101
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Waples RS, Kays R, Fredrickson RJ, Pacifici K, Mills LS. Is the Red Wolf a Listable Unit Under the US Endangered Species Act? J Hered 2018; 109:585-597. [PMID: 29889268 PMCID: PMC6022562 DOI: 10.1093/jhered/esy020] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 05/08/2018] [Indexed: 11/12/2022] Open
Abstract
Defining units that can be afforded legal protection is a crucial, albeit challenging, step in conservation planning. As we illustrate with a case study of the red wolf (Canis rufus) from the southeastern United States, this step is especially complex when the evolutionary history of the focal taxon is uncertain. The US Endangered Species Act (ESA) allows listing of species, subspecies, or Distinct Population Segments (DPSs) of vertebrates. Red wolves were listed as an endangered species in 1973, and their status remains precarious. However, some recent genetic studies suggest that red wolves are part of a small wolf species (C. lycaon) specialized for heavily forested habitats of eastern North America, whereas other authors suggest that red wolves arose, perhaps within the last ~400 years, through hybridization between gray wolves (C. lupus) and coyotes (C. latrans). Using published genetic, morphological, behavioral, and ecological data, we evaluated whether each evolutionary hypothesis would lead to a listable unit for red wolves. Although the potential hybrid origin of red wolves, combined with abundant evidence for recent hybridization with coyotes, raises questions about status as a separate species or subspecies, we conclude that under any proposed evolutionary scenario red wolves meet both criteria to be considered a DPS: they are Discrete compared with other conspecific populations, and they are Significant to the taxon to which they belong. As population-level units can qualify for legal protection under endangered-species legislation in many countries throughout the world, this general approach could potentially be applied more broadly.
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Affiliation(s)
- Robin S Waples
- NOAA Fisheries, Northwest Fisheries Science Center, Seattle, WA
| | - Roland Kays
- Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC
- North Carolina Museum of Natural Sciences, Raleigh, NC
| | | | - Krishna Pacifici
- Department of Forestry & Environmental Resources, North Carolina State University, Raleigh, NC
| | - L Scott Mills
- Wildlife Biology Program and the Office of Research and Creative Scholarship, University of Montana, Missoula, MT
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102
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Janssen K, Mundy NI. The genetic basis and enigmatic origin of melanic polymorphism in pomarine skuas ( Stercorarius pomarinus). Proc Biol Sci 2018; 284:rspb.2017.1735. [PMID: 29187628 DOI: 10.1098/rspb.2017.1735] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 10/27/2017] [Indexed: 01/28/2023] Open
Abstract
A key outstanding issue in adaptive evolution is the relationship between the genetics of intraspecific polymorphism and interspecific evolution. Here, we show that the pale/dark ventral plumage polymorphism that occurs in both the pomarine skua (Stercorarius pomarinus) and Arctic skua (S. parasiticus) is the result of convergent evolution at the same locus (MC1R), involving some of the same amino acid sites. The dark melanic MC1R allele in the pomarine skua is strongly divergent from the pale MC1R alleles. Whereas the dark allele is closely related to MC1R alleles in three species of great skua (S. skua, S. maccormicki, S. lonnbergi), the pale pomarine skua MC1R alleles present a star-like pattern in an intermediate position on the haplotype network, closer to alleles of the long-tailed skua (S. longicaudus). Variation at other nuclear loci confirms a close relationship between the pomarine skua and the great skuas. The plumage polymorphism in pomarine skuas might have arisen in the common ancestor of pomarine and great skuas, only being retained in pomarine skuas. Alternatively, the pale and melanic MC1R alleles may have evolved independently in different lineages and been brought together in pomarine skuas by hybridization. In this case, introgression of a pale MC1R allele into the pomarine skua from another skua lineage is most likely. Our current data do not permit us to distinguish between these hypotheses, and assaying genome-wide variation holds much promise in this regard. Nevertheless, we have uncovered an intriguing example of a functionally important allele within one species that is shared across species.
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Affiliation(s)
- Kirstin Janssen
- Department of Natural Sciences, Tromsø University Museum, UiT The Arctic University of Tromsø, 9037 Tromsø, Norway.,Centre of Forensic Genetics, Institute of Medical Biology, Faculty of Health Sciences, UIT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Nicholas I Mundy
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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103
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Nigenda‐Morales SF, Hu Y, Beasley JC, Ruiz‐Piña HA, Valenzuela‐Galván D, Wayne RK. Transcriptomic analysis of skin pigmentation variation in the Virginia opossum (
Didelphis virginiana
). Mol Ecol 2018; 27:2680-2697. [DOI: 10.1111/mec.14712] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Sergio F. Nigenda‐Morales
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
| | - Yibo Hu
- Key Lab of Animal Ecology and Conservation Biology Institute of Zoology Chinese Academy of Sciences Chaoyang, Beijing China
| | - James C. Beasley
- Savannah River Ecology Lab Warnell School of Forestry and Natural Resources University of Georgia Aiken South Carolina
| | - Hugo A. Ruiz‐Piña
- Centro de Investigaciones Regionales “Dr. Hideyo Noguchi” Universidad Autónoma de Yucatán Mérida Yucatán Mexico
| | - David Valenzuela‐Galván
- Departamento de Ecología Evolutiva Centro de Investigación en Biodiversidad y Conservación Universidad Autónoma del Estado de Morelos Cuernavaca Morelos Mexico
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles Los Angeles California
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104
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Pilot M, Greco C, vonHoldt BM, Randi E, Jędrzejewski W, Sidorovich VE, Konopiński MK, Ostrander EA, Wayne RK. Widespread, long-term admixture between grey wolves and domestic dogs across Eurasia and its implications for the conservation status of hybrids. Evol Appl 2018; 11:662-680. [PMID: 29875809 PMCID: PMC5978975 DOI: 10.1111/eva.12595] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Hybridisation between a domesticated species and its wild ancestor is an important conservation problem, especially if it results in the introgression of domestic gene variants into wild species. Nevertheless, the legal status of hybrids remains unregulated, partially because of the limited understanding of the hybridisation process and its consequences. The occurrence of hybridisation between grey wolves and domestic dogs is well documented from different parts of the wolf geographic range, but little is known about the frequency of hybridisation events, their causes and the genetic impact on wolf populations. We analysed 61K SNPs spanning the canid genome in wolves from across Eurasia and North America and compared that data to similar data from dogs to identify signatures of admixture. The haplotype block analysis, which included 38 autosomes and the X chromosome, indicated the presence of individuals of mixed wolf-dog ancestry in most Eurasian wolf populations, but less admixture was present in North American populations. We found evidence for male-biased introgression of dog alleles into wolf populations, but also identified a first-generation hybrid resulting from mating between a female dog and a male wolf. We found small blocks of dog ancestry in the genomes of 62% Eurasian wolves studied and melanistic individuals with no signs of recent admixed ancestry, but with a dog-derived allele at a locus linked to melanism. Consequently, these results suggest that hybridisation has been occurring in different parts of Eurasia on multiple timescales and is not solely a recent phenomenon. Nevertheless, wolf populations have maintained genetic differentiation from dogs, suggesting that hybridisation at a low frequency does not diminish distinctiveness of the wolf gene pool. However, increased hybridisation frequency may be detrimental for wolf populations, stressing the need for genetic monitoring to assess the frequency and distribution of individuals resulting from recent admixture.
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Affiliation(s)
| | - Claudia Greco
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
| | - Bridgett M. vonHoldt
- Department of Ecology and Evolutionary BiologyPrinceton UniversityPrincetonNJUSA
| | - Ettore Randi
- Department of Environmental Monitoring and Biodiversity ConservationItalian National Institute for Environmental Protection and ResearchBolognaItaly
- Department 18/Section of Environmental EngineeringAalborg UniversityAalborgDenmark
| | - Włodzimierz Jędrzejewski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Instituto Venezolano de Investigaciones Cientificas (IVIC)Centro de EcologiaCaracasVenezuela
| | | | | | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics BranchNational Human Genome Research InstituteNational Institutes of HealthBethesdaMDUSA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaLos AngelesCAUSA
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105
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Saleh M, Younes M, Sarhan M, Abdel-Hamid F. Melanism and coat colour polymorphism in the Egyptian Wolf Canis lupaster Hemprich & Ehrenberg (Carnivora: Canidae) from Egypt. ZOOLOGY IN THE MIDDLE EAST 2018. [DOI: 10.1080/09397140.2018.1475117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Affiliation(s)
- Mostafa Saleh
- Department of Zoology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Mahmoud Younes
- Department of Zoology, Faculty of Science, Al-Azhar University, Cairo, Egypt
| | - Moustafa Sarhan
- Department of Zoology, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Fouad Abdel-Hamid
- Department of Zoology, Faculty of Science, Al-Azhar University, Cairo, Egypt
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106
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Barcoding hybrids: heterogeneous distribution of Schistosoma haematobium × Schistosoma bovis hybrids across the Senegal River Basin. Parasitology 2018; 145:634-645. [PMID: 29667570 DOI: 10.1017/s0031182018000525] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Hybridization events between Schistosoma species (Digenea, Platyhelminthes) are reported with increasing frequency, largely due to improved access to molecular tools. Nevertheless, little is known about the distribution and frequency of hybrid schistosomes in nature. Screening for hybrids on a large scale is complicated by the need for nuclear and mitochondrial sequence information, precluding a 'simple' barcoding approach. Here we aimed to determine and understand the spatiotemporal distribution of Schistosoma haematobium × Schistosoma bovis hybrids in the Senegal River Basin. From ten villages, distributed over the four main water basins, we genotyped a total of 1236 schistosome larvae collected from human urine samples using a partial mitochondrial cox1 fragment; a subset of 268 parasites was also genotyped using ITS rDNA. Hybrid schistosomes were unevenly distributed, with substantially higher numbers in villages bordering Lac de Guiers than in villages from the Lampsar River and the Middle Valley of the Senegal River. The frequency of hybrids per village was not linked with the prevalence of urinary schistosomiasis in that village. However, we did find a significant positive association between the frequency of hybrids per village and the prevalence of Schistosoma mansoni. We discuss the potential consequences of adopting a barcoding approach when studying hybrids in nature.
