1
|
Ålund M, Cenzer M, Bierne N, Boughman JW, Cerca J, Comerford MS, Culicchi A, Langerhans B, McFarlane SE, Möst MH, North H, Qvarnström A, Ravinet M, Svanbäck R, Taylor SA. Anthropogenic Change and the Process of Speciation. Cold Spring Harb Perspect Biol 2023; 15:a041455. [PMID: 37788888 PMCID: PMC10691492 DOI: 10.1101/cshperspect.a041455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Anthropogenic impacts on the environment alter speciation processes by affecting both geographical contexts and selection patterns on a worldwide scale. Here we review evidence of these effects. We find that human activities often generate spatial isolation between populations and thereby promote genetic divergence but also frequently cause sudden secondary contact and hybridization between diverging lineages. Human-caused environmental changes produce new ecological niches, altering selection in diverse ways that can drive diversification; but changes also often remove niches and cause extirpations. Human impacts that alter selection regimes are widespread and strong in magnitude, ranging from local changes in biotic and abiotic conditions to direct harvesting to global climate change. Altered selection, and evolutionary responses to it, impacts early-stage divergence of lineages, but does not necessarily lead toward speciation and persistence of separate species. Altogether, humans both promote and hinder speciation, although new species would form very slowly relative to anthropogenic hybridization, which can be nearly instantaneous. Speculating about the future of speciation, we highlight two key conclusions: (1) Humans will have a large influence on extinction and "despeciation" dynamics in the short term and on early-stage lineage divergence, and thus potentially speciation in the longer term, and (2) long-term monitoring combined with easily dated anthropogenic changes will improve our understanding of the processes of speciation. We can use this knowledge to preserve and restore ecosystems in ways that promote (re-)diversification, increasing future opportunities of speciation and enhancing biodiversity.
Collapse
Affiliation(s)
- Murielle Ålund
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Meredith Cenzer
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Nicolas Bierne
- ISEM, Université de Montpellier, CNRS, IRD, Montpellier 34095, France
| | - Janette W Boughman
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - José Cerca
- CEES - Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo 0316, Norway
| | | | - Alessandro Culicchi
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Brian Langerhans
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - S Eryn McFarlane
- Department of Botany, University of Wyoming, Laramie, Wyoming 82071, USA
- Department of Biology, York University, Toronto, Ontario M3J 1P3, Canada
| | - Markus H Möst
- Research Department for Limnology, University of Innsbruck, Innsbruck 6020, Austria
| | - Henry North
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, United Kingdom
| | - Anna Qvarnström
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Richard Svanbäck
- Department of Ecology and Genetics, Animal Ecology, Uppsala University, Uppsala 75236, Sweden
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado 80309, USA
| |
Collapse
|
2
|
Smith WJ, Jezierski MT, Dunn JC, Clegg SM. Parasite exchange and hybridisation at a wild-feral-domestic interface. Int J Parasitol 2023; 53:797-808. [PMID: 37474096 DOI: 10.1016/j.ijpara.2023.06.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/27/2023] [Accepted: 06/06/2023] [Indexed: 07/22/2023]
Abstract
Interactions between wild, feral, and domestic animals are of economic and conservation significance. The pigeon Columba livia is a synanthropic species in a feral form, but it also includes the rare Rock Dove. Columba livia is an important player at the wild-domestic interface, acting as a carrier of avian diseases, and the feral form threatens Rock Doves with extinction via hybridisation. Despite its abundance, little is known about drivers of disease prevalence in C. livia, or how disease and hybridisation represent synergistic threats to Rock Doves. We focused on infection by the parasite Trichomonas, first collating prevalence estimates in domestic and free-living populations from relevant studies of C. livia. Second, we characterised variation in the diversity and prevalence of Trichomonas among three C. livia populations in the United Kingdom: a feral, a Rock Dove, and a feral-wild hybrid population. Across multiple continents, free-living pigeons had lower Trichomonas infection than captive conspecifics, but the effect was weak. Environmental factors which could impact Trichomonas infection status did not explain variation in infection among populations. Among the British populations, strain diversity varied, and there was lower parasite prevalence in Rock Doves than feral pigeons. Individual infection status was not explained by the available covariates, including hybrid score and site. The drivers of Trichomonas prevalence are unclear, perhaps due to idiosyncratic local-scale drivers. However, given the population-level variation in both infection prevalence and introgressive hybridisation, the potential combined effects could accelerate the extinction of the Rock Dove. Further study of the synergistic effects of multiple types of biotic interactions at the wild-feral-domestic interface is warranted, especially where vagile, globally distributed and superabundant animals are involved.
Collapse
Affiliation(s)
- William J Smith
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, UK.
| | - Michał T Jezierski
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, UK
| | - Jenny C Dunn
- School of Life and Environmental Sciences, University of Lincoln, UK; School of Biology, University of Leeds, UK
| | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, UK
| |
Collapse
|
3
|
Howard-McCombe J, Jamieson A, Carmagnini A, Russo IRM, Ghazali M, Campbell R, Driscoll C, Murphy WJ, Nowak C, O'Connor T, Tomsett L, Lyons LA, Muñoz-Fuentes V, Bruford MW, Kitchener AC, Larson G, Frantz L, Senn H, Lawson DJ, Beaumont MA. Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease. Curr Biol 2023; 33:4761-4769.e5. [PMID: 37935118 DOI: 10.1016/j.cub.2023.10.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/24/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023]
Abstract
The European wildcat population in Scotland is considered critically endangered as a result of hybridization with introduced domestic cats,1,2 though the time frame over which this gene flow has taken place is unknown. Here, using genome data from modern, museum, and ancient samples, we reconstructed the trajectory and dated the decline of the local wildcat population from viable to severely hybridized. We demonstrate that although domestic cats have been present in Britain for over 2,000 years,3 the onset of hybridization was only within the last 70 years. Our analyses reveal that the domestic ancestry present in modern wildcats is markedly over-represented in many parts of the genome, including the major histocompatibility complex (MHC). We hypothesize that introgression provides wildcats with protection against diseases harbored and introduced by domestic cats, and that this selection contributes to maladaptive genetic swamping through linkage drag. Using the case of the Scottish wildcat, we demonstrate the importance of local ancestry estimates to both understand the impacts of hybridization in wild populations and support conservation efforts to mitigate the consequences of anthropogenic and environmental change.
Collapse
Affiliation(s)
- Jo Howard-McCombe
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK; RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK.
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK; Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany
| | - Alberto Carmagnini
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany; School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | | | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK
| | - Ruairidh Campbell
- Wildlife Conservation Research Unit, Department of Zoology, University of Oxford Recanati-Kaplan Centre, Tubney House, Abingdon Road, Tubney OX13 5QL, UK; NatureScot, Great Glen House, Leachkin Road, Inverness IV3 8NW, UK
| | | | - William J Murphy
- Texas A&M University, Veterinary Integrative Biosciences, College Station, TX 77843, USA
| | - Carsten Nowak
- Senckenberg Research Institute and Natural History Museum, Center for Wildlife Genetics, 63571 Weimar, Germany
| | - Terry O'Connor
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Louise Tomsett
- Mammal Section, Science Department, Natural History Museum, London SW7 5BD, UK
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Violeta Muñoz-Fuentes
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | | | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh EH1 1JF, UK; School of Geosciences, University of Edinburgh, Drummond Street, Edinburgh EH8 9XP, UK
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilians University of Munich, Munich, Germany; School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK
| | - Helen Senn
- RZSS WildGenes Laboratory, Conservation Department, Royal Zoological Society of Scotland, Edinburgh EH12 6TS, UK.
| | - Daniel J Lawson
- School of Mathematics, University of Bristol, Bristol BS8 1UG, UK.
| | - Mark A Beaumont
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK.
| |
Collapse
|
4
|
Dubiner S, Namir I, Chen R, Levin E. Distance from human settlements favors wild-type appearance of feral cats ( Felis catus) in Mediterranean woodland. Ecol Evol 2023; 13:e10261. [PMID: 37404701 PMCID: PMC10316376 DOI: 10.1002/ece3.10261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
Camouflage is a common trait enabling animals to avoid detection by predators and prey. Patterns such as spots and stripes are convergent across carnivore families, including felids, and are hypothesized to have adaptive value through camouflage. House cats (Felis catus) were domesticated thousands of years ago, but despite artificial selection for a wide variety of coat colors, the wild-type pattern of tabby cats is very common. We aimed to determine whether this pattern grants an advantage over other morphs in natural environments. We collected cat images taken with camera traps in natural areas near and far from 38 rural settlements in Israel, to compare the habitat use by feral cats of different colors. We tested the effect of proximity to villages and habitat vegetation (normalized difference vegetation index, NDVI) on the probability of space use by the tabby morph compared to the others. NDVI had a positive effect on site use in both morphs, but non-tabby cats had a 2.1 higher probability of using the near sites than the far sites, independent of NDVI. The wild-type tabby cats' probability of site use were equally likely to be unaffected by proximity, or have an interaction of proximity with NDVI whereby the far transects are used with increasing probability in sites of denser vegetation. We hypothesize that the camouflage of tabby cats, more than other colors and patterns, confers an advantage in roaming the woodland habitats for which this pattern evolved. This has both theoretical implications as rare empirical evidence of the adaptive value of fur coloration, and practical implications on managing the ecological impact of feral cats worldwide.
