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Molecular analysis of blood-associated pathogens in European wildcats (Felis silvestris silvestris) from Germany. Int J Parasitol Parasites Wildl 2022; 19:128-137. [PMID: 36119442 PMCID: PMC9477852 DOI: 10.1016/j.ijppaw.2022.08.012] [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: 07/20/2022] [Revised: 08/29/2022] [Accepted: 08/29/2022] [Indexed: 12/05/2022]
Abstract
European wildcats (Felis silvestris silvestris) have not been investigated in large numbers for blood-associated pathogens in Germany, because wildcats, being a protected species, may not be hunted, and the collection of samples is therefore difficult. Thus, spleen tissue and whole blood from 96 wildcats from Germany found as roadkill or dead from other causes in the years 1998–2020 were examined for the prevalence of blood associated pathogens using molecular genetic tools. PCR was used to screen for haemotrophic Mycoplasma spp., Hepatozoon spp., Cytauxzoon spp., Bartonella spp., Filarioidea, Anaplasmataceae, and Rickettsiales, and positive samples were subsequently sequenced. Phylogenetic analyses were performed for Mycoplasma spp. and Hepatozoon spp. by calculating phylogenetic trees and DNA haplotype networks. The following pathogens were found: Candidatus Mycoplasma haematominutum (7/96), Mycoplasma ovis (1/96), Hepatozoon silvestris (34/96), Hepatozoon felis (6/96), Cytauxzoon europaeus (45/96), and Bartonella spp. (3/96). This study elucidates the prevalence of blood-associated pathogens in wildcats from Germany. European wildcats from Germany carry different blood-associated pathogens. Pathogens can also affect domestic cats. Transmision by vectors or other transmisison routes are possible.
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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.
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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]
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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.
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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
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Abundance and use pattern of wildcats of ancient human-modified cattle pastures in northern Iberian Peninsula. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01533-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
AbstractThe wildcat is typically found in low densities. Here, we estimated wildcat abundance in cattle pastures interspersed between forests in northern Iberian Peninsula, and their patterns of intra-annual and daily use. We censused wildcats three times daily (morning, afternoon, and night) from a car during 4 years in summer season. We also carried out four monthly tracks (two in the morning and two in the afternoon) for a complete year. Overall, we recorded 191 wildcats in pastures and 5 on the road in forest zones. Thirteen different individual wildcats were identified during the summer censuses, but only 29.9% of the wildcats observed (n = 196) could be assigned to an individual wildcat. The number of wildcats sighted decreased especially during the last year, when sightings were 52–67% lower than in previous years. Wildcats were seen significantly more during the morning and night censuses than during the afternoon ones. Estimated annual summer densities in pasture areas ranged between 0.11 and 0.46 sightings/km2. Throughout the year, wildcats were observed 5.9 times more during summer-autumn than during winter-spring, and they could be observed in any time of the day, but more often close to dusk. It is noteworthy that the ancient human-transformed landscapes for cattle pastures could be an important habitat for wildcats in northern Iberian Peninsula, and conserving these areas should be important to maintaining wildcat populations.
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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.
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Westekemper K, Tiesmeyer A, Steyer K, Nowak C, Signer J, Balkenhol N. Do all roads lead to resistance? State road density is the main impediment to gene flow in a flagship species inhabiting a severely fragmented anthropogenic landscape. Ecol Evol 2021; 11:8528-8541. [PMID: 34257914 PMCID: PMC8258205 DOI: 10.1002/ece3.7635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/10/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
AIM Connectivity conservation is ideally based on empirical information on how landscape heterogeneity influences species-specific movement and gene flow. Here, we present the first large-scale evaluation of landscape impacts on genetic connectivity in the European wildcat (Felis silvestris), a flagship and umbrella species for connectivity conservation across Europe. LOCATION The study was carried out in the core area of the distributional range of wildcats in Germany, covering about 186,000 km2 of a densely populated and highly fragmented landscape. METHODS We used data of 975 wildcats genotyped at 14 microsatellites and an individual-based landscape genetic framework to assess the importance of twelve landscape variables for explaining observed genetic connectivity. For this, we optimized landscape resistance surfaces for all variables and compared their relative impacts using multiple regression on distance matrices and commonality analysis. RESULTS Genetic connectivity was best explained by a synergistic combination of six landscape variables and isolation by distance. Of these variables, road density had by far the strongest individual impact followed by synergistic effects of agricultural lands and settlements. Subsequent analyses involving different road types revealed that the strong effect of road density was largely due to state roads, while highways and federal roads had a much smaller, and county roads only a negligible impact. MAIN CONCLUSIONS Our results highlight that landscape-wide genetic connectivity in wildcats across Germany is strongly shaped by the density of roads and in particular state roads, with higher densities providing larger resistance to successful dispersal. These findings have important implications for conservation planning, as measures to mitigate fragmentation effects of roads (e.g., over- or underpasses) often focus on large, federally managed transportation infrastructures. While these major roads exert local barrier effects, other road types can be more influential on overall connectivity, as they are more abundant and more widespread across the landscape.