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107
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Zimova M, Hackländer K, Good JM, Melo‐Ferreira J, Alves PC, Mills LS. Function and underlying mechanisms of seasonal colour moulting in mammals and birds: what keeps them changing in a warming world? Biol Rev Camb Philos Soc 2018; 93:1478-1498. [DOI: 10.1111/brv.12405] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 02/06/2018] [Accepted: 02/09/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Marketa Zimova
- Wildlife Biology Program University of Montana Missoula MT 59812 U.S.A
- Fisheries, Wildlife, and Conservation Biology Program, Department of Forestry and Environmental Resources North Carolina State University Raleigh NC 27695 U.S.A
| | - Klaus Hackländer
- Fisheries, Wildlife, and Conservation Biology Program, Department of Forestry and Environmental Resources North Carolina State University Raleigh NC 27695 U.S.A
- Institute of Wildlife Biology and Game Management BOKU ‐ University of Natural Resources and Life Sciences Vienna 1180 Austria
| | - Jeffrey M. Good
- Division of Biological Sciences University of Montana Missoula MT 59812 USA
| | - José Melo‐Ferreira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Campus Agrário de Vairão, 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Rua do Campo Alegre, 4169‐007 Porto Portugal
| | - Paulo Célio Alves
- Wildlife Biology Program University of Montana Missoula MT 59812 U.S.A
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado Universidade do Porto Campus Agrário de Vairão, 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências da Universidade do Porto Rua do Campo Alegre, 4169‐007 Porto Portugal
| | - L. Scott Mills
- Wildlife Biology Program and Office of Research and Creative Scholarship University of Montana Missoula MT 59812 USA
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108
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Russo IRM, Hoban S, Bloomer P, Kotzé A, Segelbacher G, Rushworth I, Birss C, Bruford MW. ‘Intentional Genetic Manipulation’ as a conservation threat. CONSERV GENET RESOUR 2018. [DOI: 10.1007/s12686-018-0983-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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109
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Sasamori S, Wiewel AS, Thomson VA, Kobayashi M, Nakata K, Suzuki H. Potential Causative Mutation for Melanism in Rats Identified in the Agouti Signaling Protein Gene (Asip) of the Rattus rattus Species Complex on Okinawa Island, Japan. Zoolog Sci 2017; 34:513-522. [PMID: 29219041 DOI: 10.2108/zs170027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The occurrence of black fur, or melanism, in many mammalian species is known to be linked to DNA sequence variation in the agouti signaling protein (Asip) gene, which is a major determinant of eumelanin and pheomelanin pigments in coat color. We investigated 38 agouti (i.e., banded wildtype) and four melanistic Rattus rattus species complex (RrC) lineage II specimens from Okinawa Island, Ryukyu Islands, Japan, for genetic variation in three exons and associated flanking regions in the Asip gene. On Okinawa, a predicted loss-of-function mutation caused by a cysteine to serine amino acid change at p.124C>S (c.370T>A) in the highly conserved functional domain of Asip was found in melanistic rats, but was absent in agouti specimens, suggesting that the p.124C>S mutation is responsible for the observed melanism. Phylogeographic analysis found that Asip sequences from Okinawan RrC lineage II, including both agouti and melanistic specimens, differed from: 1) both agouti and melanistic RrC lineage I from Otaru, Hokkaido, Japan, and 2) agouti RrC lineages I and II from South Australia. This suggests the possibility of in-situ mutation of the Asip gene, either within the RrC lineage II population on Okinawa or in an unsampled RrC lineage II population with biogeographic links to Okinawa, although incomplete lineage sorting could not be ruled out.
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Affiliation(s)
- Shoichi Sasamori
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Andrew S Wiewel
- 2 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Vicki A Thomson
- 2 School of Biological Sciences, University of Adelaide, North Terrace, Adelaide SA 5005, Australia
| | - Motoko Kobayashi
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Katsushi Nakata
- 3 Yambaru Wildlife Conservation Center, Ministry of the Environment, Kunigami-son, Okinawa 905-1413, Japan
| | - Hitoshi Suzuki
- 1 Division of Bioscience, Graduate School of Environmental Science, Hokkaido University, Sapporo 060-0810, Japan
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110
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Schmickl R, Marburger S, Bray S, Yant L. Hybrids and horizontal transfer: introgression allows adaptive allele discovery. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:5453-5470. [PMID: 29096001 DOI: 10.1093/jxb/erx297] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Evolution has devised countless remarkable solutions to diverse challenges. Understanding the mechanistic basis of these solutions provides insights into how biological systems can be subtly tweaked without maladaptive consequences. The knowledge gained from illuminating these mechanisms is equally important to our understanding of fundamental evolutionary mechanisms as it is to our hopes of developing truly rational plant breeding and synthetic biology. In particular, modern population genomic approaches are proving very powerful in the detection of candidate alleles for mediating consequential adaptations that can be tested functionally. Especially striking are signals gained from contexts involving genetic transfers between populations, closely related species, or indeed between kingdoms. Here we discuss two major classes of these scenarios, adaptive introgression and horizontal gene flow, illustrating discoveries made across kingdoms.
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Affiliation(s)
- Roswitha Schmickl
- Institute of Botany, The Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
- Department of Botany, Faculty of Science, Charles University in Prague, Benátská 2, 128 01 Prague, Czech Republic
| | - Sarah Marburger
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sian Bray
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Levi Yant
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, United Kingdom
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111
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Coat colour adaptation of post-glacial horses to increasing forest vegetation. Nat Ecol Evol 2017; 1:1816-1819. [PMID: 29085065 DOI: 10.1038/s41559-017-0358-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 09/25/2017] [Indexed: 11/08/2022]
Abstract
Wild horses unexpectedly survived terminal Pleistocene megafaunal extinctions until eventual European extirpation in the twentieth century. This survival is tied to either their occurrence in cryptic open habitats or their adaptation to forests. Our niche modelling inferred an increasing presence of horses in post-glacial forests, and our analysis of ancient DNA suggested significant selection for black phenotypes as indicating adaptation to forests.
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112
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Yannic G, Statham MJ, Denoyelle L, Szor G, Qulaut GQ, Sacks BN, Lecomte N. Investigating the ancestry of putative hybrids: are Arctic fox and red fox hybridizing? Polar Biol 2017. [DOI: 10.1007/s00300-017-2126-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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113
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Ostrander EA, Wayne RK, Freedman AH, Davis BW. Demographic history, selection and functional diversity of the canine genome. Nat Rev Genet 2017; 18:705-720. [DOI: 10.1038/nrg.2017.67] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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114
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Hendricks SA, Koblmüller S, Harrigan RJ, Leonard JA, Schweizer RM, Vonholdt BM, Kays R, Wayne RK. Defense of an expanded historical range for the Mexican wolf: A comment on Heffelfinger et al. J Wildl Manage 2017. [DOI: 10.1002/jwmg.21336] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sarah A. Hendricks
- Department of Biological Sciences and Institute of Bioinformatics and Evolutionary Studies; University of Idaho; Moscow ID USA
| | - Stephan Koblmüller
- Institute of Zoology; University of Graz; Universitätsplatz 2 8010 Graz Austria
| | - Ryan J. Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability; University of California; Los Angeles, 300 LaKretz Hall Los Angeles CA 90095 USA
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics Group; Estación Biológica de Doñana (EBD-CSIC); 41092 Sevilla Spain
| | - Rena M. Schweizer
- Division of Biological Sciences; University of Montana; 32 Campus Dr. Missoula MT 59812 USA
| | - Bridgett M. Vonholdt
- Department of Ecology and Evolutionary Biology; Princeton University; M151 Guyot Hall Princeton NJ 08544 USA
| | - Roland Kays
- North Carolina Museum of Natural Sciences; Biodiversity Lab; Raleigh NC 27601 USA
- Department of Forestry & Environmental Resources; North Carolina State University; Raleigh NC 27695 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology; University of California, Los Angeles; 610 Charles E. Young Drive East Los Angeles CA 90095 USA
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115
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Enciso-Romero J, Pardo-Díaz C, Martin SH, Arias CF, Linares M, McMillan WO, Jiggins CD, Salazar C. Evolution of novel mimicry rings facilitated by adaptive introgression in tropical butterflies. Mol Ecol 2017; 26:5160-5172. [PMID: 28777894 DOI: 10.1111/mec.14277] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/25/2017] [Accepted: 07/31/2017] [Indexed: 12/25/2022]
Abstract
Understanding the genetic basis of phenotypic variation and the mechanisms involved in the evolution of adaptive novelty, especially in adaptive radiations, is a major goal in evolutionary biology. Here, we used whole-genome sequence data to investigate the origin of the yellow hindwing bar in the Heliconius cydno radiation. We found modular variation associated with hindwing phenotype in two narrow noncoding regions upstream and downstream of the cortex gene, which was recently identified as a pigmentation pattern controller in multiple species of Heliconius. Genetic variation at each of these modules suggests an independent control of the dorsal and ventral hindwing patterning, with the upstream module associated with the ventral phenotype and the downstream module with the dorsal one. Furthermore, we detected introgression between H. cydno and its closely related species Heliconius melpomene in these modules, likely allowing both species to participate in novel mimicry rings. In sum, our findings support the role of regulatory modularity coupled with adaptive introgression as an elegant mechanism by which novel phenotypic combinations can evolve and fuel an adaptive radiation.
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Affiliation(s)
- Juan Enciso-Romero
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | - Carolina Pardo-Díaz
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | - Simon H Martin
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Carlos F Arias
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia.,Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - Mauricio Linares
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
| | | | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Camilo Salazar
- Biology Program, Faculty of Natural Sciences and Mathematics, Universidad del Rosario, Bogotá D.C, Colombia
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116
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Galaverni M, Caniglia R, Pagani L, Fabbri E, Boattini A, Randi E. Disentangling Timing of Admixture, Patterns of Introgression, and Phenotypic Indicators in a Hybridizing Wolf Population. Mol Biol Evol 2017; 34:2324-2339. [PMID: 28549194 PMCID: PMC5850710 DOI: 10.1093/molbev/msx169] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype-phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype-phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.
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Affiliation(s)
- Marco Galaverni
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Area Conservazione, WWF Italia, Rome, Italy
| | - Romolo Caniglia
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Universita degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Tartu, Estonia
| | - Elena Fabbri
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
| | - Alessio Boattini
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Ettore Randi
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg Universitet, Aalborg, Denmark
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117
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Dzialuk A, Zastempowska E, Skórzewski R, Twarużek M, Grajewski J. High domestic pig contribution to the local gene pool of free-living European wild boar: a case study in Poland. MAMMAL RES 2017. [DOI: 10.1007/s13364-017-0331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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118
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Botigué LR, Song S, Scheu A, Gopalan S, Pendleton AL, Oetjens M, Taravella AM, Seregély T, Zeeb-Lanz A, Arbogast RM, Bobo D, Daly K, Unterländer M, Burger J, Kidd JM, Veeramah KR. Ancient European dog genomes reveal continuity since the Early Neolithic. Nat Commun 2017; 8:16082. [PMID: 28719574 PMCID: PMC5520058 DOI: 10.1038/ncomms16082] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/25/2017] [Indexed: 12/19/2022] Open
Abstract
Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. Here we sequence the genomes of an Early and End Neolithic dog from Germany, including a sample associated with an early European farming community. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. We find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication. By calibrating the mutation rate using our oldest dog, we narrow the timing of dog domestication to 20,000-40,000 years ago. Interestingly, we do not observe the extreme copy number expansion of the AMY2B gene characteristic of modern dogs that has previously been proposed as an adaptation to a starch-rich diet driven by the widespread adoption of agriculture in the Neolithic.