Collapse
Affiliation(s)
| | - Itai Namir
- Hamaarag—Israel's National Nature Assessment Program, The Steinhardt Museum of Natural HistoryTel Aviv UniversityTel AvivIsrael
| | - Ron Chen
- Hamaarag—Israel's National Nature Assessment Program, The Steinhardt Museum of Natural HistoryTel Aviv UniversityTel AvivIsrael
| | - Eran Levin
- School of ZoologyTel Aviv UniversityTel AvivIsrael
| |
Collapse
|
5
|
Nilson SM, Gandolfi B, Grahn RA, Kurushima JD, Lipinski MJ, Randi E, Waly NE, Driscoll C, Murua Escobar H, Schuster RK, Maruyama S, Labarthe N, Chomel BB, Ghosh SK, Ozpinar H, Rah HC, Millán J, Mendes-de-Almeida F, Levy JK, Heitz E, Scherk MA, Alves PC, Decker JE, Lyons LA. Genetics of randomly bred cats support the cradle of cat domestication being in the Near East. Heredity (Edinb) 2022; 129:346-355. [PMID: 36319737 PMCID: PMC9708682 DOI: 10.1038/s41437-022-00568-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/04/2022] Open
Abstract
Cat domestication likely initiated as a symbiotic relationship between wildcats (Felis silvestris subspecies) and the peoples of developing agrarian societies in the Fertile Crescent. As humans transitioned from hunter-gatherers to farmers ~12,000 years ago, bold wildcats likely capitalized on increased prey density (i.e., rodents). Humans benefited from the cats' predation on these vermin. To refine the site(s) of cat domestication, over 1000 random-bred cats of primarily Eurasian descent were genotyped for single-nucleotide variants and short tandem repeats. The overall cat population structure suggested a single worldwide population with significant isolation by the distance of peripheral subpopulations. The cat population heterozygosity decreased as genetic distance from the proposed cat progenitor's (F.s. lybica) natural habitat increased. Domestic cat origins are focused in the eastern Mediterranean Basin, spreading to nearby islands, and southernly via the Levantine coast into the Nile Valley. Cat population diversity supports the migration patterns of humans and other symbiotic species.
Collapse
Affiliation(s)
- Sara M Nilson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Robert A Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Jennifer D Kurushima
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Monika J Lipinski
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | - Ettore Randi
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, 9220, Aalborg Øst, Denmark
| | - Nashwa E Waly
- Department of Animal Medicine, Faculty of Veterinary Medicine, Assuit University, 71526, Assiut, Egypt
| | | | - Hugo Murua Escobar
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, 18055, Rostock, Germany
| | - Rolf K Schuster
- Central Veterinary Research Laboratory, Dubai, United Arab Emirates
| | - Soichi Maruyama
- Laboratory of Veterinary Public Health, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Norma Labarthe
- Programa de Bioética, Ética Aplicada e Saúde Coletiva, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, 21040-360, Brazil
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Bruno B Chomel
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA
| | | | - Haydar Ozpinar
- Graduate School of Health Sciences, Istanbul Gedik University, 34876, İstanbul, Turkey
| | - Hyung-Chul Rah
- Research Institute of Veterinary Medicine, College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Javier Millán
- Instituto Agroalimentario de Aragón-IA2 (Universidad de Zaragoza-CITA), Miguel Servet 177, 50013, Zaragoza, Spain
- Fundación ARAID, Avda. de Ranillas, 50018, Zaragoza, Spain
- Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Flavya Mendes-de-Almeida
- Programa de Pós-Graduação em Medicina Veterinária - Clínica e Reprodução Animal, Faculdade de Veterinária, Universidade Federal Fluminense, Rua Vital Brazil Filho 64, Niterói, RJ, 24230-340, Brazil
| | - Julie K Levy
- Maddie's Shelter Medicine Program, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32608, USA
| | | | | | - Paulo C Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos/InBIO Associate Lab & Faculdade de Ciências, Universidade do Porto, Campus e Vairão, 4485-661, Vila do Conde, Portugal
- Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO, 65211, USA.
| | - Leslie A Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, 95616, USA.
- Department of Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA.
| |
Collapse
|
6
|
Stable isotopes unveil one millennium of domestic cat paleoecology in Europe. Sci Rep 2022; 12:12775. [PMID: 35896571 PMCID: PMC9329303 DOI: 10.1038/s41598-022-16969-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/19/2022] [Indexed: 11/11/2022] Open
Abstract
The domestic cat is the world's most popular pet and one of the most detrimental predators in terrestrial ecosystems. Effective protection of wildlife biodiversity demands detailed tracking of cat trophic ecology, and stable isotopes serve as a powerful proxy in dietary studies. However, a variable diet can make an isotopic pattern unreadable in opportunistic predators. To evaluate the usefulness of the isotopic method in cat ecology, we measured C and N isotope ratios in hundreds of archaeological cat bones. We determined trends in cat trophic paleoecology in northern Europe by exploiting population-scale patterns in animals from diverse locations. Our dataset shows a high variability of isotopic signals related to the socio-economic and/or geomorphological context. This points toward regularities in isotopic patterns across past cat populations. We provide a generalized guide to interpret the isotopic ecology of cats, emphasizing that regional isotopic baselines have a major impact on the isotopic signal.
Collapse
|
7
|
Lazzeri L, Fazzi P, Lucchesi M, Mori E, Velli E, Cappai N, Ciuti F, Ferretti F, Fonda F, Paniccia C, Pavanello M, Pecorella S, Sangiuliano A, Sforzi A, Siclari A, Spada A. The rhythm of the night: patterns of activity of the European wildcat in the Italian peninsula. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00276-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractThe European wildcat is a threatened carnivore, whose ecology is still scarcely studied, especially in Mediterranean areas. In this study, we estimated activity rhythm patterns of this felid, by means of camera-trapping at three spatial scales: (i) whole country (Italy); (ii) biogeographical areas; (iii) latitudinal zones. The activity rhythms patterns were also calculated according to temporal scales: (1) warm semester; (2) cold semester and (3) seasonal scales. Lastly, we also tested whether the effect of moon phases affected the wildcat activity. We conducted the analysis on a total of 975 independent events collected in 2009–2021, from 285 locations, in ~ 65,800 camera days. We showed that the wildcat in Italy exhibits a > 70% nocturnal behaviour, with 20% of diurnal activity, at all spatial scales, and throughout the whole year, with peaks at 10.00 p.m. and 04.00 a.m. We observed a high overlap of wildcat activity rhythms between different biogeographical and latitudinal zones. The wildcat was mainly active on the darkest nights, reducing its activity in bright moonlight nights. Diurnal activity was greater in the warm months and decreased with the distance from shrubs and woodlands, most likely according to activity rhythms of its main prey, water presence in summer, the care of offspring and the availability of shelter sites. Conversely, the distance to paved roads seems to have no significant effects on diurnal activity, suggesting that, in presence of natural shelters, the wildcat probably may tolerate these infrastructures. We suggested limited plasticity in activity rhythm patterns of the wildcat, emphasizing the importance of dark hours for this species.
Collapse
|
8
|
Landscape genetic connectivity in European wildcat (Felis silvestris silvestris): a matter of food, shelters and demographic status of populations. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
9
|
von Thaden A, Cocchiararo B, Mueller SA, Reiners TE, Reinert K, Tuchscherer I, Janke A, Nowak C. Informing conservation strategies with museum genomics: Long-term effects of past anthropogenic persecution on the elusive European wildcat. Ecol Evol 2021; 11:17932-17951. [PMID: 35003648 PMCID: PMC8717334 DOI: 10.1002/ece3.8385] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/04/2021] [Accepted: 11/09/2021] [Indexed: 12/13/2022] Open
Abstract
Like many carnivore species, European wildcats (Felis silvestris) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck at the beginning of the 20th century. In Germany, the species has managed to survive its near extinction in small isolated areas and is currently recolonizing former habitats owing to legal protection and concerted conservation efforts. Here, we SNP-genotyped and mtDNA-sequenced 56 historical and 650 contemporary samples to assess the impact of massive persecution on genetic diversity, population structure, and hybridization dynamics of wildcats. Spatiotemporal analyses suggest that the presumed postglacial differentiation between two genetically distinct metapopulations in Germany is in fact the result of the anthropogenic bottleneck followed by re-expansion from few secluded refugia. We found that, despite the bottleneck, populations experienced no severe genetic erosion, nor suffered from elevated inbreeding or showed signs of increased hybridization with domestic cats. Our findings have significant implications for current wildcat conservation strategies, as the data analyses show that the two presently recognized wildcat population clusters should be treated as a single conservation unit. Although current populations appear under no imminent threat from genetic factors, fostering connectivity through the implementation of forest corridors will facilitate the preservation of genetic diversity and promote long-term viability. The present study documents how museum collections can be used as essential resource for assessing long-term anthropogenic effects on natural populations, for example, regarding population structure and the delineation of appropriate conservation units, potentially informing todays' species conservation.