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Affiliation(s)
| | - Annika Tiesmeyer
- Conservation Genetics SectionSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Department of Ecology and EvolutionJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Katharina Steyer
- Conservation Genetics SectionSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
- Department of Ecology and EvolutionJohann Wolfgang Goethe‐University, BiologicumFrankfurt am MainGermany
| | - Carsten Nowak
- Conservation Genetics SectionSenckenberg Research Institute and Natural History Museum FrankfurtGelnhausenGermany
| | | | - Niko Balkenhol
- Wildlife SciencesUniversity of GoettingenGoettingenGermany
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Kessler C, Brambilla A, Waldvogel D, Camenisch G, Biebach I, Leigh DM, Grossen C, Croll D. A robust sequencing assay of a thousand amplicons for the high-throughput population monitoring of Alpine ibex immunogenetics. Mol Ecol Resour 2021; 22:66-85. [PMID: 34152681 PMCID: PMC9292246 DOI: 10.1111/1755-0998.13452] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 06/10/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Polymorphism for immune functions can explain significant variation in health and reproductive success within species. Drastic loss in genetic diversity at such loci constitutes an extinction risk and should be monitored in species of conservation concern. However, effective implementations of genome‐wide immune polymorphism sets into high‐throughput genotyping assays are scarce. Here, we report the design and validation of a microfluidics‐based amplicon sequencing assay to comprehensively capture genetic variation in Alpine ibex (Capra ibex). This species represents one of the most successful large mammal restorations recovering from a severely depressed census size and a massive loss in diversity at the major histocompatibility complex (MHC). We analysed 65 whole‐genome sequencing sets of the Alpine ibex and related species to select the most representative markers and to prevent primer binding failures. In total, we designed ~1,000 amplicons densely covering the MHC, further immunity‐related genes as well as randomly selected genome‐wide markers for the assessment of neutral population structure. Our analysis of 158 individuals shows that the genome‐wide markers perform equally well at resolving population structure as RAD‐sequencing or low‐coverage genome sequencing data sets. Immunity‐related loci show unexpectedly high degrees of genetic differentiation within the species. Such information can now be used to define highly targeted individual translocations. Our design strategy can be realistically implemented into genetic surveys of a large range of species. In conclusion, leveraging whole‐genome sequencing data sets to design targeted amplicon assays allows the simultaneous monitoring of multiple genetic risk factors and can be translated into species conservation recommendations.
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Affiliation(s)
- Camille Kessler
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Alice Brambilla
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,Alpine Wildlife Research Center, Gran Paradiso National Park, Italy
| | - Dominique Waldvogel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Iris Biebach
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Deborah M Leigh
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland.,WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
| | - Christine Grossen
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
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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
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Lehmann L, Stefen C. Study of non-metric characters of the skull to determine the epigenetic variability in populations of the European wildcat (Felis silvestris silvestris) and domestic cats (Felis catus). Mamm Biol 2021. [DOI: 10.1007/s42991-021-00119-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractWe studied the variability of non-metric cranial traits, mainly foramina, of European wildcats (Felis silvestris silvestris) and domestic cats (Felis catus) from Germany based on 28 non-metric traits in 211 skulls. The domestic cats were grouped together as a statistical population. The wildcats were divided into two populations: Harz and Hesse, which were further subdivided, based on traffic infrastructure, natural landscape, and in the Harz, on time period. Epigenetic variability, epigenetic distance and the fluctuating asymmetry were calculated to assess genetic variability, possible depressions and population stability. The epigenetic variability Iev of the wildcat groups ranged from 0.27 (Hesse II) to 0.40 (Harz I). The difference in Iev between all specimens from Harz and Hesse respectively was less (Iev = 0.37 Harz and 0.31 Hesse). Compared to other studies these values are not assumed to indicate genetic depression. The epigenetic distance between the wildcat samples is 0.0774 overall, and in each case higher between sub-groups of the Harz and Hesse than between groups within these regions, respectively. The significant epigenetic distance between Harz and Hesse might indicate—at least past formerly—restricted connectivity between these regions. The fluctuating asymmetry for wildcats in total is 11.74% and in the sub-groups it ranges from 8.47 to 16.14%. These values are below 20% are at the lower range known from populations of other mammal species. The use of fluctuating asymmetry had also been discussed critically in its usefulness to assess viability of populations.
