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Abbona CC, Lebrasseur O, Prevosti FJ, Peralta E, González Venanzi L, Frantz L, Larson G, Gil AF, Neme GA. Patagonian partnerships: the extinct Dusicyon avus and its interaction with prehistoric human communities. R Soc Open Sci 2024; 11:231835. [PMID: 38601034 PMCID: PMC11004678 DOI: 10.1098/rsos.231835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
The southern Mendoza province, located in the northern region of Patagonia, was inhabited by hunter-gatherer groups until historic times. Previous archaeological studies have reported canid remains among faunal assemblages, which were assumed to be part of the human diet. However, the taxonomic identification and significance of these canids within human groups have raised questions. In this study, we used ancient DNA analysis, morphological examination and stable isotope analysis (δ13Ccol and δ15N) to re-evaluate the taxonomic assignment of a canid discovered at the Late Holocene burial site of Cañada Seca. Previous morphological identifications suggested that it belonged to the genus Lycalopex, but our results conclusively demonstrate that the individual belongs to the extinct fox species Dusicyon avus. This finding expands Dusicyon avus' known geographical distribution to Patagonia's northern extremity. Furthermore, statistical predictions based on genetic divergence undermine the hypothesis that hybridization between Canis and Dusicyon, facilitated by the introduction of domestic dogs, played a role in the extinction of Dusicyon species. On the other hand, our findings indicate that a Dusicyon avus individual shared a similar diet and was probably buried alongside humans, suggesting a close relationship between the two species during their lives and deaths.
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Affiliation(s)
- Cinthia C. Abbona
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Ophélie Lebrasseur
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Francisco J. Prevosti
- Museo de Ciencias Antropológicas y Naturales, Universidad Nacional de La Rioja (UNLaR), Avenue Luis M. de la Fuente S/N, La Rioja5300, Argentina
| | - Eva Peralta
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Lucio González Venanzi
- Div. Arqueología, Anexo Museo, Laboratory 128 (FCNyM-UNLP), La Plata, Argentina, FHumyAr (UNR), Rosario, Argentina
| | - Laurent Frantz
- Graduate School Life Science Munich, Faculty of Biology/Biocenter, Grosshadernerstr, 2-4, 82152 Planegg-Martinsried, Munich, Germany
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, School of Archaeology, University of Oxford, OxfordOX1 3TG, UK
| | - Adolfo F. Gil
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
| | - Gustavo A. Neme
- Instituto de Evolución, Ecología Histórica y Ambiente (IDEVEA), UTN-CONICET, Avenue Gral. Urquiza 314, CP5600, San Rafael, Mendoza, Argentina
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2
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Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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3
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Hinton JW, West KM, Sullivan DJ, Frair JL, Chamberlain MJ. The natural history and ecology of melanism in red wolf and coyote populations of the southeastern United States – evidence for Gloger’s rule. BMC ZOOL 2022; 7:33. [PMID: 37170305 PMCID: PMC10127370 DOI: 10.1186/s40850-022-00138-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Gloger’s rule postulates that animals should be darker colored in warm and humid regions where dense vegetation and dark environments are common. Although rare in Canis populations, melanism in wolves is more common in North America than other regions globally and is believed to follow Gloger’s rule. In the temperate forests of the southeastern United States, historical records of red wolf (Canis rufus) and coyote (Canis latrans) populations document a consistent presence of melanism. Today, the melanistic phenotype is extinct in red wolves while occurring in coyotes and red wolf-coyote hybrids who occupy the red wolf's historical range. To assess if Gloger’s rule could explain the occurrence and maintenance of melanistic phenotypes in Canis taxa, we investigated differences in morphology, habitat selection, and survival associated with pelage color using body measurements, GPS tracking data, and long-term capture-mark-recapture and radio-telemetry data collected on coyotes and hybrids across the southeastern United States.
