1
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Opatova V, Bourguignon K, Bond JE. Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae). Mol Ecol Resour 2024; 24:e13894. [PMID: 37971187 DOI: 10.1111/1755-0998.13894] [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: 07/04/2023] [Revised: 10/24/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023]
Abstract
The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.
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Affiliation(s)
- Vera Opatova
- Department of Zoology, Faculty of Sciences, Charles University, Prague 2, Czech Republic
| | - Kellie Bourguignon
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Jason E Bond
- Department of Entomology and Nematology, University of California, Davis, California, USA
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2
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Measuring the Impact of Conservation: The Growing Importance of Monitoring Fauna, Flora and Funga. DIVERSITY 2022. [DOI: 10.3390/d14100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Many stakeholders, from governments to civil society to businesses, lack the data they need to make informed decisions on biodiversity, jeopardising efforts to conserve, restore and sustainably manage nature. Here we review the importance of enhancing biodiversity monitoring, assess the challenges involved and identify potential solutions. Capacity for biodiversity monitoring needs to be enhanced urgently, especially in poorer, high-biodiversity countries where data gaps are disproportionately high. Modern tools and technologies, including remote sensing, bioacoustics and environmental DNA, should be used at larger scales to fill taxonomic and geographic data gaps, especially in the tropics, in marine and freshwater biomes, and for plants, fungi and invertebrates. Stakeholders need to follow best monitoring practices, adopting appropriate indicators and using counterfactual approaches to measure and attribute outcomes and impacts. Data should be made openly and freely available. Companies need to invest in collecting the data required to enhance sustainability in their operations and supply chains. With governments soon to commit to the post-2020 global biodiversity framework, the time is right to make a concerted push on monitoring. However, action at scale is needed now if we are to enhance results-based management adequately to conserve the biodiversity and ecosystem services we all depend on.
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3
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A decade of genetic monitoring reveals increased inbreeding for the Endangered western leopard toad, Sclerophrys pantherina. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Werhahn G, Senn H, Macdonald DW, Sillero-Zubiri C. The Diversity in the Genus Canis Challenges Conservation Biology: A Review of Available Data on Asian Wolves. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.782528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Taxa belonging to the Genus Canis can challenge taxonomists because species boundaries and distribution ranges are often gradual. Species delineation within Canis is currently not based on consistent criteria, and is hampered by geographical bias and lack of taxonomic research. But a consistent taxonomy is critical, given its importance for assigning legal protection, conservation priorities, and financial resources. We carried out a qualitative review of the major wolf lineages so far identified from Asia from historical to contemporary time and considered relevant morphological, ecological, and genetic evidence. We present full mitochondrial phylogenies and genetic distances between these lineages. This review aims to summarize the available data on contemporary Asian wolf lineages within the context of the larger phylogenetic Canis group and to work toward a taxonomy that is consistent within the Canidae. We found support for the presence and taxon eligibility of Holarctic gray, Himalayan/Tibetan, Indian, and Arabian wolves in Asia and recommend their recognition at the taxonomic levels consistent within the group.
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5
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Lugli F, Caniglia R, Mattioli L, Fabbri E, Mencucci M, Cappai N, Mucci N, Apollonio M, Scandura M. Lifelong non-invasive genetic monitoring of a philopatric female wolf in the Tuscan Apennines, Italy. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01548-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Dziech A. Identification of Wolf-Dog Hybrids in Europe – An Overview of Genetic Studies. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.760160] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Significant development of genetic tools during the last decades provided opportunities for more detailed analyses and deeper understanding of species hybridization. New genetic markers allowed for reliable identification of admixed individuals deriving from recent hybridization events (a few generations) and those originating from crossings up to 19 generations back. Implementation of microsatellites (STRs) together with Bayesian clustering provided abundant knowledge regarding presence of admixed individuals in numerous populations and helped understand the problematic nature of studying hybridization (i.a., defining a reliable thresholds for recognizing individuals as admixed or obtaining well-grounded results representing actual proportion of hybrids in a population). Nevertheless, their utilization is limited to recent crossbreeding events. Single Nucleotide Polymorphisms (SNPs) proved to be more sensible tools for admixture analyses furnishing more reliable knowledge, especially for older generation backcrosses. Small sets of Ancestry Informative Markers (AIMs) of both types of markers were effective enough to implement in monitoring programs, however, SNPs seem to be more appropriate because of their ability to identify admixed individuals up to 3rd generations. The main aim of this review is to summarize abundant knowledge regarding identification of wolf-dog hybrids in Europe and discuss the most relevant problems relating to the issue, together with advantages and disadvantages of implemented markers and approaches.