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Moczek N, Nuss M, Köhler JK. Volunteering in the Citizen Science Project "Insects of Saxony"-The Larger the Island of Knowledge, the Longer the Bank of Questions. INSECTS 2021; 12:insects12030262. [PMID: 33804789 PMCID: PMC8003976 DOI: 10.3390/insects12030262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/13/2021] [Accepted: 03/15/2021] [Indexed: 11/16/2022]
Abstract
In a cross-sectional survey study (N = 116), volunteers of the project Insects of Saxony were asked about their current and past volunteering activities, their motivations, their rating of organisational offers, their knowledge, their satisfaction with the project and their personal contribution, and their intended future involvement. Participants in the study were mostly male, well-educated, over 50 years old, and had been volunteering in biodiversity projects for a long time. They were driven by both pro-social (altruistic) and self-serving (egoistic) motivations, but rated the pro-social functions as more important for their engagement. Communication and feedback were rated the most important organisational offers. Participants also reported a knowledge increase during project participation. While the volunteers were satisfied with the overall project, they were significantly less content with their own contribution. Results from the survey were followed up with a group discussion (N = 60). The anecdotes revealed the participants' regret of not having more time for their hobby, and they emphasised the challenges that arise from the different scientific approaches of the various disciplines. Most participants indicated that they want to continue their volunteering. Implications for measuring motivations in citizen science projects and for volunteer management are discussed.
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Affiliation(s)
- Nicola Moczek
- PSY: PLAN Institute for Architectural and Environmental Psychology, 10245 Berlin, Germany
- Museum für Naturkunde, Programme Society and Nature, 10115 Berlin, Germany
- Correspondence:
| | - Matthias Nuss
- Senckenberg Natural History Collections Dresden, Museum of Zoology, Lepitoptera Section, 01109 Dresden, Germany;
| | - Jana Katharina Köhler
- Department of Cognition, Emotion, and Methods in Psychology, University of Vienna, 1010 Vienna, Austria;
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Maronde L, McClintock BT, Breitenmoser U, Zimmermann F. Spatial capture-recapture with multiple noninvasive marks: An application to camera-trapping data of the European wildcat ( Felis silvestris) using R package multimark. Ecol Evol 2020; 10:13968-13979. [PMID: 33391695 PMCID: PMC7771165 DOI: 10.1002/ece3.6990] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/07/2020] [Accepted: 10/13/2020] [Indexed: 11/12/2022] Open
Abstract
In Switzerland, the European wildcat (Felis silvestris), a native felid, is protected by national law. In recent decades, the wildcat has slowly returned to much of its original range and may have even expanded into new areas that were not known to be occupied before. For the implementation of efficient conservation actions, reliable information about the status and trend of population size and density is crucial. But so far, only one reliable estimate of density in Switzerland was produced in the northern Swiss Jura Mountains. Wildcats are relatively rare and elusive, but camera trapping has proven to be an effective method for monitoring felids. We developed and tested a monitoring protocol using camera trapping in the northern Jura Mountains (cantons of Bern and Jura) in an area of 100 km2. During 60 days, we obtained 105 pictures of phenotypical wildcats of which 98 were suitable for individual identification. We identified 13 individuals from both sides and, additionally, 5 single right-sided flanks and 3 single left-sided flanks that could not be matched to unique individuals. We analyzed the camera-trap data using the R package multimark, which has been extended to include a novel spatial capture-recapture model for encounter histories that include multiple "noninvasive" marks, such as bilaterally asymmetrical left- and right-sided flanks, that can be difficult (or impossible) to reliably match to individuals. Here, we present this model in detail for the first time. Based on a "semi-complete" data likelihood, the model is less computationally demanding than Bayesian alternatives that rely on a data-augmented complete data likelihood. The spatially explicit capture-recapture model estimated a wildcat density (95% credible interval) of 26 (17-36) per 100 km2 suitable habitat. Our integrated model produced higher abundance and density estimates with improved precision compared to single-sided analyses, suggesting spatially explicit capture-recapture methods with multiple "noninvasive" marks can improve our ability to monitor wildcat population status.