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Affiliation(s)
- Laura R Botigué
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Shiya Song
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Shyamalika Gopalan
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew Oetjens
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Angela M Taravella
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Timo Seregély
- Department of Prehistoric Archaeology, Institute of Archaeology, Heritage Sciences and Art History, University of Bamberg, 96045 Bamberg, Germany
| | - Andrea Zeeb-Lanz
- Generaldirektion Kulturelles Erbe Rheinland-Pfalz, Direktion Landesarchäologie, Außenstelle Speyer, 67346 Speyer, Germany
| | | | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - Kevin Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Martina Unterländer
- Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
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119
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Lu C, Yu H, Xing Y, Cheng YY, Wu QY, Li SM, Fu HY, Zhang X, Hao LL, Liu D. Haplotype diversity in MC1R locus between the Min and white-haired pig breeds. ACTA AGR SCAND A-AN 2017. [DOI: 10.1080/09064702.2017.1337215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- C. Lu
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - H. Yu
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - Y. Xing
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - Y.-Y. Cheng
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - Q.-Y. Wu
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - S.-M. Li
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - H.-Y. Fu
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - X. Zhang
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - L.-L. Hao
- College of Animal Science, Jilin University, Changchun, People’s Republic of China
| | - D. Liu
- Heilongjiang Academy of Agricultural Sciences, Institute of Animal Husbandry, Harbin, People’s Republic of China
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120
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vonHoldt B, Fan Z, Ortega-Del Vecchyo D, Wayne RK. EPAS1 variants in high altitude Tibetan wolves were selectively introgressed into highland dogs. PeerJ 2017; 5:e3522. [PMID: 28717592 PMCID: PMC5510585 DOI: 10.7717/peerj.3522] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/08/2017] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Admixture can facilitate adaptation. For example, black wolves have obtained the variant causing black coat color through past hybridization with domestic dogs and have higher fitness than gray colored wolves. Another recent example of the transfer of adaptive variation between the two species has been suggested by the similarity between high altitude Tibetan mastiffs and wolves at the EPAS1 gene, a transcription factor induced in low oxygen environments. METHODS Here, we investigate the directionality of admixture in EPAS1 between 28 reference highland gray wolves, 15 reference domestic dogs, and 21 putatively admixed highland wolves. This experimental design represents an expanded sample of Asian dogs and wolves from previous studies. Admixture was inferred using 17,709 publicly available SNP genotypes on canine chromosome 10. We additionally conducted a scan for positive selection in the highland dog genome. RESULTS We find an excess of highland gray wolf ancestry at the EPAS1 locus in highland domestic dogs, suggesting adaptive introgression from wolves to dogs. The signal of admixture is limited in genomic extent to a small region on chromosome 10, indicating that it is the focus of selection in an oxygen-limited environment. DISCUSSION Our results suggest that an adaptive variant of EPAS1 in highland wolves was transferred to highland dogs, carrying linked variants that potentially function in hypoxia response at high elevation. The intertwined history of dogs and wolves ensures a unique evolutionary dynamic where variants that have appeared in the history of either species can be tested for their effects on fitness under natural and artificial selection. Such coupled evolutionary histories may be key to the persistence of wild canines and their domesticated kin given the increasing anthropogenic modifications that characterize the future of both species.
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Affiliation(s)
- Bridgett vonHoldt
- Ecology & Evolutionary Biology, Princeton University, Princeton, NJ, United States of America
| | - Zhenxin Fan
- College of Life Sciences, Sichuan University, Chengdu, China
| | - Diego Ortega-Del Vecchyo
- Department of Integrative Biology, University of California, Berkeley, CA, United States of America
| | - Robert K Wayne
- Ecology & Evolutionary Biology, University of California, Los Angeles, CA, United States of America
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121
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vonHoldt BM, Shuldiner E, Koch IJ, Kartzinel RY, Hogan A, Brubaker L, Wanser S, Stahler D, Wynne CDL, Ostrander EA, Sinsheimer JS, Udell MAR. Structural variants in genes associated with human Williams-Beuren syndrome underlie stereotypical hypersociability in domestic dogs. SCIENCE ADVANCES 2017; 3:e1700398. [PMID: 28776031 PMCID: PMC5517105 DOI: 10.1126/sciadv.1700398] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/15/2017] [Indexed: 05/04/2023]
Abstract
Although considerable progress has been made in understanding the genetic basis of morphologic traits (for example, body size and coat color) in dogs and wolves, the genetic basis of their behavioral divergence is poorly understood. An integrative approach using both behavioral and genetic data is required to understand the molecular underpinnings of the various behavioral characteristics associated with domestication. We analyze a 5-Mb genomic region on chromosome 6 previously found to be under positive selection in domestic dog breeds. Deletion of this region in humans is linked to Williams-Beuren syndrome (WBS), a multisystem congenital disorder characterized by hypersocial behavior. We associate quantitative data on behavioral phenotypes symptomatic of WBS in humans with structural changes in the WBS locus in dogs. We find that hypersociability, a central feature of WBS, is also a core element of domestication that distinguishes dogs from wolves. We provide evidence that structural variants in GTF2I and GTF2IRD1, genes previously implicated in the behavioral phenotype of patients with WBS and contained within the WBS locus, contribute to extreme sociability in dogs. This finding suggests that there are commonalities in the genetic architecture of WBS and canine tameness and that directional selection may have targeted a unique set of linked behavioral genes of large phenotypic effect, allowing for rapid behavioral divergence of dogs and wolves, facilitating coexistence with humans.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Corresponding author.
| | - Emily Shuldiner
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
- Translational Genetics and Genomics Unit, National Institute of Arthritis and Musculoskeletal and Skin Disorders, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Ilana Janowitz Koch
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rebecca Y. Kartzinel
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Andrew Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren Brubaker
- Department of Animal and Rangeland Sciences, Oregon State University, OR 97331, USA
| | - Shelby Wanser
- Department of Animal and Rangeland Sciences, Oregon State University, OR 97331, USA
| | - Daniel Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY 82190, USA
| | - Clive D. L. Wynne
- Department of Psychology, Arizona State University, Tempe, AZ 85287, USA
| | - Elaine A. Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Janet S. Sinsheimer
- Departments of Human Genetics and Biomathematics, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Monique A. R. Udell
- Department of Animal and Rangeland Sciences, Oregon State University, OR 97331, USA
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122
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Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT. Genomewide analysis of admixture and adaptation in the Africanized honeybee. Mol Ecol 2017; 26:3603-3617. [PMID: 28378497 DOI: 10.1111/mec.14122] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/08/2016] [Accepted: 03/20/2017] [Indexed: 02/03/2023]
Abstract
Genetic exchange by hybridization or admixture can make an important contribution to evolution, and introgression of favourable alleles can facilitate adaptation to new environments. A small number of honeybees (Apis mellifera) with African ancestry were introduced to Brazil ~60 years ago, which dispersed and hybridized with existing managed populations of European origin, quickly spreading across much of the Americas in an example of a massive biological invasion. Here, we analyse whole-genome sequences of 32 Africanized honeybees sampled from throughout Brazil to study the effect of this process on genome diversity. By comparison with ancestral populations from Europe and Africa, we infer that these samples have 84% African ancestry, with the remainder from western European populations. However, this proportion varies across the genome and we identify signals of positive selection in regions with high European ancestry proportions. These observations are largely driven by one large gene-rich 1.4-Mbp segment on chromosome 11 where European haplotypes are present at a significantly elevated frequency and likely confer an adaptive advantage in the Africanized honeybee population. This region has previously been implicated in reproductive traits and foraging behaviour in worker bees. Finally, by analysing the distribution of ancestry tract lengths in the context of the known time of the admixture event, we are able to infer an average generation time of 2.0 years. Our analysis highlights the processes by which populations of mixed genetic ancestry form and adapt to new environments.
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Affiliation(s)
- Ronald M Nelson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Andreas Wallberg
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Zilá Luz Paulino Simões
- Department of Biology, FFCLRP, University of São Paulo, Ribeirão Preto, Brazil.,Department of Genetics, FMRP, University of São Paulo, Ribeirão Preto, Brazil
| | - Daniel J Lawson
- Department of Mathematics, University of Bristol, Bristol, UK
| | - Matthew T Webster
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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123
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Montanari SR, Hobbs JPA, Pratchett MS, Bay LK, van Herwerden L. Naturally occurring hybrids of coral reef butterflyfishes have similar fitness compared to parental species. PLoS One 2017; 12:e0173212. [PMID: 28257492 PMCID: PMC5336293 DOI: 10.1371/journal.pone.0173212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/16/2017] [Indexed: 11/18/2022] Open
Abstract
Hybridisation can produce evolutionary novelty by increasing fitness and adaptive capacity. Heterosis, or hybrid vigour, has been documented in many plant and animal taxa, and is a notable consequence of hybridisation that has been exploited for decades in agriculture and aquaculture. On the contrary, loss of fitness in naturally occurring hybrid taxa has been observed in many cases. This can have negative consequences for the parental species involved (wasted reproductive effort), and has raised concerns for species conservation. This study evaluates the relative fitness of previously documented butterflyfish hybrids of the genus Chaetodon from the Indo-Pacific suture zone at Christmas Island. Histological examination confirmed the reproductive viability of Chaetodon hybrids. Examination of liver lipid content showed that hybrid body condition was not significantly different from parent species body condition. Lastly, size at age data revealed no difference in growth rates and asymptotic length between hybrids and parent species. Based on the traits measured in this study, naturally occurring hybrids of Chaetodon butterflyfishes have similar fitness to their parental species, and are unlikely to supplant parental species under current environmental conditions at the suture zone. However, given sufficient fitness and ongoing genetic exchange between the respective parental species, hybrids are likely to persist within the suture zone.