Results
We found no correlation between morphometrics and pelage color for Canis taxa. However, we observed that melanistic coyotes and hybrids experienced greater annual survival than did their gray conspecifics. Furthermore, we observed that melanistic coyotes maintained larger home ranges and exhibited greater selection for areas with dense canopy cover and wetlands than did gray coyotes.
Conclusions
In the southeastern United States, pelage color influenced habitat selection by coyotes and annual survival of coyotes and hybrids providing evidence that Gloger’s rule is applicable to canids inhabiting regions with dense canopy cover and wetlands. Greater annual survival rates observed in melanistic Canis may be attributed to better concealment in areas with dense canopy cover such as coastal bottomland forests. We suggest that the larger home range sizes of melanistic coyotes may reflect the trade-off of reduced foraging efficiency in lower quality wetland habitat for improved survival. Larger home ranges and differential use of land cover by melanistic coyotes may facilitate weak assortative mating in eastern coyote populations, in which melanistic animals may have lower success of finding compatible mates in comparison to gray conspecifics. We offer that our observations provide a partial explanation for why melanism is relatively low (< 10%) but consistent within coyote populations throughout southeastern parts of their range.
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vonHoldt BM, Aardema ML. Updating the Bibliography of Interbreeding among Canis in North America. J Hered 2021; 111:249-262. [PMID: 32034410 DOI: 10.1093/jhered/esaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 02/05/2020] [Indexed: 01/29/2023] Open
Abstract
This bibliography provides a collection of references that documents the evolution of studies evidencing interbreeding among Canis species in North America. Over the past several decades, advances in biology and genomic technology greatly improved our ability to detect and characterize species interbreeding, which has significance for understanding species in a changing landscape as well as for endangered species management. This bibliography includes a discussion within each category of interbreeding, the timeline of developing evidence, and includes a review of past research conducted on experimental crosses. Research conducted in the early 20th century is rich with detailed records and photographs of hybrid offspring development and behavior. With the progression of molecular methods, studies can estimate historical demographic parameters and detect chromosomal patterns of ancestry. As these methods continue to increase in accessibility, the field will gain a deeper and richer understanding of the evolutionary history of North American Canis.
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Affiliation(s)
- Bridgett M vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ
| | - Matthew L Aardema
- Department of Biology, Montclair State University, Montclair, NJ.,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York City, NY
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Nagashima JB, Songsasen N. Canid Reproductive Biology: Norm and Unique Aspects in Strategies and Mechanisms. Animals (Basel) 2021; 11:653. [PMID: 33804569 PMCID: PMC8001368 DOI: 10.3390/ani11030653] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/15/2021] [Accepted: 02/20/2021] [Indexed: 12/18/2022] Open
Abstract
The reproductive physiology of canids is unique compared to other mammalian species. Specifically, the reproductive cycle of female canids is characterized by extended periods of proestrus and estrus followed by obligatory diestrus and protracted ovarian inactivity (anestrus). Although canid reproduction follows this general pattern, studies have shown variations in reproductive biology among species and geographic regions. Understanding of these differences is critical to the development of assisted reproductive technologies including estrus induction, gamete rescue, and embryo production techniques for canid conservation efforts. This review summarizes current knowledge of canid reproduction, including estrus cyclicity, seasonality, and seminal traits, with the emphasis on species diversity. The application of reproductive technologies in wild canid conservation will also be discussed.