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Affiliation(s)
- Lea Maronde
- Carnivore Ecology and Wildlife ManagementKORAMuri bei BernSwitzerland
| | - Brett T. McClintock
- Alaska Fisheries Science CenterMarine Mammal LaboratoryNOAA‐NMFSSeattleWashingtonUSA
| | - Urs Breitenmoser
- Carnivore Ecology and Wildlife ManagementKORAMuri bei BernSwitzerland
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Abstract
AbstractFollowing severe population decline and local extinction due to massive habitat destruction and persecution, wildcats have recently reappeared in several parts of Germany’s low mountain region. It remains unknown how this reemergence occurred, specifically if local populations have been overlooked at low densities or if the species has successfully spread across the highly fragmented anthropogenic landscape. In the central German Rhön Mountains, for instance, wildcats were believed to be extinct during most of the twentieth century, however, the species was recently detected and subsequent genetic monitoring found the presence of a sizeable population. In this study, we used microsatellite and SNP genotypes from 146 wildcat individuals from 2008 to 2017 across a ~ 15,000 km2 area in the central German low mountain region to understand the population re-establishment of wildcats in the region. Bayesian clustering and subsequent analyses revealed that animals in the Rhön Mountains appear to be a mix from the two adjacent populations in the North and South of the area, suggesting a recent range expansion from two different directions. Both populations meet in the Rhön Biosphere Reserve, leading to an admixture of the northern, autochthonous, and the southern reintroduced wildcat population. While we cannot completely exclude the possibility of undetected population persistence, the high genetic homogeneity in the central German wildcat population and the lack of any signatures of past population decline in the Rhön favor a scenario of natural expansion. Our findings thus suggest that wildcats are well capable of rapid range expansion across richly structured landscape mosaics consisting of open land, settlements, and forest patches and document the potential of massive non-invasive genetic sampling when aiming to reconstruct the complex population and range dynamics of wildlife.
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First report of Cytauxzoon sp. infection in Germany: organism description and molecular confirmation in a domestic cat. Parasitol Res 2020; 119:3005-3011. [PMID: 32677003 PMCID: PMC7366483 DOI: 10.1007/s00436-020-06811-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 07/09/2020] [Indexed: 01/24/2023]
Abstract
Cytauxzoonosis is described as an emerging tick-borne disease of domestic and wild felids caused by protozoans of the genus Cytauxzoon. While in the Americas the condition is described as a fatal disease, in Europe, reports on the clinical expression of the infection are scarce. This study describes the first case of Cytauxzoon sp. infection in Germany, in a domestic cat. A 6-year-old male domestic cat living in Saarlouis (Saarland) was presented with anorexia, lethargy and weight loss. The cat had an outdoor lifestyle and had not travelled abroad. Serum clinical chemistry analysis revealed azotaemia with markedly increased symmetric dimethylarginine, hypercreatinemia, hyperphosphatemia and hypoalbuminemia. Moreover, a mild non-regenerative anaemia was present. Approximately 1 year prior to these findings, the domestic cat was diagnosed with a feline immunodeficiency virus (FIV) infection. These results pointed toward a decreased glomerular filtration rate, presumably as a result of kidney dysfunction. Round to oval signet ring–shaped intraerythrocytic organisms, morphologically suggestive for a piroplasm, were revealed during blood smear evaluation with a degree of parasitaemia of 33.0%. PCR analyses and sequencing of a region of the 18S rRNA gene confirmed the presence of a Cytauxzoon sp. infection, with 99–100% nucleotide sequence identity with previously published Cytauxzoon sp. isolates. As this is the first molecularly confirmed Cytauxzoon sp. infection in a domestic cat in Germany, these findings suggest that cytauxzoonosis should be considered as a differential diagnosis in cases of anaemia in outdoor domestic cats, particularly in areas where wild felid populations are present.