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Affiliation(s)
- Stefano R. Montanari
- AIMS@JCU, Australian Institute of Marine Science, College of Science and Engineering, James Cook University of North Queensland, Townsville, QLD, Australia
- * E-mail:
| | - Jean-Paul A. Hobbs
- Department of Environment and Agriculture, Curtin University, Bentley, WA, Australia
| | - Morgan S. Pratchett
- ARC Centre of Excellence for Coral Reef Studies, James Cook University of North Queensland, Townsville, QLD, Australia
| | - Line K. Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Lynne van Herwerden
- College of Science and Engineering, James Cook University of North Queensland, Townsville, QLD, Australia
- Centre for Comparative Genomics, James Cook University of North Queensland, Townsville, QLD, Australia
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124
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The Evolution and Genetics of Carotenoid Processing in Animals. Trends Genet 2017; 33:171-182. [DOI: 10.1016/j.tig.2017.01.002] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 12/29/2016] [Accepted: 01/09/2017] [Indexed: 02/06/2023]
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125
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Spatial assessment of wolf-dog hybridization in a single breeding period. Sci Rep 2017; 7:42475. [PMID: 28195213 PMCID: PMC5307949 DOI: 10.1038/srep42475] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/11/2017] [Indexed: 11/17/2022] Open
Abstract
Understanding the dynamics of wolf-dog hybridization and delineating evidence-based conservation strategies requires information on the spatial extent of wolf-dog hybridization in real-time, which remains largely unknown. We collected 332 wolf-like scats over ca. 5,000km2 in the NW Iberian Peninsula to evaluate wolf-dog hybridization at population level in a single breeding/pup-rearing season. Mitochondrial DNA (MtDNA) and 18 ancestry informative markers were used for species and individual identification, and to detect wolf-dog hybrids. Genetic relatedness was assessed between hybrids and wolves. We identified 130 genotypes, including 67 wolves and 7 hybrids. Three of the hybrids were backcrosses to dog whereas the others were backcrosses to wolf, the latter accounting for a 5.6% rate of introgression into the wolf population. Our results show a previously undocumented scenario of multiple and widespread wolf-dog hybridization events at the population level. However, there is a clear maintenance of wolf genetic identity, as evidenced by the sharp genetic identification of pure individuals, suggesting the resilience of wolf populations to a small amount of hybridization. We consider that real-time population level assessments of hybridization provide a new perspective into the debate on wolf conservation, with particular focus on current management guidelines applied in wolf-dog hybridization events.
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126
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Eroh GD, Clayton FC, Florell SR, Cassidy PB, Chirife A, Marón CF, Valenzuela LO, Campbell MS, Seger J, Rowntree VJ, Leachman SA. Cellular and ultrastructural characterization of the grey-morph phenotype in southern right whales (Eubalaena australis). PLoS One 2017; 12:e0171449. [PMID: 28170433 PMCID: PMC5295704 DOI: 10.1371/journal.pone.0171449] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/20/2017] [Indexed: 11/18/2022] Open
Abstract
Southern right whales (SRWs, Eubalena australis) are polymorphic for an X-linked pigmentation pattern known as grey morphism. Most SRWs have completely black skin with white patches on their bellies and occasionally on their backs; these patches remain white as the whale ages. Grey morphs (previously referred to as partial albinos) appear mostly white at birth, with a splattering of rounded black marks; but as the whales age, the white skin gradually changes to a brownish grey color. The cellular and developmental bases of grey morphism are not understood. Here we describe cellular and ultrastructural features of grey-morph skin in relation to that of normal, wild-type skin. Melanocytes were identified histologically and counted, and melanosomes were measured using transmission electron microscopy. Grey-morph skin had fewer melanocytes when compared to wild-type skin, suggesting reduced melanocyte survival, migration, or proliferation in these whales. Grey-morph melanocytes had smaller melanosomes relative to wild-type skin, normal transport of melanosomes to surrounding keratinocytes, and normal localization of melanin granules above the keratinocyte nuclei. These findings indicate that SRW grey-morph pigmentation patterns are caused by reduced numbers of melanocytes in the skin, as well as by reduced amounts of melanin production and/or reduced sizes of mature melanosomes. Grey morphism is distinct from piebaldism and albinism found in other species, which are genetic pigmentation conditions resulting from the local absence of melanocytes, or the inability to synthesize melanin, respectively.
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Affiliation(s)
- Guy D. Eroh
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- University of Georgia, Athens, Georgia, United States of America
| | - Fred C. Clayton
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States of America
| | - Scott R. Florell
- Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America
| | - Pamela B. Cassidy
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Andrea Chirife
- Programa de Monitoreo Sanitario Ballena Franca Austral, Puerto Madryn, Chubut, Argentina
| | - Carina F. Marón
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
| | - Luciano O. Valenzuela
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Sociales, Universidad Nacional del Centro de la Provincia de Buenos Aires, Buenos Aires, Argentina
| | - Michael S. Campbell
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, United States of America
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | - Jon Seger
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Victoria J. Rowntree
- Programa de Monitoreo Sanitario Ballena Franca Austral, Puerto Madryn, Chubut, Argentina
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
- Instituto de Conservación de Ballenas, Buenos Aires, Argentina
- Ocean Alliance/Whale Conservation Institute, Gloucester, Massachusetts, United States of America
| | - Sancy A. Leachman
- Huntsman Cancer Institute, Salt Lake City, Utah, United States of America
- Department of Dermatology, Oregon Health & Science University, Portland, Oregon, United States of America
- * E-mail:
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127
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Cassidy KA, Mech LD, MacNulty DR, Stahler DR, Smith DW. Sexually dimorphic aggression indicates male gray wolves specialize in pack defense against conspecific groups. Behav Processes 2017; 136:64-72. [PMID: 28143722 DOI: 10.1016/j.beproc.2017.01.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 11/25/2016] [Accepted: 01/18/2017] [Indexed: 10/20/2022]
Abstract
Aggression directed at conspecific groups is common among gregarious, territorial species, and for some species such as gray wolves (Canis lupus) intraspecific strife is the leading cause of natural mortality. Each individual in a group likely has different measures of the costs and benefits associated with a group task, such as an aggressive attack on another group, which can alter motivation and behavior. We observed 292 inter-pack aggressive interactions in Yellowstone National Park between 1 April 1995 and 1 April 2011 (>5300days of observation) in order to determine the role of both sexes, and the influence of pack, age, and other traits on aggression. We recorded the behaviors and characteristics of all individuals present during the interactions (n=534 individuals) and which individuals participated in each step (i.e. chase, attack, kill, flight) of the interaction. Overall, all wolves were more likely to chase rivals if they outnumbered their opponent, suggesting packs accurately assess their opponent's size during encounters and individuals adjust their behavior based on relative pack size. Males were more likely than females to chase rival packs and gray-colored wolves were more aggressive than black-colored wolves. Male wolves and gray-colored wolves also recorded higher cortisol levels than females and black-colored wolves, indicating hormonal support for more intense aggressive behavior. Further, we found a positive correlation between male age and probability of chasing, while age-specific participation for females remained constant. Chasing behavior was influenced by the sex of lone intruders, with males more likely to chase male intruders. This difference in behavior suggests male and female wolves may have different strategies and motivations during inter-pack aggressive interactions related to gray wolf mating systems. A division of labor between pack members concerning resource and territory defense suggests selection for specific traits related to aggression is an adaptive response to intense competition between groups of conspecifics.
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Affiliation(s)
- Kira A Cassidy
- Natural Resource Science and Management, 115 Green Hall, 1530 Cleveland Avenue N, University of Minnesota, St. Paul, MN, 55108, USA; Yellowstone Wolf Project, PO Box 168, Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA.
| | - L David Mech
- U. S. Geological Survey, Northern Prairie Wildlife Research Center, 8711-37th St., S.E., Jamestown, ND, 58401-7317, USA
| | - Daniel R MacNulty
- Department of Wildland Resources, Utah State University, Logan, UT, 84322, USA
| | - Daniel R Stahler
- Yellowstone Wolf Project, PO Box 168, Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA
| | - Douglas W Smith
- Yellowstone Wolf Project, PO Box 168, Yellowstone Center for Resources, Yellowstone National Park, WY, 82190, USA
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128
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Smith BP, Lucas TA, Norris RM, Henneberg M. Brain size/body weight in the dingo (Canis dingo): comparisons with domestic and wild canids. AUST J ZOOL 2017. [DOI: 10.1071/zo17040] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Endocranial volume was measured in a large sample (n = 128) of free-ranging dingoes (Canis dingo) where body size was known. The brain/body size relationship in the dingoes was compared with populations of wild (Family Canidae) and domestic canids (Canis familiaris). Despite a great deal of variation among wild and domestic canids, the brain/body size of dingoes forms a tight cluster within the variation of domestic dogs. Like dogs, free-ranging dingoes have paedomorphic crania; however, dingoes have a larger brain and are more encephalised than most domestic breeds of dog. The dingo’s brain/body size relationship was similar to those of other mesopredators (medium-sized predators that typically prey on smaller animals), including the dhole (Cuon alpinus) and the coyote (Canis latrans). These findings have implications for the antiquity and classification of the dingo, as well as the impact of feralisation on brain size. At the same time, it highlights the difficulty in using brain/body size to distinguish wild and domestic canids.
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129
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Overview on the Role of Advance Genomics in Conservation Biology of Endangered Species. Int J Genomics 2016; 2016:3460416. [PMID: 28025636 PMCID: PMC5153469 DOI: 10.1155/2016/3460416] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/23/2016] [Accepted: 11/08/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent era, due to tremendous advancement in industrialization, pollution and other anthropogenic activities have created a serious scenario for biota survival. It has been reported that present biota is entering a “sixth” mass extinction, because of chronic exposure to anthropogenic activities. Various ex situ and in situ measures have been adopted for conservation of threatened and endangered plants and animal species; however, these have been limited due to various discrepancies associated with them. Current advancement in molecular technologies, especially, genomics, is playing a very crucial role in biodiversity conservation. Advance genomics helps in identifying the segments of genome responsible for adaptation. It can also improve our understanding about microevolution through a better understanding of selection, mutation, assertive matting, and recombination. Advance genomics helps in identifying genes that are essential for fitness and ultimately for developing modern and fast monitoring tools for endangered biodiversity. This review article focuses on the applications of advanced genomics mainly demographic, adaptive genetic variations, inbreeding, hybridization and introgression, and disease susceptibilities, in the conservation of threatened biota. In short, it provides the fundamentals for novice readers and advancement in genomics for the experts working for the conservation of endangered plant and animal species.