Collapse
Affiliation(s)
- Alina von Thaden
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Berardino Cocchiararo
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| | - Sarah Ashley Mueller
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Tobias Erik Reiners
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
| | - Katharina Reinert
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Department of Physical GeographyJohann Wolfgang Goethe‐UniversityFrankfurt am MainGermany
| | - Iris Tuchscherer
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Axel Janke
- Institute of Ecology, Evolution & DiversityJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
- Senckenberg Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungFrankfurt am MainGermany
| | - Carsten Nowak
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE‐TBG)Frankfurt am MainGermany
| |
Collapse
|
10
|
Population genetic structure of European wildcats inhabiting the area between the Dinaric Alps and the Scardo-Pindic mountains. Sci Rep 2021; 11:17984. [PMID: 34504218 PMCID: PMC8429547 DOI: 10.1038/s41598-021-97401-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/12/2021] [Indexed: 11/09/2022] Open
Abstract
Habitat fragmentation and loss have contributed significantly to the demographic decline of European wildcat populations and hybridization with domestic cats poses a threat to the loss of genetic purity of the species. In this study we used microsatellite markers to analyse genetic variation and structure of the wildcat populations from the area between the Dinaric Alps and the Scardo-Pindic mountains in Slovenia, Croatia, Serbia and North Macedonia. We also investigated hybridisation between populations of wildcats and domestic cats in the area. One hundred and thirteen samples from free-leaving European wildcats and thirty-two samples from domestic cats were analysed. Allelic richness across populations ranged from 3.61 to 3.98. The observed Ho values ranged between 0.57 and 0.71. The global FST value for the four populations was 0.080 (95% CI 0.056-0.109) and differed significantly from zero (P < 0.001). The highest FST value was observed between the populations North Macedonia and Slovenia and the lowest between Slovenia and Croatia. We also found a signal for the existence of isolation by distance between populations. Our results showed that wildcats are divided in two genetic clusters largely consistent with a geographic division into a genetically diverse northern group (Slovenia, Croatia) and genetically eroded south-eastern group (Serbia, N. Macedonia). Hybridisation rate between wildcats and domestic cats varied between 13% and 52% across the regions.
Collapse
|
11
|
First Description of Sarcoptic Mange in a Free-Ranging European Wildcat ( Felis silvestris silvestris) from Spain. Animals (Basel) 2021; 11:ani11092494. [PMID: 34573459 PMCID: PMC8466406 DOI: 10.3390/ani11092494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/15/2021] [Accepted: 08/23/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Sarcoptic mange caused by the mite Sarcoptes scabiei is a worldwide-distributed skin infestation with a wide range of hosts, among them several species within the Felidae family. Sarcoptes scabiei was diagnosed in a dead adult female European wildcat (Felis silvestris silvestris) from Spain. This is the first description of Sarcoptes scabiei in a European wildcat. Since this is a species of conservation concern due to its critical demography in the southernmost population of the Iberian Peninsula, the impacts of infectious diseases, including sarcoptic mange, should be considered during disease surveillance programs of the species’ populations. Abstract Sarcoptic mange caused by the mite Sarcoptes scabiei is a worldwide-distributed skin infestation with a wide range of hosts, among them several species within the Felidae family. Sarcoptes scabiei was diagnosed in a dead adult female European wildcat (Felis silvestris silvestris) from Spain, based on histological evaluation of skin biopsies and identification of the arthropod from skin scrapings and molecular methods. This is the first description of Sarcoptes scabiei in a European wildcat. Due to its critical demography in the southernmost population of the Iberian Peninsula, the impacts of infectious diseases, including sarcoptic mange, as a new potential threat should be considered during disease surveillance programs of the species’ populations.
Collapse
|
12
|
Howard-McCombe J, Ward D, Kitchener AC, Lawson D, Senn HV, Beaumont M. On the use of genome-wide data to model and date the time of anthropogenic hybridisation: An example from the Scottish wildcat. Mol Ecol 2021; 30:3688-3702. [PMID: 34042240 DOI: 10.1111/mec.16000] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
While hybridisation has long been recognised as an important natural phenomenon in evolution, the conservation of taxa subject to introgressive hybridisation from domesticated forms is a subject of intense debate. Hybridisation of Scottish wildcats and domestic cats is a good example in this regard. Here, we developed a modelling framework to determine the timescale of introgression using approximate Bayesian computation (ABC). Applying the model to ddRAD-seq data from 129 individuals, genotyped at 6546 loci, we show that a population of wildcats genetically distant from domestic cats is still present in Scotland. These individuals were found almost exclusively within the captive breeding programme. Most wild-living cats sampled were introgressed to some extent. The demographic model predicts high levels of gene-flow between domestic cats and Scottish wildcats (13% migrants per generation) over a short timeframe, the posterior mean for the onset of hybridisation (T1 ) was 3.3 generations (~10 years) before present. Although the model had limited power to detect signals of ancient admixture, we found evidence that significant recent hybridisation may have occurred subsequent to the founding of the captive breeding population (T2 ). The model consistently predicts T1 after T2 , estimated here to be 19.3 generations (~60 years) ago, highlighting the importance of this population as a resource for conservation management. Additionally, we evaluate the effectiveness of current methods to classify hybrids. We show that an optimised 35 SNP panel is a better predictor of the ddRAD-based hybrid score in comparison with a morphological method.
Collapse
Affiliation(s)
| | - Daniel Ward
- School of Mathematics, University of Bristol, Bristol, UK
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Daniel Lawson
- School of Mathematics, University of Bristol, Bristol, UK
| | - Helen V Senn
- RZSS WildGenes Laboratory, Royal Zoological Society of Scotland, Edinburgh, UK
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, UK
| |
Collapse
|
13
|
Porto-Hannes I, Burlakova LE, Zanatta DT, Lasker HR. Boundaries and hybridization in a secondary contact zone between freshwater mussel species (Family:Unionidae). Heredity (Edinb) 2021; 126:955-973. [PMID: 33883699 PMCID: PMC8178349 DOI: 10.1038/s41437-021-00424-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 03/02/2021] [Accepted: 03/02/2021] [Indexed: 02/02/2023] Open
Abstract
Correct species identification and delineation are crucial for effective conservation and management. However, species delineation can be problematic in the presence of morphological ambiguities due to phenotypic plasticity, convergence, and/or interspecific hybridization. Here, we investigated the degree of hybridization between two closely related freshwater mussel species [Bivalvia: Unionidae; Lampsilis siliquoidea (Barnes) and L. radiata (Gmelin)] that present intermediate forms in areas of sympatry. Unionids have a distinct form of mitochondrial DNA (mtDNA) inheritance, termed doubly uniparental inheritance (DUI) where female mtDNA (F-type) is transmitted to all progeny but male mtDNA (M-type) is mostly inherited by the males resulting in mostly homoplasmic females and heteroplasmic males. An individual was identified as hybrid when F-type and M-type mtDNA of the two different species were found in the same individual. Twelve out of 116 sequenced males were identified as hybrids indicating that these species hybridize where their geographic range overlaps in the lower Great Lakes and St. Lawrence basins. Microsatellite analyses further support the occurrence of hybridization but at a larger spatial scale than indicated by the mitochondrial analyses. We also found that strong within-species population genetic structure affects the detection of purebred individuals overestimating the number of hybrids. Given the large geographic scale and proportion of hybrids found in this study, natural hybridization and introgression need to be considered when implementing local biodiversity inventories, identifying waterbodies as source of organisms for relocation and restoration projects and when setting appropriate conservation policies.
Collapse
Affiliation(s)
- Isabel Porto-Hannes
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA.
| | | | - David T Zanatta
- Institute for Great Lakes Research, Biology Department, Central Michigan University, Mount Pleasant, MI, USA
| | - Howard R Lasker
- Graduate Program in Evolution, Ecology and Behavior, University at Buffalo, Buffalo, NY, USA
- Department of Environment and Sustainability, University at Buffalo, Buffalo, NY, USA
| |
Collapse
|
14
|
Matias G, Rosalino LM, Rosa JL, Monterroso P. Wildcat population density in
NE
Portugal: A regional stronghold for a nationally threatened felid. POPUL ECOL 2021. [DOI: 10.1002/1438-390x.12088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gonçalo Matias
- cE3c‐Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - Luís Miguel Rosalino
- cE3c‐Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências Universidade de Lisboa Lisbon Portugal
| | - José Luís Rosa
- Instituto da Conservação da Natureza e Florestas Bragança Portugal
| | - Pedro Monterroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos Universidade do Porto Vairão Portugal
| |
Collapse
|
15
|
Interspecific hybrids of animals - in nature, breeding and science – a review. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2020-0082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
Interspecific hybrids called hybrids are individuals obtained by crossing two different species. Hybrids are found both in nature among wild animals but also have become attractive in animal husbandry due to the high production features of the F1 generation. Interspecific hybrids are observed in nature most often as a result of crossing closely related species, which is a great danger to the purity of the population of starting species. Interspecies hybrids are also created by man for production purposes. Due to disturbances in gametogenesis processes, they have become a valuable research model. In the article, we describe interspecific hybrids occurring in nature and related problems, interspecific hybrids created for production purposes in animal husbandry, but also research using hybrids as a research model. In the article we also highlight the issues of fertility of individuals obtained from such matings.
Collapse
|
16
|
Ravagni S, Sanchez-Donoso I, Vilà C. Biased assessment of ongoing admixture using STRUCTURE in the absence of reference samples. Mol Ecol Resour 2020; 21:677-689. [PMID: 33085825 DOI: 10.1111/1755-0998.13286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 11/30/2022]
Abstract
Detection of hybridization and introgression is important in ecological research as in conservation and evolutionary biology. STRUCTURE is one of the most popular software to study introgression and allows estimating what proportion of the genome of each individual belongs to each ancestral population, even in cases where no reference sample from the ancestral nonadmixed populations is previously identified. In spite of its frequent use, some studies have indicated that ancestry estimates may not always be reliable. We simulated population data under different conditions with regard to the genetic differentiation between ancestral populations, number of loci considered, number of alleles per marker and hybridization rate, and analysed data with STRUCTURE. When reference samples were not included, the comparison of the known degree of admixture for each simulated individual and the value estimated with STRUCTURE revealed a strong underestimation of the level of introgression, classifying many admixed individuals as nonadmixed. This derives from an inaccurate estimation of the ancestral allele frequencies. When samples from the nonadmixed ancestral population were included as reference in the analyses, the bias in the estimations was reduced. The most accurate estimates were obtained when potentially admixed samples were few in relation to reference samples. Thus, whenever possible, a very large proportion of nonadmixed reference samples should be included in admixture assessments and different approaches should be combined. The misestimate of the amount of introgression can impair our understanding of the evolutionary history of species and misguide conservation efforts.