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15
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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.
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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
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16
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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.
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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
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17
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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.
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18
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Koch K, Pink C, Hamilton N, Algar D. A population genetic study of feral cats on Christmas Island. AUST J ZOOL 2020. [DOI: 10.1071/zo20081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Feral and stray cats are a major threat for endemic species on Christmas Island and have been contributing to their decline. Cats were introduced to Christmas Island in 1888 and are now distributed across the whole island. We analysed the genetic population structure and diversity of feral and stray cats on Christmas Island to evaluate connectivity across the island and the possibility of discernible populations that could be targeted separately. Results indicate no differentiated population structure across the island, with cats facing no habitat obstacles to reduce their dispersal abilities across the island. We found high kin structure, suggesting individuals breeding successfully on the whole island. With the management of domestic and feral/stray cats since 2010, removal efforts targeting the whole island have successfully reduced the effective population size of feral/stray cats in the last five years. We suggest the use of various management techniques to facilitate future removal efforts, especially in areas on the island that are difficult to access.
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19
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Anile S, Devillard S, Ragni B, Rovero F, Mattucci F, Valvo ML. Habitat fragmentation and anthropogenic factors affect wildcat Felis silvestris silvestris occupancy and detectability on Mt Etna. WILDLIFE BIOLOGY 2019. [DOI: 10.2981/wlb.00561] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Stefano Anile
- S. Anile, (https://orcid.org/0000-0001-8871-9615) ✉ , Cooperative Wildlife Research Laboratory, Southern Illinois Univ., Carbondale, IL 62901, USA
| | - Sebastien Devillard
- S. Devillard, Univ Lyon, Université Claude Bernard Lyon, CNRS, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Bernardino Ragni
- B. Ragni, Dipto di Chimica, Biologia e Biotecnologie, Univ. degli Studi di Perugia, Perugia, Italy
| | - Francesco Rovero
- F. Rovero, Dept of Biology, Univ. of Florence, Sesto Fiorentino, Italy, and: Sezione di Biodiversità Tropicale, MUSE – Museo delle Scienze di Trento, Trento, Italy
| | - Federica Mattucci
- F. Mattucci, Laboratorio di Genetica, Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Bologna, Italy
| | - Mario Lo Valvo
- M. Lo Valvo, Dipto STEBICEF, Univ. di Palermo, Palermo, Italy
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20
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Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R. 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] [Key Words] [MESH Headings] [Grants] [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.
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Affiliation(s)
- Federica Mattucci
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy.
| | | | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, USA
| | - Paulo C Alves
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio - Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Edoardo Velli
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Università degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Romolo Caniglia
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
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21
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Iacolina L, Pertoldi C, Amills M, Kusza S, Megens HJ, Bâlteanu VA, Bakan J, Cubric-Curik V, Oja R, Saarma U, Scandura M, Šprem N, Stronen AV. Hotspots of recent hybridization between pigs and wild boars in Europe. Sci Rep 2018; 8:17372. [PMID: 30478374 PMCID: PMC6255867 DOI: 10.1038/s41598-018-35865-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 11/09/2018] [Indexed: 01/06/2023] Open
Abstract
After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.
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Affiliation(s)
- Laura Iacolina
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark. .,Aalborg Zoo, Mølleparkvej 63, 9000, Aalborg, Denmark.