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7
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Cozzi G, Hollerbach L, Suter SM, Reiners TE, Kunz F, Tettamanti F, Ozgul A. Eyes, ears, or nose? Comparison of three non-invasive methods to survey wolf recolonisation. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00167-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AbstractThe development and use of cost-effective and appropriate survey methods to assess species distribution and to monitor range expansion and contraction of wild populations is crucial due to the limited financial resources for conservation. Of particular importance, yet little studied, is the ability to collect information before a wild population is well established, i.e. at the early stages of recolonisation. During 2018 and 2019, we used camera traps, audio recorders, and scat detection dogs simultaneously to investigate composition, detection probability, and territorial extent of a pack of wolves in the Swiss Alps. We compared the efficacy of these survey methods by assessing sampling effort, data obtained, and costs. We show that, under the presented setup, camera traps and scat detection dogs substantially outperformed audio recorders in detecting wolves, representing the packs’ territorial extent, and revealing the number of adult wolves. The detection dogs did not detect pups but, unlike the other methods, allowed the identification of single individuals. The use of four camera traps during 13 weeks, a 24-km-long transect walked with the detection dog, or the use of one audio recorder during 148 weeks were necessary to obtain a comparable wolf detection probability. Our results show that no single method was able to return all information that we hoped to collect. Comprehensive and cost-effective information was best obtained by combining data from camera traps and detection dogs. We suggest both methods to be simultaneously used to successfully investigate wolf recolonisation into historical range.
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8
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Kloch A, Biedrzycka A, Szewczyk M, Nowak S, Niedźwiedzka N, Kłodawska M, Hájková A, Hulva P, Jędrzejewska B, Mysłajek R. High genetic diversity of immunity genes in an expanding population of a highly mobile carnivore, the grey wolf
Canis
lupus
, in Central Europe. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
- Agnieszka Kloch
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
| | | | - Maciej Szewczyk
- Department of Vertebrate Ecology and Zoology Faculty of Biology University of Gdańsk Gdańsk Poland
| | - Sabina Nowak
- Association for Nature “Wolf” Twardorzeczka Poland
| | | | - Monika Kłodawska
- Department of Zoology Faculty of Science Charles University Prague Czech Republic
| | - Andrea Hájková
- State Nature Conservancy of the Slovak Republic Spišská Nová Ves Slovakia
| | - Pavel Hulva
- Department of Zoology Faculty of Science Charles University Prague Czech Republic
- Department of Biology and Ecology Faculty of Science University of Ostrava Ostrava Czech Republic
| | | | - Robert Mysłajek
- Department of Ecology, Institute of Functional Biology and Ecology, Faculty of Biology, Biological and Chemical Research Centre University of Warsaw Warszawa Poland
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9
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Genome-Wide SNPs Detect Hybridisation of Marsupial Gliders ( Petaurus breviceps breviceps × Petaurus norfolcensis) in the Wild. Genes (Basel) 2021; 12:genes12091327. [PMID: 34573311 PMCID: PMC8467023 DOI: 10.3390/genes12091327] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 08/20/2021] [Accepted: 08/25/2021] [Indexed: 11/17/2022] Open
Abstract
Petaurus breviceps and Petaurus norfolcensis have produced hybrids in captivity, however there are no reported cases of Petaurus hybridisation in the wild. This study uses morphological data, mitochondrial DNA, and nuclear genome-wide SNP markers to confirm P. breviceps breviceps × P. norfolcensis hybridisation within their natural range on the central coast of New South Wales, Australia. Morphological data identified a potential hybrid that was confirmed with next-generation sequencing technology and 10,111 genome-wide SNPs. Both STRUCTURE and NewHybrid analyses identified the hybrid as a P. norfolcensis backcross, which suggests an initial F1 hybrid was fertile. The mitochondrial DNA matched that of a P. b. breviceps, indicating that a P. b. breviceps female initially mated with a P. norfolcensis male to produce a fertile female offspring. Our study is an important example of how genome-wide SNPs can be used to identify hybrids where the distribution of congeners overlaps. Hybridisation between congeners is likely to become more frequent as climate changes and habitats fragment, resulting in increased interactions and competition for resources and mates.