Collapse
Affiliation(s)
- Sara Ravagni
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Doñana Biological Station (EBD-CSIC), Seville, Spain
| |
Collapse
|
17
|
Quilodrán CS, Nussberger B, Macdonald DW, Montoya‐Burgos JI, Currat M. Projecting introgression from domestic cats into European wildcats in the Swiss Jura. Evol Appl 2020; 13:2101-2112. [PMID: 32908607 PMCID: PMC7463310 DOI: 10.1111/eva.12968] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 03/06/2020] [Accepted: 03/24/2020] [Indexed: 02/02/2023] Open
Abstract
Hybridization between wild and domesticated organisms is a worldwide conservation issue. In the Jura Mountains, threatened European wildcats (Felis silvestris) have been demographically spreading for approximately the last 50 years, but this recovery is coupled with hybridization with domestic cats (Felis catus). Here, we project the pattern of future introgression using different spatially explicit scenarios to model the interactions between the two species, including competition and different population sizes. We project the fast introgression of domestic cat genes into the wildcat population under all scenarios if hybridization is not severely restricted. If the current hybridization rate and population sizes remain unchanged, we expect the loss of genetic distinctiveness between wild and domestic cats at neutral nuclear, mitochondrial and Y chromosome markers in one hundred years. However, scenarios involving a competitive advantage for wildcats and a future increase in the wildcat population size project a slower increase in introgression. We recommend that future studies assess the fitness of these hybrids and better characterize their ecological niche and their ecological interactions with parental species to elucidate effective conservation measures.
Collapse
Affiliation(s)
- Claudio S. Quilodrán
- Department of ZoologyUniversity of OxfordOxfordUK
- Department of Genetics and Evolution ‐ Anthropology UnitLaboratory of AnthropologyGenetics and Peopling HistoryUniversity of GenevaGenevaSwitzerland
| | - Beatrice Nussberger
- Institute of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - David W. Macdonald
- Department of ZoologyWildlife Conservation Research UnitThe Recanati‐Kaplan CentreUniversity of OxfordOxfordUK
| | - Juan I. Montoya‐Burgos
- Department of Genetics and EvolutionLaboratory of Vertebrate EvolutionUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in Geneva (IGE3)GenevaSwitzerland
| | - Mathias Currat
- Department of Genetics and Evolution ‐ Anthropology UnitLaboratory of AnthropologyGenetics and Peopling HistoryUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in Geneva (IGE3)GenevaSwitzerland
| |
Collapse
|
18
|
Spatial Segregation between Red Foxes (Vulpes vulpes), European Wildcats (Felis silvestris) and Domestic Cats (Felis catus) in Pastures in a Livestock Area of Northern Spain. DIVERSITY 2020. [DOI: 10.3390/d12070268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Red foxes, European wildcats and domestic cats share cattle pastures for hunting in La Pernía Valley, northern Spain. To understand the mechanisms that allow the coexistence of these mesopredators in a habitat characterized by its anthropogenic modifications, we recorded sightings of these species in pastures in the summers of 2016, 2017, 2018 and 2019. We tested if the species preferred specific areas of pastures and if they exhibited any spatial segregation in the use of pastures. Red foxes did not show consistent preferences for any area of the pastures. European wildcats preferred pasture areas closer to streams and forest edges, whereas domestic cats preferred areas closer to buildings and paved roads whilst avoiding forest edges. All species pairs showed strong spatial segregation with less than 7% overlap. We hypothesize that spatial segregation is the mechanism used by European wildcats and domestic cats to avoid dangerous interactions with other predators and which characterizes their preference of specific areas on pastures, using areas near places that may protect them from other predators. Ultimately, the influence of fox presence (and probably that of other larger potential predators) on the use of pastures by European wildcats and domestic cats is decreasing the number of interactions between them and may help to prevent hybridization in this area.
Collapse
|
19
|
von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020. [PMID: 31925943 DOI: 10.1111/1755-0998.13136.applying] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
Collapse
Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| |
Collapse
|
20
|
Crawford HM, Calver MC, Fleming PA. Subsidised by junk foods: factors influencing body condition in stray cats (Felis catus). JOURNAL OF URBAN ECOLOGY 2020. [DOI: 10.1093/jue/juaa004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
AbstractDomestic cats (Felis catus) are one of the most widely distributed and successful carnivores globally. While cats are popular pets, many unowned, ‘stray’ cats live freely in anthropogenic environments at high densities where they make use of anthropogenic resources. These stray cats present a management challenge due to concerns about wildlife predation, pathogen transmission, public nuisance and threats to cat welfare (e.g. vehicle collisions). In Australia, there are few studies of strays compared with pet cats or feral cats (free-roaming cats in rural areas that are independent of resources provided by humans). To contribute original data about stray cat biology, the carcasses of 188 euthanised stray cats were collected from Perth, Western Australia. Cats were assessed for general health, age, reproduction, diet and gastrointestinal parasite biomass. The influence of cat demographics, collection location, season, parasite biomass, diet and history of supplemental feeding by people were tested against body condition. Overall, strays were physically healthy and reproductive, with few life-threatening injuries or macroscopic evidence of disease; however, helminths were extremely common (95% of cats) and pose a threat. Nearly 40% of strays consumed wildlife, including two species of endemic marsupial. Alarmingly, 57.5% of strays were scavenging vast amounts of refuse, including life-threatening items in volumes that blocked their gastrointestinal tracts. These findings illustrate that strays need to be removed from anthropogenic environments for their own health and welfare and to prevent continued breeding. Targeted control programmes should prioritise removal of cats from areas where refuse is common and where valued native fauna exist.
Collapse
Affiliation(s)
- H M Crawford
- Environmental and Conservation Sciences, Murdoch University, 90 South Street, Murdoch 6150, Western Australia
| | - M C Calver
- Environmental and Conservation Sciences, Murdoch University, 90 South Street, Murdoch 6150, Western Australia
| | - P A Fleming
- Environmental and Conservation Sciences, Murdoch University, 90 South Street, Murdoch 6150, Western Australia
| |
Collapse
|
21
|
Sauther ML, Bertolini F, Dollar LJ, Pomerantz J, Alves PC, Gandolfi B, Kurushima JD, Mattucci F, Randi E, Rothschild MF, Cuozzo FP, Larsen RS, Moresco A, Lyons LA, Jacky IAY. Taxonomic identification of Madagascar’s free-ranging “forest cats”. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01261-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
22
|
Renal accumulation of prooxidant mineral elements and CKD in domestic cats. Sci Rep 2020; 10:3160. [PMID: 32081923 PMCID: PMC7035273 DOI: 10.1038/s41598-020-59876-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/17/2020] [Indexed: 01/16/2023] Open
Abstract
Felids have a high incidence of chronic kidney disease (CKD), for which the most common renal lesion is chronic interstitial nephritis (CIN). CIN can be induced by tissue oxidative stress, which is determined by the cellular balance of pro- and anti-oxidant metabolites. Fish-flavoured foods are more often fed to cats than dogs, and such foods tend to have higher arsenic content. Arsenic is a pro-oxidant metallic element. We propose that renal accumulation of pro-oxidant elements such as arsenic and depletion of anti-oxidant elements such as zinc, underpin the high incidence of CIN in domestic cats. Total arsenic and other redox-reactive metal elements were measured in kidneys (after acid-digestion) and urine (both by inductively-coupled plasma-mass spectrometry) of domestic cats (kidneys, n = 56; urine, n = 21), domestic dogs (kidneys, n = 54; urine, n = 28) and non-domesticated Scottish Wildcats (kidneys, n = 17). Renal lesions were graded by severity of CIN. In our randomly sampled population, CIN was more prevalent in domestic cat versus domestic dog (51%, n = 32 of 62 cats; 15%, 11 of 70 dogs were positive for CIN, respectively). CIN was absent from all Scottish wildcats. Tissue and urinary (corrected for creatinine) arsenic content was higher in domestic cats, relative to domestic dogs and wildcats. Urine arsenic was higher in domestic cats and dogs with CIN. Arsenobetaine, an organic and relatively harmless species of arsenic, was the primary form of arsenic found in pet foods. In summary, the kidneys of domestic cats appear to have greater levels of pro-oxidant trace elements, as compared to dogs and wildcats. Since there was no difference in renal arsenic levels in cats with or without CIN, renal arsenic accumulation does not appear a primary driver of excess CIN in cats. Given clear differences in renal handling of pro vs. anti-oxidant minerals between cats and dogs, further in vivo balance studies are warranted. These may then inform species-specific guidelines for trace element incorporation into commercial diets.