| | - Cino Pertoldi
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark.,Aalborg Zoo, Mølleparkvej 63, 9000, Aalborg, Denmark
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus de la Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Szilvia Kusza
- Animal Genetics Laboratory, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi 138, 4032, Debrecen, Hungary
| | - Hendrik-Jan Megens
- Wageningen University & Research, Animal Breeding and Genomics, Droevendaalsesteeg 1, Wageningen, 6708PD, The Netherlands
| | - Valentin Adrian Bâlteanu
- Institute of Life Sciences, Faculty of Animal Science and Biotechnologies, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăştur 3-5, 400372, Cluj-Napoca, Romania
| | - Jana Bakan
- Technical University of Zvolen, Department of Phytology, Ul. T. G. Masaryka 24, 96053, Zvolen, Slovakia
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Ragne Oja
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Urmas Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, 51003, Tartu, Estonia
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, via Muroni 25, I-07100, Sassari, Italy
| | - Nikica Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - Astrid Vik Stronen
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, 9220, Aalborg, Denmark.,Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia
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22
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Andrews KR, Adams JR, Cassirer EF, Plowright RK, Gardner C, Dwire M, Hohenlohe PA, Waits LP. A bioinformatic pipeline for identifying informative SNP panels for parentage assignment from RADseq data. Mol Ecol Resour 2018; 18:1263-1281. [PMID: 29870119 PMCID: PMC6207459 DOI: 10.1111/1755-0998.12910] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 05/18/2018] [Accepted: 05/24/2018] [Indexed: 11/30/2022]
Abstract
The development of high-throughput sequencing technologies is dramatically increasing the use of single nucleotide polymorphisms (SNPs) across the field of genetics, but most parentage studies of wild populations still rely on microsatellites. We developed a bioinformatic pipeline for identifying SNP panels that are informative for parentage analysis from restriction site-associated DNA sequencing (RADseq) data. This pipeline includes options for analysis with or without a reference genome, and provides methods to maximize genotyping accuracy and select sets of unlinked loci that have high statistical power. We test this pipeline on small populations of Mexican gray wolf and bighorn sheep, for which parentage analyses are expected to be challenging due to low genetic diversity and the presence of many closely related individuals. We compare the results of parentage analysis across SNP panels generated with or without the use of a reference genome, and between SNPs and microsatellites. For Mexican gray wolf, we conducted parentage analyses for 30 pups from a single cohort where samples were available from 64% of possible mothers and 53% of possible fathers, and the accuracy of parentage assignments could be estimated because true identities of parents were known a priori based on field data. For bighorn sheep, we conducted maternity analyses for 39 lambs from five cohorts where 77% of possible mothers were sampled, but true identities of parents were unknown. Analyses with and without a reference genome produced SNP panels with ≥95% parentage assignment accuracy for Mexican gray wolf, outperforming microsatellites at 78% accuracy. Maternity assignments were completely consistent across all SNP panels for the bighorn sheep, and were 74.4% consistent with assignments from microsatellites. Accuracy and consistency of parentage analysis were not reduced when using as few as 284 SNPs for Mexican gray wolf and 142 SNPs for bighorn sheep, indicating our pipeline can be used to develop SNP genotyping assays for parentage analysis with relatively small numbers of loci.
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Affiliation(s)
- Kimberly R. Andrews
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
- Current address: Genetics and Genomics Group, University of Washington JISAO and NOAA Pacific Marine Environmental Lab, Seattle, WA 98115, USA
| | - Jennifer R. Adams
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
| | - E. Frances Cassirer
- Idaho Department of Fish and Game, 3316 16th Street, Lewiston, ID 83501, USA
| | - Raina K. Plowright
- Department of Microbiology and Immunology, Montana State University, 109 Lewis Hall, Bozeman, MT 59717, USA
| | - Colby Gardner
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Maggie Dwire
- U.S. Fish and Wildlife Service, 2105 Osuna Road NE, Albuquerque, NM 87113, USA
| | - Paul A. Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID 83844, USA
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23
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Heddergott M, Steeb S, Osten-Sacken N, Steinbach P, Schneider S, Pir JP, Müller F, Pigneur LM, Frantz AC. Serological survey of feline viral pathogens in free-living European wildcats (Felis s. silvestris) from Luxembourg. Arch Virol 2018; 163:3131-3134. [PMID: 30062638 PMCID: PMC7087253 DOI: 10.1007/s00705-018-3972-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/27/2018] [Indexed: 11/30/2022]
Abstract
European populations of free-living wildcats have been shown to be exposed to cat viruses. Luxembourg has a high degree of habitat fragmentation, and hybridisation rates between domestic cats and wildcats are high. We therefore assessed the seroprevalence of six viruses in 34 serum samples collected between 2001 and 2016 from wildcats in Luxembourg. The values for feline leukemia virus (FeLV; 52.9%) and feline coronavirus (FCoV; 47.1%) were amongst the highest reported for wildcats. We found evidence for the cumulative likelihood of exposure to FCoV affecting its seroprevalence. Routine monitoring of viral agents in this strictly protected species should be considered.