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Affiliation(s)
- Jennifer B. Nagashima
- Center for Species Survival, Smithsonian Conservation Biology Institute, 1500 Remount Rd., Front Royal, VA 22630, USA;
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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vonHoldt B, Heppenheimer E, Petrenko V, Croonquist P, Rutledge LY. Ancestry-Specific Methylation Patterns in Admixed Offspring from an Experimental Coyote and Gray Wolf Cross. J Hered 2017; 108:341-348. [PMID: 28182234 DOI: 10.1093/jhered/esx004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 01/19/2017] [Indexed: 12/18/2022] Open
Abstract
Reduced fitness of admixed individuals is typically attributed to genetic incompatibilities. Although mismatched genomes can lead to fitness changes, in some cases the reduction in hybrid fitness is subtle. The potential role of transcriptional regulation in admixed genomes could provide a mechanistic explanation for these discrepancies, but evidence is lacking for nonmodel organisms. Here, we explored the intersection of genetics and gene regulation in admixed genomes derived from an experimental cross between a western gray wolf and western coyote. We found a significant positive association between methylation and wolf ancestry, and identified outlier genes that have been previously implicated in inbreeding-related, or otherwise deleterious, phenotypes. We describe a pattern of site-specific, rather than genome-wide, methylation driven by inter-specific hybridization. Epigenetic variation is thus suggested to play a nontrivial role in both maintaining and combating mismatched genotypes through putative transcriptional mechanisms. We conclude that the regulation of gene expression is an underappreciated key component of hybrid genome functioning, but could also act as a potential source of novel and beneficial adaptive variation in hybrid offspring.
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Affiliation(s)
- Bridgett vonHoldt
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Elizabeth Heppenheimer
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Vladimir Petrenko
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Paula Croonquist
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
| | - Linda Y Rutledge
- From the Ecology & Evolutionary Biology Department, Princeton University, 106A Guyot Hall, Princeton, NJ 08544 (vonHoldt, Heppenheimer, and Rutledge); and Biology Department, Anoka-Ramsey Community College, Coon Rapids, MN 55433 (Petrenko and Croonquist)
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8
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Mech LD, Asa CS, Callahan M, Christensen BW, Smith F, Young JK. Studies of wolf x coyote hybridization via artificial insemination. PLoS One 2017; 12:e0184342. [PMID: 28863171 DOI: 10.1371/journal.pone.0184342] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022] Open
Abstract
Following the production of western gray wolf (Canis lupus) x western coyote (Canis latrans) hybrids via artificial insemination (AI), the present article documents that the hybrids survived in captivity for at least 4 years and successfully bred with each other. It further reports that backcrossing one of the hybrids to a male gray wolf by AI also resulted in the birth of live pups that have survived for at least 10 months. All male hybrids (F1 and F2) produced sperm by about 10 months of age, and sperm quality of the F1 males fell within the fertile range for domestic dogs, but sperm motility and morphology, in particular, were low in F2 males at 10 months but improved in samples taken at 22 months of age. These studies are relevant to a long-standing controversy about the identity of the red wolf (Canis rufus), the existence of a proposed new species (Canis lycaon) of gray wolf, and to the role of hybridization in mammalian evolution.
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Abstract
A response to Hohenlohe et al.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Laboratory of Neurogenetics of Language, Rockefeller University, New York, NY 10065, USA
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46510, Israel
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jeff Wall
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90094, USA
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10
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Hohenlohe PA, Rutledge LY, Waits LP, Andrews KR, Adams JR, Hinton JW, Nowak RM, Patterson BR, Wydeven AP, Wilson PA, White BN. Comment on "Whole-genome sequence analysis shows two endemic species of North American wolf are admixtures of the coyote and gray wolf". Sci Adv 2017; 3:e1602250. [PMID: 28630899 PMCID: PMC5462499 DOI: 10.1126/sciadv.1602250] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 04/19/2017] [Indexed: 05/05/2023]
Abstract
Whole-genome data do not support a recent hybrid origin for red and eastern wolves.