Collapse
|
23
|
Trouwborst A, McCormack PC, Martínez Camacho E. Domestic cats and their impacts on biodiversity: A blind spot in the application of nature conservation law. PEOPLE AND NATURE 2020. [DOI: 10.1002/pan3.10073] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Arie Trouwborst
- Tilburg Law School Tilburg University Tilburg The Netherlands
| | | | | |
Collapse
|
24
|
von Thaden A, Nowak C, Tiesmeyer A, Reiners TE, Alves PC, Lyons LA, Mattucci F, Randi E, Cragnolini M, Galián J, Hegyeli Z, Kitchener AC, Lambinet C, Lucas JM, Mölich T, Ramos L, Schockert V, Cocchiararo B. Applying genomic data in wildlife monitoring: Development guidelines for genotyping degraded samples with reduced single nucleotide polymorphism panels. Mol Ecol Resour 2020; 20. [PMID: 31925943 DOI: 10.1111/1755-0998.13136] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/24/2019] [Accepted: 01/05/2020] [Indexed: 01/16/2023]
Abstract
The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.
Collapse
Affiliation(s)
- Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Tobias E Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
| | - Paulo C Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Federica Mattucci
- Area per la Genetica della Conservazione, ISPRA, Ozzano dell'Emilia, Bologna, Italy
| | - Ettore Randi
- Department BIGEA, University of Bologna, Bologna, Italy.,Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Margherita Cragnolini
- Institut für Spezielle Zoologie und Evolutionsbiologie, Biologisch-Pharmazeutische Fakultät, Friedrich-Schiller-Universität Jena, Jena, Germany
| | - José Galián
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Zsolt Hegyeli
- "Milvus Group" Bird and Nature Protection Association, Tîrgu Mureş, Romania
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK.,Institute of Geography, School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Clotilde Lambinet
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - José M Lucas
- Departamento de Zoología y Antropología Física, Facultad de Veterinaria, Universidad de Murcia, Murcia, Spain
| | - Thomas Mölich
- Landesverband Thüringen e.V., BUND für Umwelt und Naturschutz Deutschland (BUND), Erfurt, Germany
| | - Luana Ramos
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO - Laboratório Associado, Universidade do Porto, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
| | - Vinciane Schockert
- Department of Science and Environmental Management, University of Liège, Liège, Belgium
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| |
Collapse
|
25
|
Gil-Sánchez JM, Barea-Azcón JM, Jaramillo J, Herrera-Sánchez FJ, Jiménez J, Virgós E. Fragmentation and low density as major conservation challenges for the southernmost populations of the European wildcat. PLoS One 2020; 15:e0227708. [PMID: 31990935 PMCID: PMC6986748 DOI: 10.1371/journal.pone.0227708] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/26/2019] [Indexed: 11/18/2022] Open
Abstract
Knowledge of population dynamics of threatened species in the wild is key to effective conservation actions. However, at present, there are many examples of endangered animals for which their current situation is unknown, and not just in remote areas and less developed countries. We have explored this topic by studying the paradigmatic case of the European wildcat (Felis silvestris silvestris), an endangered small carnivore whose status has been subjectively established on the basis of non-systematic approaches and opportunistic records. Little is known about its demographic situation, prompting the need for information to improve conservation measures. However, the secretive behaviour of felines along with its low density in natural conditions have prevented the gathering of sufficient data. We developed a field sampling strategy for one of the largest populations (Andalusia, South Spain, 87,268 km2), based on a logistically viable systematic non-intrusive survey by camera-trapping. This study offers the first large-scale estimation for any European wildcat population, based on analytical approaches applied on Species Distribution Models. A hierarchical approach based on a Maxent model for distribution estimation was used, along with Generalised Linear Models for density estimation from explicit spatial capture-recapture data. Our results show that the distribution range is smaller and more highly fragmented than previously assumed. The overall estimated density was very low (0.069 ±0.0019 wildcats/km2) and the protected areas network seems to be insufficient to cover a significant part of the population or a viable nucleus in demographic terms. Indeed, the most important areas remain unprotected. Our main recommendations are to improve the protected area network and/or vigilance programs in hunting estates, in addition to studying and improving connectivity between the main population patches.
Collapse
Affiliation(s)
| | - Jose Miguel Barea-Azcón
- Agencia de Medio Ambiente y Agua (Consejería de Agricultura, Ganadería, Pesca y Desarrollo Sostenible, Junta de Andalucía), Gerencia de Granada, Edificio Zeus III, Granada, Spain
| | - Javier Jaramillo
- Agencia de Medio Ambiente y Agua (Consejería de Agricultura, Ganadería, Pesca y Desarrollo Sostenible, Junta de Andalucía), Gerencia de Granada, Edificio Zeus III, Granada, Spain
| | | | - José Jiménez
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC-UCLM-JCCM), Ciudad Real, Spain
| | - Emilio Virgós
- Department of Biology, Geology, Physics and Inorganic Chemistry, ESCET, Universidad Rey Juan Carlos, C/Tulipán, Móstoles, Madrid, Spain
| |
Collapse
|
26
|
Tiesmeyer A, Ramos L, Manuel Lucas J, Steyer K, Alves PC, Astaras C, Brix M, Cragnolini M, Domokos C, Hegyeli Z, Janssen R, Kitchener AC, Lambinet C, Mestdagh X, Migli D, Monterroso P, Mulder JL, Schockert V, Youlatos D, Pfenninger M, Nowak C. Range-wide patterns of human-mediated hybridisation in European wildcats. CONSERV GENET 2020. [DOI: 10.1007/s10592-019-01247-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
AbstractHybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.
Collapse
|
27
|
Soyumert A. Camera-Trapping Two Felid Species: Monitoring Eurasian Lynx (Lynx lynx) and Wildcat (Felis silvestris) Populations in Mixed Temperate Forest Ecosystems. MAMMAL STUDY 2020. [DOI: 10.3106/ms2019-0046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Anıl Soyumert
- Game and Wildlife Programme, Kastamonu University, Araç, 37800, Kastamonu, Turkey
| |
Collapse
|
28
|
Beugin M, Salvador O, Leblanc G, Queney G, Natoli E, Pontier D. Hybridization between Felis silvestris silvestris and Felis silvestris catus in two contrasted environments in France. Ecol Evol 2020; 10:263-276. [PMID: 31988727 PMCID: PMC6972816 DOI: 10.1002/ece3.5892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 11/30/2022] Open
Abstract
European wildcat (Felis silvestris silvestris) populations are fragmented throughout most of the whole range of the subspecies and may be threatened by hybridization with the domestic cat F.s. catus. The underlying ecological processes promoting hybridization remain largely unknown. In France, wildcats are mainly present in the northeast and signs of their presence in the Pyrenees have been recently provided. However, no studies have been carried out in the French Pyrenees to assess their exposure to hybridization. We compared two local populations of wildcats, one living in a continuous forest habitat in the French Pyrenees, the other living in a highly fragmented forest-agricultural landscape in northeastern France to get insights into the variability of hybridization rates. Strong evidence of hybridization was detected in northeastern France and not in the Pyrenees. Close kin in the Pyrenees were not found in the same geographic location contrary to what was previously reported for females in the northeastern wildcat population. The two wildcat populations were significantly differentiated (F ST = 0.072) to an extent close to what has been reported (F ST = 0.103) between the Iberian population, from which the Pyrenean population may originate, and the German population, which is connected to the northeastern population. The genetic diversity of the Pyrenean wildcats was lower than that of northeastern wildcat populations in France and in other parts of Europe. The lower hybridization in the Pyrenees may result from the continuity of natural forest habitats. Further investigations should focus on linking landscape features to hybridization rates working on local populations.
Collapse
Affiliation(s)
- Marie‐Pauline Beugin
- Laboratoire de Biométrie et Biologie Evolutive UMR5558CNRSUniv LyonUniversité Lyon 1VilleurbanneFrance
- Animal Genomics LaboratoryANTAGENELa tour de SalvagnyFrance
| | - Olivier Salvador
- Réserve naturelle nationale de Jujols et de NohèdesRéserves Naturelles CatalanesPradesFrance
| | | | | | | | - Dominique Pontier
- Laboratoire de Biométrie et Biologie Evolutive UMR5558CNRSUniv LyonUniversité Lyon 1VilleurbanneFrance
| |
Collapse
|
29
|
Dickman CR, Legge SM, Woinarski JCZ. Assessing Risks to Wildlife from Free-Roaming Hybrid Cats: The Proposed Introduction of Pet Savannah Cats to Australia as a Case Study. Animals (Basel) 2019; 9:ani9100795. [PMID: 31615026 PMCID: PMC6826879 DOI: 10.3390/ani9100795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The domestic cat, Felis catus, is often cross-bred with other species in the cat family to produce hybrid or ‘designer’ cats that are sought by people as pets. However, hybrid cats are often surrendered to wildlife shelters, or released, which leads to concern that they may establish free-roaming populations and damage native wildlife. In 2008, the Australian government rejected an application, on precautionary grounds, to import savannah cats (hybrids of the domestic cat and serval Leptailurus serval) into the country. We review the limited information informing this decision and then present a framework that identifies the native mammal species likely to have been most at risk of predation from savannah cats if importation and establishment had occurred. Assuming that savannah cats hunt similar prey to those that are hunted by both parent species, we estimate that 91% of Australia’s extant terrestrial mammal fauna would likely face some risk of predation from savannah cats, including 93% of non-volant mammal species that have threatened conservation status. The framework results strongly validate the decision to ban savannah cats from Australia. We suggest that our framework approach could be adapted to assess the likely risks that are posed by the arrival of other hybrid cats or hybrids of other animals. Abstract Hybrid cats—created by crossing different species within the family Felidae—are popular pets, but they could potentially threaten native species if they escape and establish free-roaming populations. To forestall this possibility, the Australian government imposed a specific ban on importation of the savannah cat, a hybrid created by crossing the domestic cat Felis catus and serval Leptailurus serval, in 2008. We develop a decision–framework that identifies those species of non-volant native mammals in Australia that would likely have been susceptible to predation by savannah cats if importation and establishment had occurred. We assumed that savannah cats would hunt ecologically similar prey to those that are depredated by both the domestic cat and the serval, and categorised native mammals as having different levels of susceptibility to predation by savannah cats based on their size, habitat range, and behaviour. Using this framework, we assessed savannah cats as likely to add at least 28 extant native mammal species to the 168 that are known already to be susceptible to predation by the domestic cat, posing a risk to 91% of Australia’s extant non-volant terrestrial mammal species (n = 216) and to 93% of threatened mammal species. The framework could be generalised to assess risks from any other hybrid taxa.