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130
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Abstract
Understanding the timing and geographic context of dog origins is a crucial component for understanding human history, as well as the evolutionary context in which the morphological and behavioral divergence of dogs from wolves occurred. A substantial challenge to understanding domestication is that dogs have experienced a complicated demographic history. An initial severe bottleneck was associated with domestication followed by postdivergence gene flow between dogs and wolves, as well as population expansions, contractions, and replacements. In addition, because the domestication of dogs occurred in the relatively recent past, much of the observed polymorphism may be shared between dogs and wolves, limiting the power to distinguish between alternative models of dog history. Greater insight into the domestication process will require explicit tests of alternative models of domestication through the joint analysis of whole genomes from modern lineages and ancient wolves and dogs from across Eurasia.
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Affiliation(s)
- Adam H Freedman
- Informatics Group, Faculty of Arts & Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095;
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Freedman AH, Lohmueller KE, Wayne RK. Evolutionary History, Selective Sweeps, and Deleterious Variation in the Dog. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032155] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The dog is our oldest domesticate and has experienced a wide variety of demographic histories, including a bottleneck associated with domestication and individual bottlenecks associated with the formation of modern breeds. Admixture with gray wolves, and among dog breeds and populations, has also occurred throughout its history. Likewise, the intensity and focus of selection have varied, from an initial focus on traits enhancing cohabitation with humans, to more directed selection on specific phenotypic characteristics and behaviors. In this review, we summarize and synthesize genetic findings from genome-wide and complete genome studies that document the genomic consequences of demography and selection, including the effects on adaptive and deleterious variation. Consistent with the evolutionary history of the dog, signals of natural and artificial selection are evident in the dog genome. However, conclusions from studies of positive selection are fraught with the problem of false positives given that demographic history is often not taken into account.
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Affiliation(s)
- Adam H. Freedman
- Informatics Group, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095
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132
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Cairns KM, Wilton AN. New insights on the history of canids in Oceania based on mitochondrial and nuclear data. Genetica 2016; 144:553-565. [PMID: 27640201 DOI: 10.1007/s10709-016-9924-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022]
Abstract
How and when dingoes arrived in Oceania poses a fascinating question for scientists with interest in the historical movements of humans and dogs. The dingo holds a unique position as top terrestrial predator of Australia and exists in a wild state. In the first geographical survey of genetic diversity in the dingo using whole mitochondrial genomes, we analysed 16,428 bp in 25 individuals from five separate populations. We also investigated 13 nuclear loci to compare with the mitochondrial population history patterns. Phylogenetic analyses based upon mitochondrial DNA and nuclear DNA support the hypothesis that there are at least two distinct populations of dingo, one of which occurs in the northwest and the other in the southeast of the continent. Conservative molecular dating based upon mitochondrial DNA suggest that the lineages split approximately 8300 years before present, likely outside Australia but within Oceania. The close relationship between dingoes and New Guinea Singing Dogs suggests that plausibly dingoes spread into Australia via the land bridge between Papua New Guinea and Australia although seafaring introductions cannot be rejected. The geographical distribution of these divergent lineages suggests there were multiple independent dingo immigrations. Importantly, the observation of multiple dingo populations suggests the need for revision of existing conservation and management programs that treat dingoes as a single homogeneous population.
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Affiliation(s)
- Kylie M Cairns
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Alan N Wilton
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia
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133
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Janssens L, Miller R, Van Dongen S. The morphology of the mandibular coronoid process does not indicate that Canis lupus chanco is the progenitor to dogs. ZOOMORPHOLOGY 2016; 135:269-277. [PMID: 27340333 PMCID: PMC4871911 DOI: 10.1007/s00435-015-0298-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/12/2015] [Accepted: 12/30/2015] [Indexed: 12/18/2022]
Abstract
The domestication of wolves is currently under debate. Where, when and from which wolf sub-species dogs originated are being investigated both by osteoarchaeologists and geneticists. While DNA research is rapidly becoming more active and popular, morphological methods have been the gold standard in the past. But even today morphological details are routinely employed to discern archaeological wolves from dogs. One such morphological similarity between Canis lupus chanco and dogs was published in 1977 by Olsen and Olsen. This concerns the “turned back” anatomy of the dorsal part of the vertical ramus of the mandible that was claimed to be specific to domestic dogs and Chinese wolves C. lupus chanco, and “absent from other canids”. Based on this characteristic, C. lupus chanco was said to be the progenitor of Asian and American dogs, and this specific morphology has been continuously used as an argument to assign archaeological specimens, including non-Asian and non-American, to the dog clade. We challenged this statement by examining 384 dog skulls of 72 breeds and 60 skulls of four wolf sub-species. Only 20 % of dog mandibles and 80 % of C. lupus chanco showed the specific anatomy. In addition, 12 % of Canis lupus pallipes mandibles showed the “turned back” morphology. It can be concluded that the shape of the coronoid process of the mandible cannot be used as a morphological trait to determine whether a specimen belongs to a dog or as an argument in favour of chanco as the progenitor to dogs.
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Affiliation(s)
- Luc Janssens
- Department of Archaeology, Leiden University, Einsteinweg 2, 2333 CC Leiden, The Netherlands
| | - Rebecca Miller
- Service of Prehistory, University of Liège, quai Roosevelt, 1, 4000 Liège, Belgium
| | - Stefan Van Dongen
- Department of Evolutionary Ecology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
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134
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Fulgione D, Rippa D, Buglione M, Trapanese M, Petrelli S, Maselli V. Unexpected but welcome. Artificially selected traits may increase fitness in wild boar. Evol Appl 2016; 9:769-76. [PMID: 27330553 PMCID: PMC4908463 DOI: 10.1111/eva.12383] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 03/12/2016] [Indexed: 01/13/2023] Open
Abstract
Artificial selection affects phenotypes differently by natural selection. Domestic traits, which pass into the wild, are usually negatively selected. Yet, exceptionally, this axiom may fail to apply if genes, from the domestic animals, increase fertility in the wild. We studied a rare case of a wild boar population under the framework of Wright's interdemic selection model, which could explain gene flow between wild boar and pig, both considered as demes. We analysed the MC1R gene and microsatellite neutral loci in 62 pregnant wild boars as markers of hybridization, and we correlated nucleotide mutations on MC1R (which are common in domestic breeds) to litter size, as an evaluation of fitness in wild sow. Regardless of body size and phyletic effects, wild boar sows bearing nonsynonymous MC1R mutations produced larger litters. This directly suggests that artificially selected traits reaching wild populations, through interdemic gene flow, could bypass natural selection if and only if they increase the fitness in the wild.
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Affiliation(s)
| | - Daniela Rippa
- Department of Biology University of Naples Federico II Naples Italy
| | - Maria Buglione
- Department of Biology University of Naples Federico II Naples Italy
| | | | - Simona Petrelli
- Department of Biology University of Naples Federico II Naples Italy
| | - Valeria Maselli
- Department of Biology University of Naples Federico II Naples Italy
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135
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vonHoldt BM, Kays R, Pollinger JP, Wayne RK. Admixture mapping identifies introgressed genomic regions in North American canids. Mol Ecol 2016; 25:2443-53. [PMID: 27106273 DOI: 10.1111/mec.13667] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/12/2016] [Accepted: 04/15/2016] [Indexed: 12/21/2022]
Abstract
Hybrid zones typically contain novel gene combinations that can be tested by natural selection in a unique genetic context. Parental haplotypes that increase fitness can introgress beyond the hybrid zone, into the range of parental species. We used the Affymetrix canine SNP genotyping array to identify genomic regions tagged by multiple ancestry informative markers that are more frequent in an admixed population than expected. We surveyed a hybrid zone formed in the last 100 years as coyotes expanded their range into eastern North America. Concomitant with expansion, coyotes hybridized with wolves and some populations became more wolflike, such that coyotes in the northeast have the largest body size of any coyote population. Using a set of 3102 ancestry informative markers, we identified 60 differentially introgressed regions in 44 canines across this admixture zone. These regions are characterized by an excess of exogenous ancestry and, in northeastern coyotes, are enriched for genes affecting body size and skeletal proportions. Further, introgressed wolf-derived alleles have penetrated into Southern US coyote populations. Because no wolves currently exist in this area, these alleles are unlikely to have originated from recent hybridization. Instead, they probably originated from intraspecific gene flow or ancient admixture. We show that grey wolf and coyote admixture has far-reaching effects and, in addition to phenotypically transforming admixed populations, allows for the differential movement of alleles from different parental species to be tested in new genomic backgrounds.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Roland Kays
- North Carolina Museum of Natural Science and NC State University, Raleigh, NC, 27612, USA
| | - John P Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, 90095, USA
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136
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137
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Mckean NE, Trewick SA, Morgan-Richards M. Little or no gene flow despite F1 hybrids at two interspecific contact zones. Ecol Evol 2016; 6:2390-404. [PMID: 27066230 PMCID: PMC4783458 DOI: 10.1002/ece3.1942] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 12/01/2015] [Indexed: 11/28/2022] Open
Abstract
Hybridization can create the selective force that promotes assortative mating but hybridization can also select for increased hybrid fitness. Gene flow resulting from hybridization can increase genetic diversity but also reduce distinctiveness. Thus the formation of hybrids has important implications for long‐term species coexistence. This study compares the interaction between the tree wētā Hemideina thoracica and its two neighboring species; H. crassidens and H. trewicki. We examined the ratio of parent and hybrid forms in natural areas of sympatry. Individuals with intermediate phenotype were confirmed as first generation hybrids using nine independent genetic markers. Evidence of gene flow from successful hybridization was sought from the distribution of morphological and genetic characters. Both species pairs appear to be largely retaining their own identity where they live in sympatry, each with a distinct karyotype. Hemideina thoracica and H. trewicki are probably reproductively isolated, with sterile F1 hybrids. This species pair shows evidence of niche differences with adult size and timing of maturity differing where Hemideina thoracica is sympatric with H. trewicki. In contrast, evidence of a low level of introgression was detected in phenotypes and genotypes where H. thoracica and H. crassidens are sympatric. We found no evidence of size divergence although color traits in combination with hind tibia spines reliably distinguish the two species. This species pair show a bimodal hybrid zone in the absence of assortative mating and possible sexual exclusion by H. thoracica males in the formation of F1 hybrids.
