P L Toews
- Department of Biology, Pennylvania State University, University Park, Pennsylvania, USA
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9
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Campagna L, Toews DP. The genomics of adaptation in birds. Curr Biol 2022; 32:R1173-R1186. [DOI: 10.1016/j.cub.2022.07.076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Toews DPL, Rhinehart TA, Mulvihill R, Galen S, Gosser SM, Johnson T, Williamson JL, Wood AW, Latta SC. Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose-breasted grosbeak ( Pheucticus ludovicianus) and a scarlet tanager ( Piranga olivacea). Ecol Evol 2022; 12:e9152. [PMID: 35928797 PMCID: PMC9343856 DOI: 10.1002/ece3.9152] [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: 02/03/2022] [Revised: 06/26/2022] [Accepted: 07/07/2022] [Indexed: 12/04/2022] Open
Abstract
Using low‐coverage whole‐genome sequencing, analysis of vocalizations, and inferences from natural history, we document a first‐generation hybrid between a rose‐breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). These two species occur sympatrically throughout much of eastern North America, although were not previously known to interbreed. Following the field identification of a putative hybrid, we use genetic and bioacoustic data to show that a rose‐breasted grosbeak was the maternal parent and a scarlet tanager was the paternal parent of the hybrid, whose song was similar to the latter species. These two species diverged >10 million years ago, and thus it is surprising to find a hybrid formed under natural conditions in the wild. Notably, the hybrid has an exceptionally heterozygous genome, with a conservative estimate of a heterozygous base every 100 bp. The observation that this hybrid of such highly divergent parental taxa has survived until adulthood serves as another example of the capacity for hybrid birds to survive with an exceptionally divergent genomic composition.
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Affiliation(s)
- David P L Toews
- Department of Biology, 619 Mueller Laboratory Pennsylvania State University University Park Pennsylvania USA
| | - Tessa A Rhinehart
- Department of Biological Sciences University of Pittsburgh Pittsburgh Pennsylvania USA
| | - Robert Mulvihill
- Department of Conservation and Field Research National Aviary Pittsburgh Pennsylvania USA
| | - Spencer Galen
- Biology Department University of Scranton Scranton Pennsylvania USA
| | | | - Tom Johnson
- The Academy of Natural Sciences of Drexel University Philadelphia Pennsylvania USA
| | - Jessie L Williamson
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque New Mexico USA
| | - Andrew W Wood
- Department of Biology, 619 Mueller Laboratory Pennsylvania State University University Park Pennsylvania USA
| | - Steven C Latta
- Department of Conservation and Field Research National Aviary Pittsburgh Pennsylvania USA
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11
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Minor NR, Dougherty PJ, Taylor SA, Carling MD. Estimating hybridization in the wild using citizen science data: a path forward. Evolution 2021; 76:362-372. [PMID: 34708408 DOI: 10.1111/evo.14392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/15/2021] [Accepted: 09/19/2021] [Indexed: 11/28/2022]
Abstract
Genomic evidence of introgression in natural populations has reinvigorated the study of hybridization in recent years. Still, it is largely unknown how frequently individual organisms mate across species lines. Recently, Justyn et al. 2020 suggested that eBird, one of the world's largest citizen science databases, may supply adequate data for estimating hybridization rates. Here, we compare Justyn et al.'s estimates-and their conclusions that hybridization is rare-with estimates from museum and molecular data. We also estimate hybridization using eBird observations from areas and times when hybridization is possible, namely, in contact zones during the breeding season. These estimates are all considerably higher than those reported in Justyn et al., emphasizing that inferences from multiple datasets can differ radically. Finally, we demonstrate an approach for predicting the location of hybrid zones using eBird data, which can be done with high confidence and with unprecedented resolution. We show that citizen science data, far from settling the question of how frequently bird species hybridize, instead offer a promising step toward more focused study of hybrid zones. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nicholas R Minor
- University of Wyoming Department of Zoology & Physiology.,University of Wyoming Museum of Vertebrates
| | - Paul J Dougherty
- University of Wyoming Department of Zoology & Physiology.,University of Wyoming Program in Ecology.,University of Wyoming Museum of Vertebrates
| | | | - Matthew D Carling
- University of Wyoming Department of Zoology & Physiology.,University of Wyoming Program in Ecology.,University of Wyoming Museum of Vertebrates
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12
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Enbody ED, Sprehn CG, Abzhanov A, Bi H, Dobreva MP, Osborne OG, Rubin CJ, Grant PR, Grant BR, Andersson L. A multispecies BCO2 beak color polymorphism in the Darwin's finch radiation. Curr Biol 2021; 31:5597-5604.e7. [PMID: 34687609 DOI: 10.1016/j.cub.2021.09.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/25/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Carotenoid-based polymorphisms are widespread in populations of birds, fish, and reptiles,1 but generally little is known about the factors affecting their maintenance in populations.2 We report a combined field and molecular-genetic investigation of a nestling beak color polymorphism in Darwin's finches. Beaks are pink or yellow, and yellow is recessive.3 Here we show that the polymorphism arose in the Galápagos half a million years ago through a mutation associated with regulatory change in the BCO2 gene and is shared by 14 descendant species. The polymorphism is probably a balanced polymorphism, maintained by ecological selection associated with survival and diet. In cactus finches, the frequency of the yellow genotype is correlated with cactus fruit abundance and greater hatching success and may be altered by introgressive hybridization. Polymorphisms that are hidden as adults, as here, may be far more common than is currently recognized, and contribute to diversification in ways that are yet to be discovered.