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10
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Carrillo-Bilbao G, Martin-Solano S, Saegerman C. Zoonotic Blood-Borne Pathogens in Non-Human Primates in the Neotropical Region: A Systematic Review. Pathogens 2021; 10:1009. [PMID: 34451473 PMCID: PMC8400055 DOI: 10.3390/pathogens10081009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 07/29/2021] [Accepted: 08/05/2021] [Indexed: 01/17/2023] Open
Abstract
Background: Understanding which non-human primates (NHPs) act as a wild reservoir for blood-borne pathogens will allow us to better understand the ecology of diseases and the role of NHPs in the emergence of human diseases in Ecuador, a small country in South America that lacks information on most of these pathogens. Methods and principal findings: A systematic review was carried out using PRISMA guidelines from 1927 until 2019 about blood-borne pathogens present in NHPs of the Neotropical region (i.e., South America and Middle America). Results: A total of 127 publications were found in several databases. We found in 25 genera (132 species) of NHPs a total of 56 blood-borne pathogens in 197 records where Protozoa has the highest number of records in neotropical NHPs (n = 128) compared to bacteria (n = 12) and viruses (n = 57). Plasmodium brasilianum and Trypanosoma cruzi are the most recorded protozoa in NHP. The neotropical primate genus with the highest number of blood-borne pathogens recorded is Alouatta sp. (n = 32). The use of non-invasive samples for neotropical NHPs remains poor in a group where several species are endangered or threatened. A combination of serological and molecular techniques is common when detecting blood-borne pathogens. Socioecological and ecological risk factors facilitate the transmission of these parasites. Finally, a large number of countries remain unsurveyed, such as Ecuador, which can be of public health importance. Conclusions and significance: NHPs are potential reservoirs of a large number of blood-borne pathogens. In Ecuador, research activities should be focused on bacteria and viruses, where there is a gap of information for neotropical NHPs, in order to implement surveillance programs with regular and effective monitoring protocols adapted to NHPs.
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Affiliation(s)
- Gabriel Carrillo-Bilbao
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Fundamental and Applied Research for Animal and Health (FARAH) Center, Department of Infections and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium;
- Facultad de Filosofía y Letras y Ciencias de la Educación, Universidad Central del Ecuador, 170521 Quito, Ecuador
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, 170521 Quito, Ecuador;
| | - Sarah Martin-Solano
- Instituto de Investigación en Zoonosis (CIZ), Universidad Central del Ecuador, 170521 Quito, Ecuador;
- Grupo de Investigación en Sanidad Animal y Humana (GISAH), Carrera Ingeniería en Biotecnología, Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas—ESPE, 171103 Sangolquí, Ecuador
| | - Claude Saegerman
- Research Unit of Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Fundamental and Applied Research for Animal and Health (FARAH) Center, Department of Infections and Parasitic Diseases, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium;
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11
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Podbielska A, Piórkowska K, Szmatoła T. Microsatellite-Based Genetic Structure and Hybrid Detection in Alpacas Bred in Poland. Animals (Basel) 2021; 11:ani11082193. [PMID: 34438651 PMCID: PMC8388510 DOI: 10.3390/ani11082193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/17/2021] [Accepted: 07/18/2021] [Indexed: 11/16/2022] Open
Abstract
This study aimed to characterize the population structure and genetic diversity of alpacas maintained in Poland using 17 microsatellite markers recommended by the International Society for Animal Genetics. The classification of llamas, alpacas, and hybrids of both based on phenotype is often difficult due to long-term admixture. Our results showed that microsatellite markers can distinguish alpacas from llamas and provide information about the level of admixture of one species in another. Alpacas admixed with llamas constituted 8.8% of the tested individuals, with the first-generation hybrid displaying only 7.4% of llama admixture. The results showed that Poland hosts a high alpaca genetic diversity as a consequence of their mixed origin. More than 200 different alleles were identified and the average observed heterozygosity and expected heterozygosity values were 0.745 and 0.768, respectively, the average coefficient of inbreeding was 0.034, and the average polymorphism information content value was 0.741. The probability of exclusion for one parent was estimated at 0.99995 and for two parents at 0.99999.