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Affiliation(s)
- Natasha E Mckean
- Ecology Group Institute of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Steven A Trewick
- Ecology Group Institute of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Mary Morgan-Richards
- Ecology Group Institute of Agriculture and Environment Massey University Palmerston North New Zealand
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138
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Hedrick PW, Smith DW, Stahler DR. Negative-assortative mating for color in wolves. Evolution 2016; 70:757-66. [PMID: 26988852 DOI: 10.1111/evo.12906] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/13/2016] [Accepted: 03/01/2016] [Indexed: 12/01/2022]
Abstract
There is strong negative-assortative mating for gray and black pelage color in the iconic wolves in Yellowstone National Park. This is the first documented case of significant negative-assortative mating in mammals and one of only a very few cases in vertebrates. Of 261 matings documented from 1995 to 2015, 63.6% were between gray and black wolves and the correlation between mates for color was -0.266. There was a similar excess of matings of both gray males × black females and black males × gray females. Using the observed frequency of negative-assortative mating in a model with both random and negative-assortative mating, the estimated proportion of negative-assortative mating was 0.430. The estimated frequency of black wolves in the population from 1996 to 2014 was 0.452 and these frequencies appear stable over this 19-year period. Using the estimated level of negative-assortative mating, the predicted equilibrium frequency of the dominant allele was 0.278, very close to the mean value of 0.253 observed. In addition, the patterns of genotype frequencies, that is, the observed proportion of black homozygotes and the observed excess of black heterozygotes, are consistent with negative-assortative mating. Importantly these results demonstrate that negative-assortative mating could be entirely responsible for the maintenance of this well-known color polymorphism.
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Affiliation(s)
- Philip W Hedrick
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85287.
| | - Douglas W Smith
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, 82190
| | - Daniel R Stahler
- Yellowstone Wolf Project, Yellowstone Center for Resources, Yellowstone National Park, Wyoming, 82190
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139
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Janowitz Koch I, Clark MM, Thompson MJ, Deere-Machemer KA, Wang J, Duarte L, Gnanadesikan GE, McCoy EL, Rubbi L, Stahler DR, Pellegrini M, Ostrander EA, Wayne RK, Sinsheimer JS, vonHoldt BM. The concerted impact of domestication and transposon insertions on methylation patterns between dogs and grey wolves. Mol Ecol 2016; 25:1838-55. [PMID: 27112634 PMCID: PMC4849173 DOI: 10.1111/mec.13480] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 11/09/2015] [Accepted: 11/12/2015] [Indexed: 12/21/2022]
Abstract
The process of domestication can exert intense trait-targeted selection on genes and regulatory regions. Specifically, rapid shifts in the structure and sequence of genomic regulatory elements could provide an explanation for the extensive, and sometimes extreme, variation in phenotypic traits observed in domesticated species. Here, we explored methylation differences from >24 000 cytosines distributed across the genomes of the domesticated dog (Canis familiaris) and the grey wolf (Canis lupus). PCA and model-based cluster analyses identified two primary groups, domestic vs. wild canids. A scan for significantly differentially methylated sites (DMSs) revealed species-specific patterns at 68 sites after correcting for cell heterogeneity, with weak yet significant hypermethylation typical of purebred dogs when compared to wolves (59% and 58%, P < 0.05, respectively). Additionally, methylation patterns at eight genes significantly deviated from neutrality, with similar trends of hypermethylation in purebred dogs. The majority (>66%) of differentially methylated regions contained or were associated with repetitive elements, indicative of a genotype-mediated trend. However, DMSs were also often linked to functionally relevant genes (e.g. neurotransmitters). Finally, we utilized known genealogical relationships among Yellowstone wolves to survey transmission stability of methylation marks, from which we found a substantial fraction that demonstrated high heritability (both H(2) and h(2 ) > 0.99). These analyses provide a unique epigenetic insight into the molecular consequences of recent selection and radiation of our most ancient domesticated companion, the dog. These findings suggest selection has acted on methylation patterns, providing a new genomic perspective on phenotypic diversification in domesticated species.
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Affiliation(s)
- Ilana Janowitz Koch
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
| | - Michelle M Clark
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48085, USA
| | - Lionel Duarte
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Eskender L McCoy
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Daniel R Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, WY, 82190, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Elaine A Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Robert K Wayne
- Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Janet S Sinsheimer
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Department of Human Genetics and Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, 08544, USA
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140
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Pereira RJ, Martínez-Solano I, Buckley D. Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Mol Ecol 2016; 25:1551-65. [DOI: 10.1111/mec.13575] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 01/11/2016] [Accepted: 02/01/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Ricardo J. Pereira
- Centre for GeoGenetics; Natural History Museum of Denmark; University of Copenhagen; Øster Voldgade 5-7 1350 Copenhagen Denmark
| | - Iñigo Martínez-Solano
- Instituto de Investigación en Recursos Cinegéticos (IREC-UCLM-CSIC-JCCM); Ronda de Toledo, s/n 13005 Ciudad Real Spain
- Ecology, Evolution and Development Group; Department of Wetland Ecology; Estación Biológica de Doñana (EBD-CSIC); Avenida Américo Vespucio, s/n 41092 Sevilla Spain
| | - David Buckley
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales MNCN-CSIC; c/José Gutiérrez Abascal 2 28006 Madrid Spain
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141
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Freedman AH, Schweizer RM, Ortega-Del Vecchyo D, Han E, Davis BW, Gronau I, Silva PM, Galaverni M, Fan Z, Marx P, Lorente-Galdos B, Ramirez O, Hormozdiari F, Alkan C, Vilà C, Squire K, Geffen E, Kusak J, Boyko AR, Parker HG, Lee C, Tadigotla V, Siepel A, Bustamante CD, Harkins TT, Nelson SF, Marques-Bonet T, Ostrander EA, Wayne RK, Novembre J. Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs. PLoS Genet 2016; 12:e1005851. [PMID: 26943675 PMCID: PMC4778760 DOI: 10.1371/journal.pgen.1005851] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/18/2016] [Indexed: 12/31/2022] Open
Abstract
Controlling for background demographic effects is important for accurately identifying loci that have recently undergone positive selection. To date, the effects of demography have not yet been explicitly considered when identifying loci under selection during dog domestication. To investigate positive selection on the dog lineage early in the domestication, we examined patterns of polymorphism in six canid genomes that were previously used to infer a demographic model of dog domestication. Using an inferred demographic model, we computed false discovery rates (FDR) and identified 349 outlier regions consistent with positive selection at a low FDR. The signals in the top 100 regions were frequently centered on candidate genes related to brain function and behavior, including LHFPL3, CADM2, GRIK3, SH3GL2, MBP, PDE7B, NTAN1, and GLRA1. These regions contained significant enrichments in behavioral ontology categories. The 3rd top hit, CCRN4L, plays a major role in lipid metabolism, that is supported by additional metabolism related candidates revealed in our scan, including SCP2D1 and PDXC1. Comparing our method to an empirical outlier approach that does not directly account for demography, we found only modest overlaps between the two methods, with 60% of empirical outliers having no overlap with our demography-based outlier detection approach. Demography-aware approaches have lower-rates of false discovery. Our top candidates for selection, in addition to expanding the set of neurobehavioral candidate genes, include genes related to lipid metabolism, suggesting a dietary target of selection that was important during the period when proto-dogs hunted and fed alongside hunter-gatherers.
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Affiliation(s)
- Adam H. Freedman
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Rena M. Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Diego Ortega-Del Vecchyo
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eunjung Han
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Brian W. Davis
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ilan Gronau
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | | | | | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment, Sichuan University, Chengdu, China
| | - Peter Marx
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, Hungary
| | - Belen Lorente-Galdos
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Oscar Ramirez
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Farhad Hormozdiari
- Department of Computer Science, University of California, Los Angeles, Los Angeles, California, United States of America
| | | | - Carles Vilà
- Estación Biológia de Doñana EBD-CSIC, Sevilla, Spain
| | - Kevin Squire
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Eli Geffen
- Department of Zoology, Tel Aviv University, Tel Aviv, Israel
| | - Josip Kusak
- Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Adam R. Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, New York, United States of America
| | - Heidi G. Parker
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Clarence Lee
- Life Technologies, Foster City, California, United States of America
| | - Vasisht Tadigotla
- Life Technologies, Foster City, California, United States of America
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America
| | | | | | - Stanley F. Nelson
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Tomas Marques-Bonet
- ICREA at Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
- Centro Nacional de Analisis Genomico (CNAG/PCB), Baldiri Reixach 4–8, Barcelona, Spain
| | - Elaine A. Ostrander
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
| | - John Novembre
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, California, United States of America
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142
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Schneiderová I, Zouhar J, Štefanská L, Bolfíková BČ, Lhota S, Brandl P. Vocal activity of lesser galagos (Galago spp.) at zoos. Zoo Biol 2016; 35:147-56. [PMID: 26741794 DOI: 10.1002/zoo.21261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 12/16/2015] [Indexed: 11/06/2022]
Abstract
Almost nothing is known about the natural vocal behavior of lesser galagos living in zoos. This is perhaps because they are usually kept in nocturnal exhibits separated from the visitors by a transparent and acoustically insulating glass barrier. The aim of the present study was therefore to fill this gap in knowledge of the vocal behavior of lesser galagos from zoos. This knowledge might be beneficial because the vocalizations of these small primates can be used for species determination. We performed a 10-day-long acoustic monitoring of vocal activity in each of seven various groups of Galago senegalensis and G. moholi living at four zoos. We quantitatively evaluated the occurrence of four loud vocalization types present in both species, including the most species-specific advertisement call. We found that qualitative as well as quantitative differences exist in the vocal behavior of the studied groups. We confirmed that the observed vocalization types can be collected from lesser galagos living at zoos, and the success can be increased by selecting larger and more diverse groups. We found two distinct patterns of diel vocal activity in the most vocally active groups. G. senegalensis groups were most vocally active at the beginning and at the end of their activity period, whereas one G. moholi group showed an opposite pattern. The latter is surprising, as it is generally accepted that lesser galagos emit advertisement calls especially at dawn and dusk, i.e., at the beginning and at the end of their diel activity.