Collapse
Affiliation(s)
- Christopher R Dickman
- National Environmental Science Program Threatened Species Recovery Hub, Desert Ecology Research Group, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Sarah M Legge
- National Environmental Science Program Threatened Species Recovery Hub, Centre for Biodiversity and Conservation Science, University of Queensland, St Lucia, QLD 4072, Australia.
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT 2601, Australia.
- National Environmental Science Program Threatened Species Recovery Hub, Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT 0909, Australia.
| | - John C Z Woinarski
- National Environmental Science Program Threatened Species Recovery Hub, Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina, NT 0909, Australia.
| |
Collapse
|
30
|
Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. Sci Rep 2019; 9:11612. [PMID: 31406125 PMCID: PMC6691104 DOI: 10.1038/s41598-019-48002-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.
Collapse
|
31
|
Zhigileva ON, Uslamina IM, Gimranov DO, Chernova AA. Mitochondrial DNA markers for the study of introgression between the sable and the pine marten. CONSERV GENET RESOUR 2019. [DOI: 10.1007/s12686-019-01098-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
32
|
A Case of Letting the Cat out of The Bag-Why Trap-Neuter-Return Is Not an Ethical Solution for Stray Cat ( Felis catus) Management. Animals (Basel) 2019; 9:ani9040171. [PMID: 30995809 PMCID: PMC6523511 DOI: 10.3390/ani9040171] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 04/01/2019] [Accepted: 04/10/2019] [Indexed: 11/16/2022] Open
Abstract
Trap-Neuter-Return (TNR) programs, in which stray cats are captured, neutered and returned to the environment are advocated as a humane, ethical alternative to euthanasia. We review the TNR literature in light of current debate over whether or not there should be further TNR trials in Australia. We revisit the problems arising from stray cats living in association with human habitation and estimate how many stray cats would have to be processed through a scientifically-guided TNR program to avoid high euthanasia rates. We also identify 10 ethical and welfare challenges that have to be addressed: we consider the quality of life for stray cats, where they would live, whether the TNR process itself is stressful, whether TNR cats are vulnerable to injury, parasites and disease, can be medically treated, stray cats' body condition and diet, and their impacts on people, pet cats, and urban wildlife, especially endemic fauna. We conclude that TNR is unsuitable for Australia in almost all situations because it is unlikely to resolve problems caused by stray cats or meet ethical and welfare challenges. Targeted adoption, early-age desexing, community education initiatives and responsible pet ownership have greater promise to minimize euthanasia, reduce numbers rapidly, and address the identified issues.
Collapse
|
33
|
McFarlane SE, Pemberton JM. Detecting the True Extent of Introgression during Anthropogenic Hybridization. Trends Ecol Evol 2019; 34:315-326. [DOI: 10.1016/j.tree.2018.12.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 12/10/2018] [Accepted: 12/18/2018] [Indexed: 10/27/2022]
|
34
|
Senn HV, Ghazali M, Kaden J, Barclay D, Harrower B, Campbell RD, Macdonald DW, Kitchener AC. Distinguishing the victim from the threat: SNP-based methods reveal the extent of introgressive hybridization between wildcats and domestic cats in Scotland and inform future in situ and ex situ management options for species restoration. Evol Appl 2019; 12:399-414. [PMID: 30828363 PMCID: PMC6383845 DOI: 10.1111/eva.12720] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/15/2018] [Accepted: 09/18/2018] [Indexed: 02/06/2023] Open
Abstract
The degree of introgressive hybridization between the Scottish wildcat and domestic cat has long been suspected to be advanced. Here, we use a 35-SNP-marker test, designed to assess hybridization between wildcat and domestic cat populations in Scotland, to assess a database of 295 wild-living and captive cat samples, and test the assumptions of the test using 3,097 SNP markers generated independently in a subset of the data using ddRAD. We discovered that despite increased genetic resolution provided by these methods, wild-living cats in Scotland show a complete genetic continuum or hybrid swarm structure when judged against reference data. The historical population of wildcats, although hybridized, clearly groups at one end of this continuum, as does the captive population of wildcats. The interpretation of pelage scores against nuclear genetic data continues to be problematic. This is probably because of a breakdown in linkage equilibrium between wildcat pelage genes as the two populations have become increasingly mixed, meaning that pelage score or SNP score alone is poor diagnostic predictors of hybrid status. Until better tools become available, both should be used jointly, where possible, when making management decisions about individual cats. We recommend that the conservation community in Scotland must now define clearly what measures are to be used to diagnose a wildcat in the wild in Scotland, if future conservation action is to be effective.
Collapse
Affiliation(s)
- Helen V. Senn
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Muhammad Ghazali
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Jennifer Kaden
- RZSS WildGenes Laboratory, Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - David Barclay
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | - Ben Harrower
- Conservation DepartmentRoyal Zoological Society of ScotlandEdinburghUK
| | | | - David W. Macdonald
- Wildlife Conservation Research Unit, Zoology, Recanati Kaplan Centre, Zoology DepartmentOxford UniversityOxfordUK
| | - Andrew C. Kitchener
- Department Natural SciencesNational Museums ScotlandEdinburghUK
- Institute of Geography, School of GeosciencesUniversity of EdinburghEdinburghUK
| |
Collapse
|
35
|
Wellenreuther M, Muñoz J, Chávez‐Ríos JR, Hansson B, Cordero‐Rivera A, Sánchez‐Guillén RA. Molecular and ecological signatures of an expanding hybrid zone. Ecol Evol 2018; 8:4793-4806. [PMID: 29876058 PMCID: PMC5980427 DOI: 10.1002/ece3.4024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 02/19/2018] [Accepted: 02/20/2018] [Indexed: 01/17/2023] Open
Abstract
Many species are currently changing their distributions and subsequently form sympatric zones with hybridization between formerly allopatric species as one possible consequence. The damselfly Ischnura elegans has recently expanded south into the range of its ecologically and morphologically similar sister species Ischnura graellsii. Molecular work shows ongoing introgression between these species, but the extent to which this species mixing is modulated by ecological niche use is not known. Here, we (1) conduct a detailed population genetic analysis based on molecular markers and (2) model the ecological niche use of both species in allopatric and sympatric regions. Population genetic analyses showed chronic introgression between I. elegans and I. graellsii across a wide part of Spain, and admixture analysis corroborated this, showing that the majority of I. elegans from the sympatric zone could not be assigned to either the I. elegans or I. graellsii species cluster. Niche modeling demonstrated that I. elegans has modified its environmental niche following hybridization and genetic introgression with I. graellsii, making niche space of introgressed I. elegans populations more similar to I. graellsii. Taken together, this corroborates the view that adaptive introgression has moved genes from I. graellsii into I. elegans and that this process is enabling Spanish I. elegans to occupy a novel niche, further facilitating its expansion. Our results add to the growing evidence that hybridization can play an important and creative role in the adaptive evolution of animals.
Collapse
Affiliation(s)
- Maren Wellenreuther
- Department of BiologyLund UniversityLundSweden
- The New Zealand Institute for Plant & Food Research LtdNelsonNew Zealand
| | | | - Jesús R. Chávez‐Ríos
- Departamento de Biología Celular y FisiologíaUnidad Periférica TlaxcalaInstituto de Investigaciones BiomédicasUniversidad Nacional Autónoma de MéxicoTlaxcalaMéxico
| | | | | | | |
Collapse
|
36
|
Ferreira da Silva MJ, Kopp GH, Casanova C, Godinho R, Minhós T, Sá R, Zinner D, Bruford MW. Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa. PLoS One 2018; 13:e0194189. [PMID: 29614097 PMCID: PMC5882123 DOI: 10.1371/journal.pone.0194189] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/27/2018] [Indexed: 12/04/2022] Open
Abstract
Dispersal is a demographic process that can potentially counterbalance the negative impacts of anthropogenic habitat fragmentation. However, mechanisms of dispersal may become modified in populations living in human-dominated habitats. Here, we investigated dispersal in Guinea baboons (Papio papio) in areas with contrasting levels of anthropogenic fragmentation, as a case study. Using molecular data, we compared the direction and extent of sex-biased gene flow in two baboon populations: from Guinea-Bissau (GB, fragmented distribution, human-dominated habitat) and Senegal (SEN, continuous distribution, protected area). Individual-based Bayesian clustering, spatial autocorrelation, assignment tests and migrant identification suggested female-mediated gene flow at a large spatial scale for GB with evidence of contact between genetically differentiated males at one locality, which could be interpreted as male-mediated gene flow in southern GB. Gene flow was also found to be female-biased in SEN for a smaller scale. However, in the southwest coastal part of GB, at the same geographic scale as SEN, no sex-biased dispersal was detected and a modest or recent restriction in GB female dispersal seems to have occurred. This population-specific variation in dispersal is attributed to behavioural responses to human activity in GB. Our study highlights the importance of considering the genetic consequences of disrupted dispersal patterns as an additional impact of anthropogenic habitat fragmentation and is potentially relevant to the conservation of many species inhabiting human-dominated environments.