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Affiliation(s)
- Angelika Podbielska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
- Correspondence:
| | - Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
| | - Tomasz Szmatoła
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland; (K.P.); (T.S.)
- Center for Experimental and Innovative Medicine, University of Agriculture in Krakow, Rędzina 1c, 30-248 Kraków, Poland
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12
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Santostasi NL, Gimenez O, Caniglia R, Fabbri E, Molinari L, Reggioni W, Ciucci P. Estimating Admixture at the Population Scale: Taking Imperfect Detectability and Uncertainty in Hybrid Classification Seriously. J Wildl Manage 2021. [DOI: 10.1002/jwmg.22038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Nina L. Santostasi
- Department of Biology and Biotechnologies “Charles Darwin” University of Rome La Sapienza Rome Italy
| | - Olivier Gimenez
- CEFE, CNRS University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
| | - Romolo Caniglia
- Italian Institute for Environmental Protection and Research (ISPRA), Unit for Conservation Genetics (BIO–CGE), Ozzano dell'Emilia Italy
| | - Elena Fabbri
- Italian Institute for Environmental Protection and Research (ISPRA), Unit for Conservation Genetics (BIO–CGE), Ozzano dell'Emilia Italy
| | - Luigi Molinari
- Wolf Apennine Center, Appennino Tosco‐Emiliano National Park, Ligonchio Italy
| | - Willy Reggioni
- Wolf Apennine Center, Appennino Tosco‐Emiliano National Park, Ligonchio Italy
| | - Paolo Ciucci
- CEFE, CNRS University of Montpellier, University Paul Valéry Montpellier 3, EPHE, IRD Montpellier France
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13
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Harmoinen J, von Thaden A, Aspi J, Kvist L, Cocchiararo B, Jarausch A, Gazzola A, Sin T, Lohi H, Hytönen MK, Kojola I, Stronen AV, Caniglia R, Mattucci F, Galaverni M, Godinho R, Ruiz-González A, Randi E, Muñoz-Fuentes V, Nowak C. Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples. BMC Genomics 2021; 22:473. [PMID: 34171993 PMCID: PMC8235813 DOI: 10.1186/s12864-021-07761-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/01/2021] [Indexed: 12/25/2022] Open
Abstract
Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07761-5.
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Affiliation(s)
- Jenni Harmoinen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.