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Affiliation(s)
- Erik D Enbody
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.
| | - C Grace Sprehn
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Arhat Abzhanov
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Huijuan Bi
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Mariya P Dobreva
- Department of Life Sciences, Imperial College London, Silwood Park Campus, SL5 7PY Ascot, UK
| | - Owen G Osborne
- School of Natural Sciences, Bangor University, Environment Centre Wales, Deiniol Road, Bangor LL57 2UW, UK
| | - Carl-Johan Rubin
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - B Rosemary Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Leif Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden; Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843-4458, USA.
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13
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Wang S, Ore MJ, Mikkelsen EK, Lee-Yaw J, Toews DPL, Rohwer S, Irwin D. Signatures of mitonuclear coevolution in a warbler species complex. Nat Commun 2021; 12:4279. [PMID: 34257313 PMCID: PMC8277850 DOI: 10.1038/s41467-021-24586-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
Divergent mitonuclear coadaptation could facilitate speciation. We investigate this possibility in two hybridizing species of warblers, Setophaga occidentalis and S. townsendi, in western North America. Inland S. townsendi harbor distinct mitochondrial DNA haplotypes from those of S. occidentalis. These populations also differ in several nuclear DNA regions. Coastal S. townsendi demonstrate mixed mitonuclear ancestry from S. occidentalis and inland S. townsendi. Of the few highly-differentiated chromosomal regions between inland S. townsendi and S. occidentalis, a 1.2 Mb gene block on chromosome 5 is also differentiated between coastal and inland S. townsendi. Genes in this block are associated with fatty acid oxidation and energy-related signaling transduction, thus linked to mitochondrial functions. Genetic variation within this candidate gene block covaries with mitochondrial DNA and shows signatures of divergent selection. Spatial variation in mitonuclear ancestries is correlated with climatic conditions. Together, these observations suggest divergent mitonuclear coadaptation underpins cryptic differentiation in this species complex.
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Affiliation(s)
- Silu Wang
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada.
- Department of Integrative Biology, University of California, Berkeley, CA, USA.
| | - Madelyn J Ore
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
- Cornell Lab of Ornithology, Ithaca, NY, USA
| | - Else K Mikkelsen
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Julie Lee-Yaw
- Department of Botany, 3200-6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
- Biological Sciences, 4401 University Drive, University of Lethbridge, Lethbridge, AB, Canada
| | - David P L Toews
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sievert Rohwer
- Department of Biology and Burke Museum, Box 353010, University of Washington, Seattle, WA, USA
| | - Darren Irwin
- Department of Zoology, and Biodiversity Research Centre, 6270 University Blvd, University of British Columbia, Vancouver, BC, Canada
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14
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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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15
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Baiz MD, Wood AW, Toews DPL. Rare hybrid solves "genetic problem" of linked plumage traits. Ecology 2021; 102:e03424. [PMID: 34086359 DOI: 10.1002/ecy.3424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 12/23/2020] [Accepted: 03/21/2021] [Indexed: 11/10/2022]
Affiliation(s)
- Marcella D Baiz
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Andrew W Wood
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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16
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Szarmach SJ, Brelsford A, Witt CC, Toews DPL. Comparing divergence landscapes from reduced-representation and whole genome resequencing in the yellow-rumped warbler (Setophaga coronata) species complex. Mol Ecol 2021; 30:5994-6005. [PMID: 33934424 DOI: 10.1111/mec.15940] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/23/2021] [Accepted: 04/19/2021] [Indexed: 12/01/2022]
Abstract
Researchers seeking to generate genomic data for non-model organisms are faced with a number of trade-offs when deciding which method to use. The selection of reduced representation approaches versus whole genome resequencing will ultimately affect the marker density, sequencing depth, and the number of individuals that can multiplexed. These factors can affect researchers' ability to accurately characterize certain genomic features, such as landscapes of divergence-how FST varies across the genomes. To provide insight into the effect of sequencing method on the estimation of divergence landscapes, we applied an identical bioinformatic pipeline to three generations of sequencing data (GBS, ddRAD, and WGS) produced for the same system, the yellow-rumped warbler species complex. We compare divergence landscapes generated using each method for the myrtle warbler (Setophaga coronata coronata) and the Audubon's warbler (S. c. auduboni), and for Audubon's warblers with deeply divergent mtDNA resulting from mitochondrial introgression. We found that most high-FST peaks were not detected in the ddRAD data set, and that while both GBS and WGS were able to identify the presence of large peaks, WGS was superior at a finer scale. Comparing Audubon's warblers with divergent mitochondrial haplotypes, only WGS allowed us to identify small (10-20 kb) regions of elevated differentiation, one of which contained the nuclear-encoded mitochondrial gene NDUFAF3. We calculated the cost per base pair for each method and found it was comparable between GBS and WGS, but significantly higher for ddRAD. These comparisons highlight the advantages of WGS over reduced representation methods when characterizing landscapes of divergence.
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Affiliation(s)
| | - Alan Brelsford
- Evolution, Ecology, and Organismal Biology Department, University of California Riverside, Riverside, CA, USA
| | - Christopher C Witt
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, New Mexico, USA
| | - David P L Toews
- Department of Biology, Pennsylvania State University, University Park, PA, USA
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17
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Dog colour patterns explained by modular promoters of ancient canid origin. Nat Ecol Evol 2021; 5:1415-1423. [PMID: 34385618 PMCID: PMC8484016 DOI: 10.1038/s41559-021-01524-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023]
Abstract
Distinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.
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