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Affiliation(s)
- Irena Schneiderová
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Jan Zouhar
- Department of Econometrics, Faculty of Informatics and Statistics, University of Economics, Prague, Czech Republic
| | - Lucie Štefanská
- Department of Game Management and Wildlife Biology, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Barbora Černá Bolfíková
- Department of Animal Science and Food Processing, Faculty of Tropical Agrisciences, Czech University of Life Sciences, Prague, Czech Republic
| | - Stanislav Lhota
- Department of Husbandry and Ethology of Animals, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences, Prague, Czech Republic.,Ústí nad Labem Zoo, Ústí nad Labem, Czech Republic
| | - Pavel Brandl
- Prague Zoological Garden, Prague, Czech Republic
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143
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Lifshitz N, St Clair CC. Coloured ornamental traits could be effective and non-invasive indicators of pollution exposure for wildlife. CONSERVATION PHYSIOLOGY 2016; 4:cow028. [PMID: 27766151 PMCID: PMC5069843 DOI: 10.1093/conphys/cow028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 06/09/2016] [Accepted: 06/22/2016] [Indexed: 05/21/2023]
Abstract
Growth in human populations causes habitat degradation for other species, which is usually gauged by physical changes to landscapes. Corresponding habitat degradation to air and water is also common, but its effects on individuals can be difficult to detect until they result in the decline or disappearance of populations. More proactive measures of pollution usually combine abiotic samples of soil, water or air with invasive sampling of expendable species, but this approach sometimes creates ethical dilemmas and has limited application for threatened species. Here, we describe the potential to measure the effects of pollution on many species of birds and fish by using ornamental traits that are expressed as coloured skin, feathers and scales. As products of sexual selection, these traits are sensitive to environmental conditions, thereby providing honest information about the condition of their bearers as ready-made biomarkers. We review the documented effects of several classes of pollutants, including pharmaceuticals, pesticides, industry-related compounds and metals, on two classes of colour pigments, namely melanins and carotenoids. We find that several pollutants impede the expression of both carotenoids and brown melanin, while enhancing traits coloured by black melanin. We also review some of the current limitations of using ornamental colour as an indicator of pollution exposure, suggest avenues for future research and speculate about how advances in robotics and remote imagery will soon make it possible to measure these traits remotely and in a non-invasive manner. Wider awareness of this potential by conservation managers could foster the development of suitable model species and comparative metrics and lay a foundation for pollution monitoring that is more generalizable and biologically relevant than existing standards.
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Affiliation(s)
- Natalia Lifshitz
- Corresponding author: Department of Biological Sciences, University of Alberta, Z-708, 11455 Saskatchewan Drive, Edmonton, Alberta, Canada T6G 2E9. Tel: +1 780 492 9685.
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144
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Schweizer RM, Robinson J, Harrigan R, Silva P, Galverni M, Musiani M, Green RE, Novembre J, Wayne RK. Targeted capture and resequencing of 1040 genes reveal environmentally driven functional variation in grey wolves. Mol Ecol 2015; 25:357-79. [DOI: 10.1111/mec.13467] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/29/2022]
Affiliation(s)
- Rena M. Schweizer
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
| | - Ryan Harrigan
- Center for Tropical Research Institute of the Environment and Sustainability University of California 619 Charles E. Young Drive East Los Angeles CA 90095 USA
| | - Pedro Silva
- CIBIO/InBio – Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Campus Agrário de Vairão 4485‐661 Vairão Portugal
- Departamento de Biologia Faculdade de Ciências Universidade do Porto Rua do Campo Alegre s/n. 4169‐007 Porto Portugal
| | - Marco Galverni
- Laboratory of Genetics ISPRA (Istituto Superiore per la Protezione e Ricerca Ambientale) Via Cà Fornacetta 9 40064 Ozzano dell'Emilia BO Italy
| | - Marco Musiani
- Faculties of Environmental Design and Veterinary Medicine (Joint Appointment) EVDS University of Calgary 2500 University Dr NW Calgary Alberta Canada T2N 1N4
| | - Richard E. Green
- Department of Biomolecular Engineering University of California Santa Cruz CA 95060 USA
| | - John Novembre
- Department of Human Genetics University of Chicago 920 E. 58th Street Chicago IL 60637 USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology University of California, Los Angeles 610 Charles E Young Dr East Los Angeles CA 90095 USA
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145
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Fan Z, Silva P, Gronau I, Wang S, Armero AS, Schweizer RM, Ramirez O, Pollinger J, Galaverni M, Ortega Del-Vecchyo D, Du L, Zhang W, Zhang Z, Xing J, Vilà C, Marques-Bonet T, Godinho R, Yue B, Wayne RK. Worldwide patterns of genomic variation and admixture in gray wolves. Genome Res 2015; 26:163-73. [PMID: 26680994 PMCID: PMC4728369 DOI: 10.1101/gr.197517.115] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 12/15/2015] [Indexed: 12/25/2022]
Abstract
The gray wolf (Canis lupus) is a widely distributed top predator and ancestor of the domestic dog. To address questions about wolf relationships to each other and dogs, we assembled and analyzed a data set of 34 canine genomes. The divergence between New and Old World wolves is the earliest branching event and is followed by the divergence of Old World wolves and dogs, confirming that the dog was domesticated in the Old World. However, no single wolf population is more closely related to dogs, supporting the hypothesis that dogs were derived from an extinct wolf population. All extant wolves have a surprisingly recent common ancestry and experienced a dramatic population decline beginning at least ∼30 thousand years ago (kya). We suggest this crisis was related to the colonization of Eurasia by modern human hunter–gatherers, who competed with wolves for limited prey but also domesticated them, leading to a compensatory population expansion of dogs. We found extensive admixture between dogs and wolves, with up to 25% of Eurasian wolf genomes showing signs of dog ancestry. Dogs have influenced the recent history of wolves through admixture and vice versa, potentially enhancing adaptation. Simple scenarios of dog domestication are confounded by admixture, and studies that do not take admixture into account with specific demographic models are problematic.
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Affiliation(s)
- Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA
| | - Pedro Silva
- CIBIO-UP, University of Porto, Vairão, 4485-661, Portugal
| | - Ilan Gronau
- Efi Arazi School of Computer Science, the Herzliya Interdisciplinary Center (IDC), Herzliya 46150, Israel
| | - Shuoguo Wang
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | | | - Rena M Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA
| | - Oscar Ramirez
- ICREA at Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain
| | - John Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA
| | | | - Diego Ortega Del-Vecchyo
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, California 90095-1606, USA
| | - Lianming Du
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
| | - Wenping Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, People's Republic of China, 610081
| | - Zhihe Zhang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, Sichuan Province, People's Republic of China, 610081
| | - Jinchuan Xing
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA; Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Carles Vilà
- Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Tomas Marques-Bonet
- ICREA at Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain; Centro Nacional de Análisis Genómico (CNAG), Parc Científic de Barcelona, 08028 Barcelona, Spain
| | - Raquel Godinho
- CIBIO-UP, University of Porto, Vairão, 4485-661, Portugal
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu 610064, People's Republic of China
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California 90095-1606, USA
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146
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Semple F, MacPherson H, Webb S, Kilanowski F, Lettice L, McGlasson SL, Wheeler AP, Chen V, Millhauser GL, Melrose L, Davidson DJ, Dorin JR. Human β-Defensin 3 [corrected] Exacerbates MDA5 but Suppresses TLR3 Responses to the Viral Molecular Pattern Mimic Polyinosinic:Polycytidylic Acid. PLoS Genet 2015; 11:e1005673. [PMID: 26646717 PMCID: PMC4672878 DOI: 10.1371/journal.pgen.1005673] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/26/2015] [Indexed: 11/19/2022] Open
Abstract
Human β-defensin 3 (hBD3) is a cationic host defence peptide and is part of the innate immune response. HBD3 is present on a highly copy number variable block of six β-defensin genes, and increased copy number is associated with the autoimmune disease psoriasis. It is not known how this increase influences disease development, but psoriasis is a T cell-mediated disease and activation of the innate immune system is required for the initial trigger that leads to the amplification stage. We investigated the effect of hBD3 on the response of primary macrophages to various TLR agonists. HBD3 exacerbated the production of type I Interferon-β in response to the viral ligand mimic polyinosinic:polycytidylic acid (polyI:C) in both human and mouse primary cells, although production of the chemokine CXCL10 was suppressed. Compared to polyI:C alone, mice injected with both hBD3 peptide and polyI:C also showed an enhanced increase in Interferon-β. Mice expressing a transgene encoding hBD3 had elevated basal levels of Interferon-β, and challenge with polyI:C further increased this response. HBD3 peptide increased uptake of polyI:C by macrophages, however the cellular response and localisation of polyI:C in cells treated contemporaneously with hBD3 or cationic liposome differed. Immunohistochemistry showed that hBD3 and polyI:C do not co-localise, but in the presence of hBD3 less polyI:C localises to the early endosome. Using bone marrow derived macrophages from knockout mice we demonstrate that hBD3 suppresses the polyI:C-induced TLR3 response mediated by TICAM1 (TRIF), while exacerbating the cytoplasmic response through MDA5 (IFIH1) and MAVS (IPS1/CARDIF). Thus, hBD3, a highly copy number variable gene in human, influences cellular responses to the viral mimic polyI:C implying that copy number may have a significant phenotypic effect on the response to viral infection and development of autoimmunity in humans. Defensins are classically known as antimicrobial peptides due to their ability to rapidly kill pathogens including bacteria, viruses and fungi. They are produced in the presence of infectious agents at body surfaces exposed to the environment. Increasingly, their functional repertoire is expanding, and they have been shown to modulate the immune system. In humans, there is a block of six β-defensin genes that varies in copy number in the population. Individuals with an increased number of β-defensin genes have an increased likelihood of developing the skin autoimmune disease psoriasis. It is not known how this increase in gene copy number influences development of the disease, and psoriasis is a complex interplay of genomic and environmental factors that trigger disease progression and include exposure to viruses. We examined whether a molecular pattern characteristic of viruses produces an altered immune response in the presence of the defensin human β-defensin 3 (hBD3). We find that hBD3 triggers a larger interferon defence response to this viral mimic by increasing accessibility to a cellular receptor that recognises viral patterns. Interferon is known to be important in autoimmunity and our work may explain why individuals with increased β-defensin number are predisposed to develop psoriasis.
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Affiliation(s)
- Fiona Semple
- MRC Centre for Inflammation Research, University of Edinburgh, Queen’s Medical Research Institute (QMRI), Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Heather MacPherson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Sheila Webb
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Fiona Kilanowski
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Lettice
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah L. McGlasson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Ann P. Wheeler
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
| | - Valerie Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Glenn L. Millhauser
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Lauren Melrose
- MRC Centre for Inflammation Research, University of Edinburgh, Queen’s Medical Research Institute (QMRI), Edinburgh, United Kingdom
| | - Donald J. Davidson
- MRC Centre for Inflammation Research, University of Edinburgh, Queen’s Medical Research Institute (QMRI), Edinburgh, United Kingdom
| | - Julia R. Dorin
- MRC Centre for Inflammation Research, University of Edinburgh, Queen’s Medical Research Institute (QMRI), Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
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147
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Smetanová M, Černá Bolfíková B, Randi E, Caniglia R, Fabbri E, Galaverni M, Kutal M, Hulva P. From Wolves to Dogs, and Back: Genetic Composition of the Czechoslovakian Wolfdog. PLoS One 2015; 10:e0143807. [PMID: 26636975 PMCID: PMC4670199 DOI: 10.1371/journal.pone.0143807] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/10/2015] [Indexed: 11/18/2022] Open
Abstract
The Czechoslovakian Wolfdog is a unique dog breed that originated from hybridization between German Shepherds and wild Carpathian wolves in the 1950s as a military experiment. This breed was used for guarding the Czechoslovakian borders during the cold war and is currently kept by civilian breeders all round the world. The aim of our study was to characterize, for the first time, the genetic composition of this breed in relation to its known source populations. We sequenced the hypervariable part of the mtDNA control region and genotyped the Amelogenin gene, four sex-linked microsatellites and 39 autosomal microsatellites in 79 Czechoslovakian Wolfdogs, 20 German Shepherds and 28 Carpathian wolves. We performed a range of population genetic analyses based on both empirical and simulated data. Only two mtDNA and two Y-linked haplotypes were found in Czechoslovakian Wolfdogs. Both mtDNA haplotypes were of domestic origin, while only one of the Y-haplotypes was shared with German Shepherds and the other was unique to Czechoslovakian Wolfdogs. The observed inbreeding coefficient was low despite the small effective population size of the breed, possibly due to heterozygote advantages determined by introgression of wolf alleles. Moreover, Czechoslovakian Wolfdog genotypes were distinct from both parental populations, indicating the role of founder effect, drift and/or genetic hitchhiking. The results revealed the peculiar genetic composition of the Czechoslovakian Wolfdog, showing a limited introgression of wolf alleles within a higher proportion of the dog genome, consistent with the reiterated backcrossing used in the pedigree. Artificial selection aiming to keep wolf-like phenotypes but dog-like behavior resulted in a distinctive genetic composition of Czechoslovakian Wolfdogs, which provides a unique example to study the interactions between dog and wolf genomes.