| | - 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, Biologicum, Frankfurt am Main, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - 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
| | - Anne Jarausch
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Biologicum, Frankfurt am Main, Germany
| | - Andrea Gazzola
- Association for the Conservation of Biological Diversity, Focşani, Romania
| | - Teodora Sin
- Association for the Conservation of Biological Diversity, Focşani, Romania.,Department of Systems Ecology and Sustainability, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Marjo K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Eteläranta 55, FI-96300, Rovaniemi, Finland
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research, Bologna, Italy
| | | | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - Aritz Ruiz-González
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research, Bologna, Italy.,Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - 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
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - 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
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14
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Smeds L, Aspi J, Berglund J, Kojola I, Tirronen K, Ellegren H. Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations. Evol Appl 2021; 14:721-734. [PMID: 33767747 PMCID: PMC7980305 DOI: 10.1111/eva.13151] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 01/02/2023] Open
Abstract
Hybridization and admixture can threaten the genetic integrity of populations and be of particular concern to endangered species. Hybridization between grey wolves and dogs has been documented in many wolf populations worldwide and is a prominent example of human-mediated hybridization between a domesticated species and its wild relative. We analysed whole-genome sequences from >200 wolves and >100 dogs to study admixture in Fennoscandian wolf populations. A principal component analysis of genetic variation and admixture showed that wolves and dogs were well-separated, without evidence for introgression. Analyses of local ancestry revealed that wolves had <1% mixed ancestry, levels comparable to the degree of mixed ancestry in many dogs, and likely not resulting from recent wolf-dog hybridization. We also show that the founders of the Scandinavian wolf population were genetically inseparable from Finnish and Russian Karelian wolves, pointing at the geographical origin of contemporary Scandinavian wolves. Moreover, we found Scandinavian-born animals among wolves sampled in Finland, demonstrating bidirectional gene flow between the Scandinavian Peninsula and eastern countries. The low incidence of admixture between wolves and dogs in Fennoscandia may be explained by the fact that feral dogs are rare in this part of Europe and that careful monitoring and management act to remove hybrids before they backcross into wolf populations.
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Affiliation(s)
- Linnéa Smeds
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Jouni Aspi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Jonas Berglund
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke)RovaniemiFinland
| | - Konstantin Tirronen
- Institute of BiologyKarelian Research Centre of the Russian Academy of SciencePetrozavodskRussian Federation
| | - Hans Ellegren
- Department of Ecology and GeneticsUppsala UniversityUppsalaSweden
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15
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Schenker L, Bollmann K, Rehnus M, Brodbeck S, Gugerli F. Hare's affairs: Lessons learnt from a noninvasive genetic monitoring for tracking mountain hare individuals. Ecol Evol 2020; 10:10150-10166. [PMID: 33005371 PMCID: PMC7520196 DOI: 10.1002/ece3.6676] [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: 11/04/2019] [Revised: 06/29/2020] [Accepted: 07/20/2020] [Indexed: 01/31/2023] Open
Abstract
Systematic monitoring of individuals and their abundance over time has become an important tool to provide information for conservation. For genetic monitoring studies, noninvasive sampling has emerged as a valuable approach, particularly so for elusive or rare animals. Here, we present the 5-year results of an ongoing noninvasive genetic monitoring of mountain hares (Lepus timidus) in a protected area in the Swiss Alps. We used nuclear microsatellites and a sex marker to identify individuals and assign species to noninvasively collected feces samples. Through including a marker for sex identification, we were able to assess sex ratio changes and sex-specific demographic parameters over time. Male abundance in the area showed high fluctuations and apparent survival for males was lower than for females. Generally, males and females showed only little temporary migration into and out of the study area. Additionally, using genotyped tissue samples from mountain hares, European hares (Lepus europaeus) and their hybrids, we were able to provide evidence for the first occurrence of a European hare in the study area at an elevation of 2,300 m a.s.l. in spring 2016. For future monitoring studies, we suggest to include complementary analysis methods to reliably infer species identities of the individuals analyzed and, thus, not only monitor mountain hare individual abundance, but also assess the potential threats given through competitive exclusion by and hybridization with the European hare.