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Affiliation(s)
- Mike Heddergott
- Musée National d'Histoire Naturelle, 25, rue Münster, 2160, Luxembourg, Luxembourg.
| | - Sandra Steeb
- Arbeitskreis Wildbiologie an der Justus-Liebig-Universität Gießen e.V., Leihgesterner Weg 217, 35392, Giessen, Germany
| | - Natalia Osten-Sacken
- Musée National d'Histoire Naturelle, 25, rue Münster, 2160, Luxembourg, Luxembourg
- Fondation Fauna-Flora, 25, rue Münster, 2160, Luxembourg, Luxembourg
| | - Peter Steinbach
- Faculty of Chemistry, University of Göttingen, Tammannstraße 4, 37077, Göttingen, Germany
| | - Simone Schneider
- Musée National d'Histoire Naturelle, 25, rue Münster, 2160, Luxembourg, Luxembourg
- Biological Station SICONA, 12, rue de Capellen, 8393, Olm, Luxembourg
| | - Jacques P Pir
- Musée National d'Histoire Naturelle, 25, rue Münster, 2160, Luxembourg, Luxembourg
| | - Franz Müller
- Arbeitskreis Wildbiologie an der Justus-Liebig-Universität Gießen e.V., Leihgesterner Weg 217, 35392, Giessen, Germany
- , Hauptstraße 22, 36129, Gersfeld, Germany
| | - Lise-Marie Pigneur
- Laboratoire de génétique de la conservation (GeCoLAB), Université de Liège, quartier vallée 1, chemin de la Vallée 4, 4000, Liège, Belgium
| | - Alain C Frantz
- Musée National d'Histoire Naturelle, 25, rue Münster, 2160, Luxembourg, Luxembourg
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Oliveira T, Urra F, López‐Martín JM, Ballesteros‐Duperón E, Barea‐Azcón JM, Moléon M, Gil‐Sánchez JM, Alves PC, Díaz‐Ruíz F, Ferreras P, Monterroso P. Females know better: Sex-biased habitat selection by the European wildcat. Ecol Evol 2018; 8:9464-9477. [PMID: 30377515 PMCID: PMC6194279 DOI: 10.1002/ece3.4442] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 01/13/2018] [Accepted: 07/06/2018] [Indexed: 02/05/2023] Open
Abstract
The interactions between animals and their environment vary across species, regions, but also with gender. Sex-specific relations between individuals and the ecosystem may entail different behavioral choices and be expressed through different patterns of habitat use. Regardless, only rarely sex-specific traits are addressed in ecological modeling approaches. The European wildcat (Felis silvestris silvestris) is a species of conservation concern in Europe, with a highly fragmented and declining distribution across most of its range. We assessed sex-specific habitat selection patterns for the European wildcat, at the landscape and home range levels, across its Iberian biogeographic distribution using a multipopulation approach. We developed resource selection functions in a use-availability framework using radio-telemetry data from five wildcat populations. At the landscape level, we observed that, while both genders preferentially established home ranges in areas close to broadleaf forests and far from humanized areas, females selected mid-range elevation areas with some topographic complexity, whereas males used lowland areas. At the home range level, both females and males selected areas dominated by scrublands or broadleaf forests, but habitat features were less important at this level. The strength of association to habitat features was higher for females at both spatial levels, suggesting a tendency to select habitats with higher quality that can grant them enhanced access to shelter and feeding resources. Based on our results, we hypothesize that sex-biased behavioral patterns may contribute to the resilience of wildcats' genetic integrity through influencing the directionality of hybridization with domestic cats. Our study provides information about European wildcats' habitat use in an Iberian context, relevant for the implementation of conservation plans, and highlights the ecological relevance of considering sex-related differences in environmental preferences.