Collapse
Affiliation(s)
- Maria Joana Ferreira da Silva
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- CAPP, School of Social and Political Sciences, University of Lisbon, Rua Almerindo Lessa, Lisboa, Portugal
- * E-mail:
| | - Gisela H. Kopp
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Catarina Casanova
- CAPP, School of Social and Political Sciences, University of Lisbon, Rua Almerindo Lessa, Lisboa, Portugal
| | - Raquel Godinho
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, Porto, Portugal
- Department of Zoology, Faculty of Sciences, University of Johannesburg, Auckland Park, South Africa
| | - Tânia Minhós
- Departamento de Antropologia, Faculdade de Ciências Sociais e Humanas, Universidade Nova de Lisboa, Lisboa, Portugal
- Centre for Research in Anthropology (CRIA), Instituto Universitário de Lisboa, Lisboa, Portugal
- IGC, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, Oeiras, Portugal
| | - Rui Sá
- Departamento de Ciências Ambientais, Universidade Lusófona da Guiné, Rua Vitorino Costa, Bissau, Guiné-Bissau
- Research Centre for Anthropology and Health, Universidade de Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Göttingen, Germany
| | - Michael W. Bruford
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, United Kingdom
- Sustainable Places Research Institute, Cardiff University, Cardiff, Wales, United Kingdom
| |
Collapse
|
37
|
Saba Rahim M, Sharma H, Parveen A, Roy JK. Trait Mapping Approaches Through Association Analysis in Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 164:83-108. [PMID: 29511776 DOI: 10.1007/10_2017_50] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Previously, association mapping (AM) methodology was used to unravel genetic complications in animal science by measuring the complex traits for candidate and non-candidate genes. Nowadays, this statistical approach is widely used to clarify the complexity in plant breeding program-based genome-wide breeding strategies, marker development, and diversity analysis. This chapter is particularly focused on methodologies with limitations and provides an overview of AM models and software used up to now. Association or linkage disequilibrium mapping has become a very popular method for discovering candidate and non-candidate genes and confirmation of quantitative trait loci (QTL) on various parts of the genome and in marker-assisted selection for breeding. Previously, various QTL investigations were carried out for different plants exclusively by linkage mapping. To help to understand the basics of modern molecular genetic techniques, in this chapter we summarize previous studies done on different crops. AM offers high-resolution power when there is large genotypic diversity and low linkage disequilibrium (LD) for the germplasm being investigated. The benefits of AM, compared with traditional QTL mapping, include a relatively detailed mapping resolution and a far less time-consuming approach since no mapping populations need to be generated. The advancements in genotyping and computational techniques have encouraged the use of AM. AM provides a fascinating approach for genetic investigation of QTLs, due to its resolution and the possibility to study the various genomic areas at the same time without construction of mapping populations. In this chapter we also discuss the advantages and disadvantages of AM, especially in the dicotyledonous crops Fabaceae and Solanaceae, with various genome-size reproductive strategies (clonal vs. sexual), and statistical models. The main objective of this chapter is to highlight the uses of association genetics in major and minor crop species that have trouble being analyzed for dissection of complex traits by identification of the factor responsible for controlling the effect of trait. Graphical Abstract.
Collapse
Affiliation(s)
- M Saba Rahim
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Afsana Parveen
- National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Joy K Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, India.
| |
Collapse
|
38
|
Steyer K, Tiesmeyer A, Muñoz‐Fuentes V, Nowak C. Low rates of hybridization between European wildcats and domestic cats in a human-dominated landscape. Ecol Evol 2018; 8:2290-2304. [PMID: 29468044 PMCID: PMC5817136 DOI: 10.1002/ece3.3650] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 10/18/2017] [Accepted: 10/27/2017] [Indexed: 01/07/2023] Open
Abstract
Hybridization between wild species and their domestic congeners is considered a major threat for wildlife conservation. Genetic integrity of the European wildcat, for instance, is a concern as they are outnumbered by domestic cats by several orders of magnitude throughout its range. We genotyped 1,071 individual wildcat samples obtained from hair traps and roadkills collected across the highly fragmented forests of western Central Europe, in Germany and Luxembourg, to assess domestic cat introgression in wildcats in human-dominated landscapes. Analyses using a panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5% of wildcat individuals being categorized as F1, F2, or backcrosses to either parental taxon. We report that results based on a set of SNPs were more consistent than on a set of 14 microsatellite markers, showed higher accuracy to detect hybrids and their class in simulation analyses, and were less affected by underlying population structure. Our results strongly suggest that very high hybridization rates previously reported for Central Europe may be partly due to inadequate choice of markers and/or sampling design. Our study documents that an adequately selected SNP panel for hybrid detection may be used as an alternative to commonly applied microsatellite markers, including studies relying on noninvasively collected samples. In addition, our finding of overall low hybridization rates in Central European wildcats provides an example of successful wildlife coexistence in human-dominated, fragmented landscapes.
Collapse
Affiliation(s)
- Katharina Steyer
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution and DiversityGoethe‐University FrankfurtFrankfurt am MainGermany
| | - Annika Tiesmeyer
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Institute of Ecology, Evolution and DiversityGoethe‐University FrankfurtFrankfurt am MainGermany
| | - Violeta Muñoz‐Fuentes
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- European Molecular Biology LaboratoryEuropean Bioinformatics InstituteWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - Carsten Nowak
- Conservation Genetics GroupSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
| |
Collapse
|
39
|
Levänen R, Thulin CG, Spong G, Pohjoismäki JLO. Widespread introgression of mountain hare genes into Fennoscandian brown hare populations. PLoS One 2018; 13:e0191790. [PMID: 29370301 PMCID: PMC5784980 DOI: 10.1371/journal.pone.0191790] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/11/2018] [Indexed: 11/29/2022] Open
Abstract
In Fennoscandia, mountain hare (Lepus timidus) and brown hare (Lepus europaeus) hybridize and produce fertile offspring, resulting in gene flow across the species barrier. Analyses of maternally inherited mitochondrial DNA (mtDNA) show that introgression occur frequently, but unavailability of appropriate nuclear DNA markers has made it difficult to evaluate the scale- and significance for the species. The extent of introgression has become important as the brown hare is continuously expanding its range northward, at the apparent expense of the mountain hare, raising concerns about possible competition. We report here, based on analysis of 6833 SNP markers, that the introgression is highly asymmetrical in the direction of gene flow from mountain hare to brown hare, and that the levels of nuclear gene introgression are independent of mtDNA introgression. While it is possible that brown hares obtain locally adapted alleles from the resident mountain hares, the low levels of mountain hare alleles among allopatric brown hares suggest that hybridization is driven by stochastic processes. Interspecific geneflow with the brown hare is unlikely to have major impacts on mountain hare in Fennoscandia, but direct competition may.
Collapse
Affiliation(s)
- Riikka Levänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Carl-Gustaf Thulin
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Spong
- Molecular Ecology Group, Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, Umeå, Sweden
- Forestry and Environmental Resources, College of Natural Resources, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Jaakko L. O. Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
- * E-mail:
| |
Collapse
|
40
|
Zwijacz-Kozica T, Ważna A, Muñoz-Fuentes V, Tiesmeyer A, Cichocki J, Nowak C. Not European Wildcats, But Domestic Cats Inhabit Tatra National Park. POLISH JOURNAL OF ECOLOGY 2017. [DOI: 10.3161/15052249pje2017.65.4.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Agnieszka Ważna
- Department of Zoology, University of Zielona Góra, Szafrana 1, 65-516 Zielona Góra, Poland
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, Gelnhausen 63571, Germany
| | - Annika Tiesmeyer
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, Gelnhausen 63571, Germany
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt, Max-von-Laue-Straße 13, Frankfurt am Main 60439, Germany
| | - Jan Cichocki
- Department of Zoology, University of Zielona Góra, Szafrana 1, 65-516 Zielona Góra, Poland
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, Gelnhausen 63571, Germany
| |
Collapse
|
41
|
Ruiz-García M, Pinedo-Castro M, Shostell JM. Small spotted bodies with multiple specific mitochondrial DNAs: existence of diverse and differentiated tigrina lineages or species (Leopardus spp: Felidae, Mammalia) throughout Latin America. Mitochondrial DNA A DNA Mapp Seq Anal 2017; 29:993-1014. [PMID: 29157065 DOI: 10.1080/24701394.2017.1404041] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
We analysed two sets of mitochondrial (mt) DNA data from tigrinas (traditionally, Leopardus tigrinus) we sampled in Costa Rica, Venezuela, Colombia, Ecuador, Peru, Bolivia, northwestern and northeastern Argentina and southern Brazil. Additionally, the analysis included some GenBank sequences from southern, central and northeastern Brazil. The first mt set (mt ATP8+mt 16S rRNA with 41 tigrina) revealed the existence of seven different tigrina-like haplogroups. They could represent, at least, 4-6 different tigrina species following the Phylogenetic Species Concept (PSC). In the second mt set (mitogenomics with 18 tigrinas), we detected six different tigrina-like haplogroups. They could represent 4-5 different tigrina species - including a possible full new species, which has gone previously unnoticed to the world of science both morphologic and molecularly. Coat patterns of several of these different tigrinas support the molecular differences. We also detected intense hybridization in many Andean tigrina with margays (Leopardus wiedii) and ocelots (Leopardus pardalis) as well as hybridization of one Bolivian tigrina with Leopardus geoffroyi. Similar hybridization was found for many of the southern Brazilian tigrina (Leopardus guttulus). All of the temporal split estimates for these tigrina haplogroups, together with those of the Leopardus species recognized to date, began in the late Pliocene but mostly occurred during the Pleistocene. In agreement with the existence of multiple species within the traditional L. tigrinus species, we detected strong and significant spatial structure in the two mt data sets. There were clear circular clines. A major part of the analyses detected more genetic resemblance between the Central American + trans Andean Colombian and Ecuadorian tigrina (L. oncilla) with the most geographically distant tigrina from central and southern Brazil (L. guttulus; pure individuals not hybridized with L. geoffroyi). In comparison, the Andean tigrina taxa had intermediate geographical origins but were highly genetically differentiated both from the Central American + trans Andean Colombian-Ecuadorian tigrina and from the central and southern Brazilian tigrina.