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Affiliation(s)
- Milena Smetanová
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Barbora Černá Bolfíková
- Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Prague, Czech Republic
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e Ricerca Ambientale (ISPRA), Ozzano Emilia (BO), Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Romolo Caniglia
- Laboratorio di Genetica, Istituto Superiore per la Protezione e Ricerca Ambientale (ISPRA), Ozzano Emilia (BO), Italy
| | - Elena Fabbri
- Laboratorio di Genetica, Istituto Superiore per la Protezione e Ricerca Ambientale (ISPRA), Ozzano Emilia (BO), Italy
| | - Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e Ricerca Ambientale (ISPRA), Ozzano Emilia (BO), Italy
| | - Miroslav Kutal
- Institute of Forest Ecology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
- Friends of the Earth Czech Republic, Olomouc branch, Olomouc, Czech Republic
| | - Pavel Hulva
- Department of Zoology, Charles University in Prague, Prague, Czech Republic
- Department of Biology and Ecology, Ostrava University, Ostrava, Czech Republic
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148
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Galov A, Fabbri E, Caniglia R, Arbanasić H, Lapalombella S, Florijančić T, Bošković I, Galaverni M, Randi E. First evidence of hybridization between golden jackal (Canis aureus) and domestic dog (Canis familiaris) as revealed by genetic markers. ROYAL SOCIETY OPEN SCIENCE 2015; 2:150450. [PMID: 27019731 PMCID: PMC4807452 DOI: 10.1098/rsos.150450] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 11/03/2015] [Indexed: 05/22/2023]
Abstract
Interspecific hybridization is relatively frequent in nature and numerous cases of hybridization between wild canids and domestic dogs have been recorded. However, hybrids between golden jackals (Canis aureus) and other canids have not been described before. In this study, we combined the use of biparental (15 autosomal microsatellites and three major histocompatibility complex (MHC) loci) and uniparental (mtDNA control region and a Y-linked Zfy intron) genetic markers to assess the admixed origin of three wild-living canids showing anomalous phenotypic traits. Results indicated that these canids were hybrids between golden jackals and domestic dogs. One of them was a backcross to jackal and another one was a backcross to dog, confirming that golden jackal-domestic dog hybrids are fertile. The uniparental markers showed that the direction of hybridization, namely females of the wild species hybridizing with male domestic dogs, was common to most cases of canid hybridization. A melanistic 3bp-deletion at the K locus (β-defensin CDB103 gene), that was absent in reference golden jackal samples, but was found in a backcross to jackal with anomalous black coat, suggested its introgression from dogs via hybridization. Moreover, we demonstrated that MHC sequences, although rarely used as markers of hybridization, can be also suitable for the identification of hybrids, as long as haplotypes are exclusive for the parental species.
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Affiliation(s)
- Ana Galov
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb 10000, Croatia
- Author for correspondence: Ana Galov e-mail:
| | - Elena Fabbri
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Romolo Caniglia
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Haidi Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, Zagreb 10000, Croatia
| | - Silvana Lapalombella
- Department of Biological, Geological and Environmental Sciences University of Bologna, Via Selmi 3, Bologna 40126, Italy
| | - Tihomir Florijančić
- Department for Hunting, Fishery and Beekeeping, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia
| | - Ivica Bošković
- Department for Hunting, Fishery and Beekeeping, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Kralja Petra Svačića 1d, Osijek 31000, Croatia
| | - Marco Galaverni
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell’Emilia (BO) 40064, Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, Aalborg 9000, Denmark
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149
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de Groot GA, Nowak C, Skrbinšek T, Andersen LW, Aspi J, Fumagalli L, Godinho R, Harms V, Jansman HA, Liberg O, Marucco F, Mysłajek RW, Nowak S, Pilot M, Randi E, Reinhardt I, Śmietana W, Szewczyk M, Taberlet P, Vilà C, Muñoz-Fuentes V. Decades of population genetic research reveal the need for harmonization of molecular markers: the grey wolf C
anis lupus
as a case study. Mamm Rev 2015. [DOI: 10.1111/mam.12052] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- G. Arjen de Groot
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Carsten Nowak
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Tomaž Skrbinšek
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Večna pot 111 Ljubljana 1000 Slovenia
| | | | - Jouni Aspi
- Department of Biology, Genetics and Physiology; University of Oulu; P.O. Box 3000 90014 Oulu Finland
| | - Luca Fumagalli
- Department of Ecology and Evolution; Laboratory for Conservation Biology; Biophore Building; University of Lausanne; 1015 Lausanne Switzerland
| | - Raquel Godinho
- Research Center in Biodiversity and Genetic Resources; CIBIO/InBio; Campus Agrário de Vairão 4485-661 Vairão Portugal
- Department of Biology; Faculty of Sciences; University of Porto; Rua do Campo Alegre s/n 4169-007 Porto Portugal
- Department of Zoology; Faculty of Sciences; University of Johannesburg; Auckland Park 2006 Johannesburg South Africa
| | - Verena Harms
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
| | - Hugh A.H. Jansman
- Animal Ecology; Alterra, Wageningen UR; P.O. Box 47 6700 AA Wageningen The Netherlands
| | - Olof Liberg
- Swedish University of Agricultural Sciences (SLU); Grimsö Wildlife Research Station SE-730 91 Riddarhyttan Sweden
| | - Francesca Marucco
- Parco Naturale Alpi Marittime; Centro Gestione e Conservazione Grandi Carnivori; Piazza Regina Elena 30 12010 Valdieri Italy
| | - Robert W. Mysłajek
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Sabina Nowak
- Association for Nature ‘Wolf’; Twardorzeczka 229 34-324 Lipowa Poland
| | - Małgorzata Pilot
- School of Life Sciences; University of Lincoln; Green Lane Lincoln LN6 7DL UK
| | - Ettore Randi
- Laboratorio di Genetica; Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA); Via Cà Fornacetta 9 40064 Ozzano dell'Emilia (BO) Italy
- Aalborg University; Department 18/Section of Environmental Engineering; Sohngårdsholmsvej 57 9000 Aalborg Denmark
| | - Ilka Reinhardt
- LUPUS - German Institute for Wolf Monitoring and Research; Dorfstraße 20 02979 Spreewitz Germany
| | - Wojciech Śmietana
- Polish Academy of Sciences; Institute of Nature Conservation; Mickiewicza 33 31-120 Kraków Poland
| | - Maciej Szewczyk
- Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw; Pawińskiego 5a 02-106 Warszawa Poland
| | - Pierre Taberlet
- Centre National de la Recherche Scientifique; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
- Université Grenoble Alpes; Laboratoire d'Ecologie Alpine (LECA); F-38000 Grenoble France
| | - Carles Vilà
- Doñana Biological Station (EBD-CSIC); Avenida Americo Vespucio s/n 41092 Sevilla Spain
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group; Senckenberg Research Institute and Natural History Museum Frankfurt; Clamecystrasse 12 63571 Gelnhausen Germany
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150
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Schweizer RM, vonHoldt BM, Harrigan R, Knowles JC, Musiani M, Coltman D, Novembre J, Wayne RK. Genetic subdivision and candidate genes under selection in North American grey wolves. Mol Ecol 2015; 25:380-402. [PMID: 26333947 DOI: 10.1111/mec.13364] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 08/05/2015] [Accepted: 08/25/2015] [Indexed: 12/12/2022]
Abstract
Previous genetic studies of the highly mobile grey wolf (Canis lupus) found population structure that coincides with habitat and phenotype differences. We hypothesized that these ecologically distinct populations (ecotypes) should exhibit signatures of selection in genes related to morphology, coat colour and metabolism. To test these predictions, we quantified population structure related to habitat using a genotyping array to assess variation in 42 036 single-nucleotide polymorphisms (SNPs) in 111 North American grey wolves. Using these SNP data and individual-level measurements of 12 environmental variables, we identified six ecotypes: West Forest, Boreal Forest, Arctic, High Arctic, British Columbia and Atlantic Forest. Next, we explored signals of selection across these wolf ecotypes through the use of three complementary methods to detect selection: FST /haplotype homozygosity bivariate percentilae, bayescan, and environmentally correlated directional selection with bayenv. Across all methods, we found consistent signals of selection on genes related to morphology, coat coloration, metabolism, as predicted, as well as vision and hearing. In several high-ranking candidate genes, including LEPR, TYR and SLC14A2, we found variation in allele frequencies that follow environmental changes in temperature and precipitation, a result that is consistent with local adaptation rather than genetic drift. Our findings show that local adaptation can occur despite gene flow in a highly mobile species and can be detected through a moderately dense genomic scan. These patterns of local adaptation revealed by SNP genotyping likely reflect high fidelity to natal habitats of dispersing wolves, strong ecological divergence among habitats, and moderate levels of linkage in the wolf genome.
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Affiliation(s)
- Rena M Schweizer
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - Bridgett M vonHoldt
- Department of Ecology & Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ, 08544-2016, USA
| | - Ryan Harrigan
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, 619 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
| | - James C Knowles
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - Marco Musiani
- Faculties of Environmental Design and Veterinary Medicine (Joint Appointment), EVDS, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada, T2N 1N4
| | - David Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada, T6G 2E9
| | - John Novembre
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095, USA
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