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Affiliation(s)
- Laura Schenker
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Kurt Bollmann
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Maik Rehnus
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Sabine Brodbeck
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
| | - Felix Gugerli
- Swiss Federal Institute for Forest, Snow and Landscape Research WSLBirmensdorfSwitzerland
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16
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Caniglia R, Galaverni M, Velli E, Mattucci F, Canu A, Apollonio M, Mucci N, Scandura M, Fabbri E. A standardized approach to empirically define reliable assignment thresholds and appropriate management categories in deeply introgressed populations. Sci Rep 2020; 10:2862. [PMID: 32071323 PMCID: PMC7028925 DOI: 10.1038/s41598-020-59521-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Anthropogenic hybridization is recognized as a major threat to the long-term survival of natural populations. While identifying F1 hybrids might be simple, the detection of older admixed individuals is far from trivial and it is still debated whether they should be targets of management. Examples of anthropogenic hybridization have been described between wolves and domestic dogs, with numerous cases detected in the Italian wolf population. After selecting appropriate wild and domestic reference populations, we used empirical and simulated 39-autosomal microsatellite genotypes, Bayesian assignment and performance analyses to develop a workflow to detect different levels of wolf x dog admixture. Membership proportions to the wild cluster (qiw) and performance indexes identified two q-thresholds which allowed to efficiently classify the analysed genotypes into three assignment classes: pure (with no or negligible domestic ancestry), older admixed (with a marginal domestic ancestry) and recent admixed (with a clearly detectable domestic ancestry) animals. Based on their potential to spread domestic variants, such classes were used to define three corresponding management categories: operational pure, introgressed and operational hybrid individuals. Our multiple-criteria approach can help wildlife managers and decision makers in more efficiently targeting the available resources for the long-term conservation of species threatened by anthropogenic hybridization.
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Affiliation(s)
- Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy.
| | | | - Edoardo Velli
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Antonio Canu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Marco Apollonio
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Nadia Mucci
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
| | - Massimo Scandura
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Elena Fabbri
- Unit for Conservation Genetics (BIO-CGE), Italian Institute for Environmental Protection and Research (ISPRA), Ozzano dell' Emilia, Bologna, Italy
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17
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Novel real-time PCR species identification assays for British and Irish bats and their application to a non-invasive survey of bat roosts in Ireland. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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18
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Dreger DL, Hooser BN, Hughes AM, Ganesan B, Donner J, Anderson H, Holtvoigt L, Ekenstedt KJ. True Colors: Commercially-acquired morphological genotypes reveal hidden allele variation among dog breeds, informing both trait ancestry and breed potential. PLoS One 2019; 14:e0223995. [PMID: 31658272 PMCID: PMC6816562 DOI: 10.1371/journal.pone.0223995] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/02/2019] [Indexed: 01/15/2023] Open
Abstract
Direct-to-consumer canine genetic testing is becoming increasingly popular among dog owners. The data collected therein provides intriguing insight into the current status of morphological variation present within purebred populations. Mars WISDOM PANELTM data from 11,790 anonymized dogs, representing 212 breeds and 4 wild canine species, were evaluated at genes associated with 7 coat color traits and 5 physical characteristics. Frequencies for all tested alleles at these 12 genes were determined by breed and by phylogenetic grouping. A sub-set of the data, consisting of 30 breeds, was divided into separate same-breed populations based on country of collection, body size, coat variation, or lineages selected for working or conformation traits. Significantly different (p ≤ 0.00167) allele frequencies were observed between populations for at least one of the tested genes in 26 of the 30 breeds. Next, standard breed descriptions from major American and international registries were used to determine colors and tail lengths (e.g. genetic bobtail) accepted within each breed. Alleles capable of producing traits incongruous with breed descriptions were observed in 143 breeds, such that random mating within breeds has probabilities of between 4.9e-7 and 0.25 of creating undesirable phenotypes. Finally, the presence of rare alleles within breeds, such as those for the recessive black coloration and natural bobtail, was combined with previously published identity-by-decent haplotype sharing levels to propose pathways by which the alleles may have spread throughout dog breeds. Taken together, this work demonstrates that: 1) the occurrence of low frequency alleles within breeds can reveal the influence of regional or functional selection practices; 2) it is possible to visualize the potential historic connections between breeds that share rare alleles; and 3) the necessity of addressing conflicting ideals in breed descriptions relative to actual genetic potential is crucial.
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Affiliation(s)
- Dayna L. Dreger
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States of America
| | - Blair N. Hooser
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States of America
| | | | | | | | | | | | - Kari J. Ekenstedt
- Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States of America
- * E-mail:
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