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Affiliation(s)
- Teresa Oliveira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
| | - Fermín Urra
- Gestión Ambiental de NavarraPamplonaNavarraSpain
| | - José María López‐Martín
- Secció d'Activitats Cinegètiques i Pesca ContinentalServeis Territorials de BarcelonaDepartment of D'Agricultura, Ramaderia, Pesca i AlimentacióGeneralitat de CatalunyaBarcelonaSpain
- Wildlife Ecology and Health GroupFacultat de VeterinàriaUniversitat Autònoma de Barcelona (UAB)BellaterraBarcelonaSpain
| | - Elena Ballesteros‐Duperón
- Agencia de Medio Ambiente y AguaConsejería de Medio Ambiente y Ordenación del TerritorioJunta de AndalucíaGranadaSpain
| | - José Miguel Barea‐Azcón
- Agencia de Medio Ambiente y AguaConsejería de Medio Ambiente y Ordenación del TerritorioJunta de AndalucíaGranadaSpain
| | - Marcos Moléon
- Department of ZoologyUniversity of GranadaGranadaSpain
| | | | - Paulo Celio Alves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
- Departamento de BiologiaFaculdade de CiênciasUniversidade do PortoPortoPortugal
- Wildlife Biology ProgramUniversity of MontanaMissoulaMontana
| | - Francisco Díaz‐Ruíz
- Biogeography, Diversity and Conservation Research TeamDepartment of Animal BiologyFaculty of SciencesUniversity of MalagaMalagaSpain
| | - Pablo Ferreras
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM‐JCCM)Ciudad RealSpain
| | - Pedro Monterroso
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoVairãoPortugal
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Carroll EL, Bruford MW, DeWoody JA, Leroy G, Strand A, Waits L, Wang J. Genetic and genomic monitoring with minimally invasive sampling methods. Evol Appl 2018; 11:1094-1119. [PMID: 30026800 PMCID: PMC6050181 DOI: 10.1111/eva.12600] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 01/02/2018] [Indexed: 12/12/2022] Open
Abstract
The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.
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Affiliation(s)
- Emma L. Carroll
- Scottish Oceans Institute and Sea Mammal Research UnitUniversity of St AndrewsSt AndrewsUK
| | - Mike W. Bruford
- Cardiff School of Biosciences and Sustainable Places Research InstituteCardiff UniversityCardiff, WalesUK
| | - J. Andrew DeWoody
- Department of Forestry and Natural Resources and Department of Biological SciencesPurdue UniversityWest LafayetteINUSA
| | - Gregoire Leroy
- Animal Production and Health DivisionFood and Agriculture Organization of the United NationsRomeItaly
| | - Alan Strand
- Grice Marine LaboratoryDepartment of BiologyCollege of CharlestonCharlestonSCUSA
| | - Lisette Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
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26
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Fischer D, Ziegler L, Hail K, Heckmann J, Reiners TE, Bauer C, Lierz M, Lang J. Clinical examination methods and investigation into the occurrence of endoparasites, Borna disease virus and genetic variability in the garden dormouse, Eliomys quercinus. FOLIA ZOOLOGICA 2018. [DOI: 10.25225/fozo.v67.i2.a1.2018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Dominik Fischer
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus Liebig University Giessen, Frankfurter Stras
| | - Luisa Ziegler
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus Liebig University Giessen, Frankfurter Stras
| | - Katrin Hail
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus Liebig University Giessen, Frankfurter Stras
| | - Julia Heckmann
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus Liebig University Giessen, Frankfurter Stras
| | - Tobias Erik Reiners
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Cl
| | - Christian Bauer
- Working Group Wildlife Biology at Justus Liebig University Giessen, Leihgesterner Weg 217, D-35392 G
| | - Michael Lierz
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus Liebig University Giessen, Frankfurter Stras
| | - Johannes Lang
- Clinic for Birds, Reptiles, Amphibians and Fish, Justus Liebig University Giessen, Frankfurter Stras
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27
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Hollerbach L, Heurich M, Reiners TE, Nowak C. Detection dogs allow for systematic non-invasive collection of DNA samples from Eurasian lynx. Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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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.
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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
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29
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Jerosch S, Kramer-Schadt S, Götz M, Roth M. The importance of small-scale structures in an agriculturally dominated landscape for the European wildcat ( Felis silvestris silvestris ) in central Europe and implications for its conservation. J Nat Conserv 2018. [DOI: 10.1016/j.jnc.2017.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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30
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Advances in Using Non-invasive, Archival, and Environmental Samples for Population Genomic Studies. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_45] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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31
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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
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32
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Assessing SNP genotyping of noninvasively collected wildlife samples using microfluidic arrays. Sci Rep 2017; 7:10768. [PMID: 28883428 PMCID: PMC5589735 DOI: 10.1038/s41598-017-10647-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/11/2017] [Indexed: 11/09/2022] Open
Abstract
Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology.
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33
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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]
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34
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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
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