Collapse
Affiliation(s)
- Manuel Ruiz-García
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Myreya Pinedo-Castro
- a Departamento de Biología, Facultad de Ciencias , Laboratorio de Genética de Poblaciones-Biología Evolutiva, Unidad de Genética, Pontificia Universidad Javeriana , Bogotá , Colombia
| | - Joseph Mark Shostell
- b Math, Science and Technology Department , University of Minnesota Crookston , Crookston , MN , USA
| |
Collapse
|
42
|
Peters KJ, Myers SA, Dudaniec RY, O'Connor JA, Kleindorfer S. Females drive asymmetrical introgression from rare to common species in Darwin's tree finches. J Evol Biol 2017; 30:1940-1952. [PMID: 28833876 DOI: 10.1111/jeb.13167] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 08/15/2017] [Indexed: 01/06/2023]
Abstract
The consequences of hybridization for biodiversity depend on the specific ecological and evolutionary context in which it occurs. Understanding patterns of gene flow among hybridizing species is crucial for determining the evolutionary trajectories of species assemblages. The recently discovered hybridization between two species of Darwin's tree finches (Camarhynchus parvulus and C. pauper) on Floreana Island, Galápagos, presents an exciting opportunity to investigate the mechanisms causing hybridization and its potential evolutionary consequences under conditions of recent habitat disturbance and the introduction of invasive pathogens. In this study, we combine morphological and genetic analysis with pairing observations to explore the extent, direction and drivers of hybridization and to test whether hybridization patterns are a result of asymmetrical pairing preference driven by females of the rarer species (C. pauper). We found asymmetrical introgression from the critically endangered, larger-bodied C. pauper to the common, smaller-bodied C. parvulus, which was associated with a lack of selection against heterospecific males by C. pauper females. Examination of pairing data showed that C. parvulus females paired assortatively, whereas C. pauper females showed no such pattern. This study shows how sex-specific drivers can determine the direction of gene flow in hybridizing species. Furthermore, our results suggest the existence of a hybrid swarm comprised of C. parvulus and hybrid birds. We discuss the influence of interspecific abundance differences and susceptibility to the invasive parasite Philornis downsi on the observed hybridization and recommend that the conservation of this iconic species group should be managed jointly rather than species-specific.
Collapse
Affiliation(s)
- K J Peters
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - S A Myers
- Southern Seas Ecology Laboratory, School of Earth and Environmental Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - R Y Dudaniec
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - J A O'Connor
- Department of Environment, Water and Natural Resources, Adelaide, SA, Australia
| | - S Kleindorfer
- School of Biological Sciences, Flinders University, Adelaide, SA, Australia
| |
Collapse
|
43
|
|
44
|
Spatial colonization by feral domestic catsFelis catus of former wildcatFelis silvestris silvestris home ranges. MAMMAL RES 2017. [DOI: 10.1007/bf03193135] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
45
|
Temporal shifts in the saltmarsh–Nelson’s sparrow hybrid zone revealed by replicated demographic and genetic surveys. CONSERV GENET 2017. [DOI: 10.1007/s10592-016-0920-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
46
|
Jerosch S, Götz M, Roth M. Spatial organisation of European wildcats (Felis silvestris silvestris) in an agriculturally dominated landscape in Central Europe. Mamm Biol 2017. [DOI: 10.1016/j.mambio.2016.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
47
|
Beutel T, Reineking B, Tiesmeyer A, Nowak C, Heurich M. Spatial patterns of co-occurrence of the European wildcatFelis silvestris silvestrisand domestic catsFelis silvestris catusin the Bavarian Forest National Park. WILDLIFE BIOLOGY 2017. [DOI: 10.2981/wlb.00284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Tanja Beutel
- T. Beutel and M. Heurich, Dept of Research and Documentation, Bavarian Forest National Park, Freyunger Straße 2, DE-94481 Grafenau, Germany. MH also at: Chair of Wildlife Ecology and Management, Univ. of Freiburg, Faculty of Environment and Natural Resources, Freiburg, Germany
| | - Björn Reineking
- B. Reineking, Univ. Grenoble Alpes, Irstea, UR EMGR, St-Martin-d'Hères, France, and: Biogeographical Modelling, Bayreuth Center of Ecology and Environmental Research BayCEER, Univ. of Bayreuth, Bayreuth, Germany
| | - Annika Tiesmeyer
- A. Tiesmeyer and C. Nowak, Senckenberg Research Inst. and Natural History Museum Frankfurt, Gelnhausen, Germany. AT also at: Inst. for Ecology, Evolution and Diversity, Goethe Univ. Frankfurt, Frankfurt am Main, Germany
| | - Carsten Nowak
- A. Tiesmeyer and C. Nowak, Senckenberg Research Inst. and Natural History Museum Frankfurt, Gelnhausen, Germany. AT also at: Inst. for Ecology, Evolution and Diversity, Goethe Univ. Frankfurt, Frankfurt am Main, Germany
| | - Marco Heurich
- T. Beutel and M. Heurich, Dept of Research and Documentation, Bavarian Forest National Park, Freyunger Straße 2, DE-94481 Grafenau, Germany. MH also at: Chair of Wildlife Ecology and Management, Univ. of Freiburg, Faculty of Environment and Natural Resources, Freiburg, Germany
| |
Collapse
|
48
|
Doherty TS, Dickman CR, Johnson CN, Legge SM, Ritchie EG, Woinarski JCZ. Impacts and management of feral catsFelis catusin Australia. Mamm Rev 2016. [DOI: 10.1111/mam.12080] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Tim S. Doherty
- School of Life and Environmental Sciences; Centre for Integrative Ecology (Burwood campus); Deakin University; Geelong Vic. Australia
| | - Chris R. Dickman
- Desert Ecology Research Group; School of Life and Environmental Sciences; University of Sydney; Sydney NSW Australia
| | - Chris N. Johnson
- School of Biological Sciences; University of Tasmania; Hobart Tas. Australia
| | - Sarah M. Legge
- Threatened Species Recovery Hub; National Environmental Science Program; Centre for Biodiversity and Conservation Science; University of Queensland; St Lucia Qld Australia
| | - Euan G. Ritchie
- School of Life and Environmental Sciences; Centre for Integrative Ecology (Burwood campus); Deakin University; Geelong Vic. Australia
| | - John C. Z. Woinarski
- Threatened Species Recovery Hub; National Environmental Science Programme; Charles Darwin University; Casuarina NT Australia
| |
Collapse
|
49
|
Xu C, Gao J, Du Z, Li D, Wang Z, Li Y, Pang X. Identifying the genetic diversity, genetic structure and a core collection of Ziziphus jujuba Mill. var. jujuba accessions using microsatellite markers. Sci Rep 2016; 6:31503. [PMID: 27531220 PMCID: PMC4987672 DOI: 10.1038/srep31503] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/21/2016] [Indexed: 01/02/2023] Open
Abstract
Ziziphus is a genus of spiny shrubs and small trees in the Rhamnaceae family. This group has a controversial taxonomy, with more than 200 species described, including Chinese jujube (Ziziphus jujuba Mill. var. jujuba) and Indian jujube (Z. mauritiana), as well as several other important cultivated fruit crops. Using 24 SSR markers distributed across the Chinese jujube genome, 962 jujube accessions from the two largest germplasm repositories were genotyped with the aim of analyzing the genetic diversity and structure and constructing a core collection that retain high genetic diversity. A molecular profile comparison revealed 622 unique genotypes, among which 123 genotypes were genetically identical to at least one other accessions. STRUCTURE analysis and multivariate analyses (Cluster and PCoA) roughly divided the accessions into three major groups, with some admixture among groups. A simulated annealing algorithm and a heuristic algorithm were chosen to construct the core collection. A final core of 150 accessions was selected, comprising 15.6% of the analyzed accessions and retaining more than 99.5% of the total alleles detected. We found no significant differences in allele frequency distributions or in genetic diversity parameters between the chosen core accessions and the 622 genetically unique accessions. This work contributes to the understanding of Chinese jujube diversification and the protection of important germplasm resources.
Collapse
Affiliation(s)
- Chaoqun Xu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Jiao Gao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Zengfeng Du
- National Foundation for Improved Cultivar of Chinese Jujube, Cangzhou Heibei, 061000, China
| | - Dengke Li
- Pomology Institute, Shanxi Academy of Agricultural Science, Taigu, Shanxi 030815, China
| | - Zhe Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing (100083), China
| |
Collapse
|
50
|
Beugin MP, Leblanc G, Queney G, Natoli E, Pontier D. Female in the inside, male in the outside: insights into the spatial organization of a European wildcat population. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0871-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|