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Affiliation(s)
- Paul A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA
| | - Linda Y. Rutledge
- Biology Department, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, USA
| | - Kimberly R. Andrews
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID 83844-1136, USA
| | - Joseph W. Hinton
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | | | - Brent R. Patterson
- Ministry of Natural Resources and Forestry, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | | | - Paul A. Wilson
- Biology Department, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Brad N. White
- Biology Department, Trent University, Peterborough, Ontario K9L 0G2, Canada
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Franco-Trecu V, Abud C, Feijoo M, Kloetzer G, Casacuberta M, Costa-Urrutia P. Sex beyond species: the first genetically analyzed case of intergeneric fertile hybridization in pinnipeds. Evol Dev 2016; 18:127-36. [PMID: 26994861 DOI: 10.1111/ede.12183] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A species, according to the biological concept, is a natural group of potentially interbreeding individuals isolated by diverse mechanisms. Hybridization is considered the production of offspring resulting from the interbreeding of two genetically distinct taxa. It has been documented in over 10% of wild animals, and at least in 34 cases for Artic marine mammals. In Otariids, intergeneric hybridization has been reported though neither confirming it through genetic analyses nor presenting evidence of fertile offspring. In this study, we report the finding of a hybrid adult female between a South American fur seal (Arctocephalus australis) and a South American sea lion (Otaria byronia), and its offspring, a male pup, in Uruguay. Further based on morphological constraints and breeding seasons, sex-biased hybridization between the two species is hypothesized. Morphological and genetic (nuclear and mitochondrial) results confirm de hybrid nature of the female-pup pair. Here we discuss a genetic dilution effect, considering other hybridization events must be occurring, and how isolation mechanisms could be circumvented. Moreover, the results obtained from stable isotope analysis suggest feeding habits may be a trait transmitted maternally, leading to consider broader issues regarding hybridization as an evolutionary innovation phenomenon.
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Affiliation(s)
- Valentina Franco-Trecu
- Departamento de Ecología & Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Carolina Abud
- Departamento de Ecología & Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Matías Feijoo
- Departamento de Ecología & Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | | | | | - Paula Costa-Urrutia
- Facultad de Ciencias Marinas, Universidad Autónoma de Baja California, Km 103 carretera Tijuana-Ensenada, 22860 Ensenada Baja California, México.,Metric Genetic Laboratory, Sport City, Blvd Adolfo López Mateos 1181, San Pedro de Los Pinos, 01180 Ciudad de México, México
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12
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vonHoldt BM, Cahill JA, Fan Z, Gronau I, Robinson J, Pollinger JP, Shapiro B, Wall J, Wayne RK. Whole-genome sequence analysis shows that two endemic species of North American wolf are admixtures of the coyote and gray wolf. Sci Adv 2016; 2:e1501714. [PMID: 29713682 PMCID: PMC5919777 DOI: 10.1126/sciadv.1501714] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 06/28/2016] [Indexed: 05/22/2023]
Abstract
Protection of populations comprising admixed genomes is a challenge under the Endangered Species Act (ESA), which is regarded as the most powerful species protection legislation ever passed in the United States but lacks specific provisions for hybrids. The eastern wolf is a newly recognized wolf-like species that is highly admixed and inhabits the Great Lakes and eastern United States, a region previously thought to be included in the geographic range of only the gray wolf. The U.S. Fish and Wildlife Service has argued that the presence of the eastern wolf, rather than the gray wolf, in this area is grounds for removing ESA protection (delisting) from the gray wolf across its geographic range. In contrast, the red wolf from the southeastern United States was one of the first species protected under the ESA and was protected despite admixture with coyotes. We use whole-genome sequence data to demonstrate a lack of unique ancestry in eastern and red wolves that would not be expected if they represented long divergent North American lineages. These results suggest that arguments for delisting the gray wolf are not valid. Our findings demonstrate how a strict designation of a species under the ESA that does not consider admixture can threaten the protection of endangered entities. We argue for a more balanced approach that focuses on the ecological context of admixture and allows for evolutionary processes to potentially restore historical patterns of genetic variation.
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Affiliation(s)
- Bridgett M. vonHoldt
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - James A. Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Zhenxin Fan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center, Herzliya 46150, Israel
| | - Jacqueline Robinson
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
| | - John P. Pollinger
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jeff Wall
- Department of Epidemiology and Biostatistics, School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA 90095–1606, USA
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13
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Affiliation(s)
- L Y Rutledge
- Department of Ecology and Evolutionary Biology, Princeton University, 106A Guyot Hall, Princeton, NJ 08544, USA
| | - S Devillard
- Université de Lyon, Lyon 69000, France; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, Villeurbanne 69622, France
| | - P A Hohenlohe
- Department of Biological Sciences and Institute of Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | - B N White
- Department of Biology, Trent University, 2140 East Bank Drive, Peterborough, Ontario, Canada K9 J 7B9
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14
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Abstract
Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes, in combination with genomic simulations, to test hypotheses of hybrid origins of Canis types in eastern North America. A principal components analysis revealed no evidence to support eastern wolves, or any other Canis type, as the product of grey wolf × western coyote hybridization. In contrast, simulations that included eastern wolves as a distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves and eastern coyotes. Our results support the eastern wolf as a distinct genomic cluster in North America and help resolve hybrid origins of Great Lakes wolves and eastern coyotes. The data provide timely information that will shed new light on the debate over wolf conservation in eastern North America.
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Affiliation(s)
- L. Y. Rutledge
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, Ontario, K9J 7B8Canada
- e-mail:
| | - S. Devillard
- Université de Lyon, F-69000, Lyon; Université Lyon 1; CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, F-69622, Villeurbanne, France
| | | | - P. A. Hohenlohe
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA
| | - B. N. White
- Biology Department, Trent University, 2140 East Bank Drive, Peterborough, Ontario, K9J 7B8Canada
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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Meachen JA, Brannick AL, Fry TJ. Extinct Beringian wolf morphotype found in the continental U.S. has implications for wolf migration and evolution. Ecol Evol 2016; 6:3430-8. [PMID: 27252837 PMCID: PMC4870223 DOI: 10.1002/ece3.2141] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/22/2016] [Accepted: 03/27/2016] [Indexed: 11/08/2022] Open
Abstract
Pleistocene diversity was much higher than today, for example there were three distinct wolf morphotypes (dire, gray, Beringian) in North America versus one today (gray). Previous fossil evidence suggested that these three groups overlapped ecologically, but split the landscape geographically. The Natural Trap Cave (NTC) fossil site in Wyoming, USA is an ideally placed late Pleistocene site to study the geographical movement of species from northern to middle North America before, during, and after the last glacial maximum. Until now, it has been unclear what type of wolf was present at NTC. We analyzed morphometrics of three wolf groups (dire, extant North American gray, Alaskan Beringian) to determine which wolves were present at NTC and what this indicates about wolf diversity and migration in Pleistocene North America. Results show NTC wolves group with Alaskan Beringian wolves. This provides the first morphological evidence for Beringian wolves in mid‐continental North America. Their location at NTC and their radiocarbon ages suggest that they followed a temporary channel through the glaciers. Results suggest high levels of competition and diversity in Pleistocene North American wolves. The presence of mid‐continental Beringian morphotypes adds important data for untangling the history of immigration and evolution of Canis in North America.
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Affiliation(s)
- Julie A Meachen
- Anatomy Department Des Moines University 3200 Grand Ave Des Moines Iowa 50312
| | | | - Trent J Fry
- Anatomy Department Des Moines University 3200 Grand Ave Des Moines Iowa 50312
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17
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Sefc KM, Koblmüller S. Ancient hybrid origin of the eastern wolf not yet off the table: a comment on Rutledge et al. (2015). Biol Lett 2016; 12:20150834. [PMID: 26843554 PMCID: PMC4780545 DOI: 10.1098/rsbl.2015.0834] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/09/2015] [Indexed: 11/12/2022] Open
Abstract
A recent study of North American canids by Rutledge et al. (Biol. Lett. 11, 20150303 (doi:10.1098/rsbl.2015.0303)) refutes the hypothesized hybrid origin of the eastern wolf (EW) based on genomic evidence against very recent hybridization. However, the analyses do not rule out the possibility of more ancient hybridization. Claims to have resolved the evolutionary origin of the EW are therefore inappropriate. Importantly, though, we plead that uncertainty about the ancient history of the taxon should not affect current conservation policy.
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Affiliation(s)
- Kristina M Sefc
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
| | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria
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