1
|
Kreling SES, Reese EM, Cavalluzzi OM, Bozzi NB, Messinger R, Schell CJ, Long RA, Prugh LR. City divided: Unveiling family ties and genetic structuring of coyotes in Seattle. Mol Ecol 2024; 33:e17427. [PMID: 38837263 DOI: 10.1111/mec.17427] [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: 04/01/2024] [Revised: 05/02/2024] [Accepted: 05/13/2024] [Indexed: 06/07/2024]
Abstract
Linear barriers pose significant challenges for wildlife gene flow, impacting species persistence, adaptation, and evolution. While numerous studies have examined the effects of linear barriers (e.g., fences and roadways) on partitioning urban and non-urban areas, understanding their influence on gene flow within cities remains limited. Here, we investigated the impact of linear barriers on coyote (Canis latrans) population structure in Seattle, Washington, where major barriers (i.e., interstate highways and bodies of water) divide the city into distinct quadrants. Just under 1000 scats were collected to obtain genetic data between January 2021 and December 2022, allowing us to identify 73 individual coyotes. Notably, private allele analysis underscored limited interbreeding among quadrants. When comparing one quadrant to each other, there were up to 16 private alleles within a single quadrant, representing nearly 22% of the population allelic diversity. Our analysis revealed weak isolation by distance, and despite being a highly mobile species, genetic structuring was apparent between quadrants even with extremely short geographic distance between individual coyotes, implying that Interstate 5 and the Ship Canal act as major barriers. This study uses coyotes as a model species for understanding urban gene flow and its consequences in cities, a crucial component for bolstering conservation of rarer species and developing wildlife friendly cities.
Collapse
Affiliation(s)
- Samantha E S Kreling
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Ellen M Reese
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Olivia M Cavalluzzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Natalee B Bozzi
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Riley Messinger
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Christopher J Schell
- Department of Environmental Science, Policy, and Management, University of California-Berkeley, Berkeley, California, USA
| | | | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| |
Collapse
|
2
|
Morris DR, McWhorter TJ, Boardman WSJ, Simpson G, Wentzel J, Coetzee J, Moodley Y. Unravelling the maternal evolutionary history of the African leopard ( Panthera pardus pardus). PeerJ 2024; 12:e17018. [PMID: 38618571 PMCID: PMC11016244 DOI: 10.7717/peerj.17018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 02/06/2024] [Indexed: 04/16/2024] Open
Abstract
The African leopard (Panthera pardus pardus) has lost a significant proportion of its historical range, notably in north-western Africa and South Africa. Recent studies have explored the genetic diversity and population structure of African leopards across the continent. A notable genetic observation is the presence of two divergent mitochondrial lineages, PAR-I and PAR-II. Both lineages appeared to be distributed widely, with PAR-II frequently found in southern Africa. Until now, no study has attempted to date the emergence of either lineage, assess haplotype distribution, or explore their evolutionary histories in any detail. To investigate these underappreciated questions, we compiled the largest and most geographically representative leopard data set of the mitochondrial NADH-5 gene to date. We combined samples (n = 33) collected in an altitudinal transect across the Mpumalanga province of South Africa, where two populations of leopard are known to be in genetic contact, with previously published sequences of African leopard (n = 211). We estimate that the maternal PAR-I and PAR-II lineages diverged approximately 0.7051 (0.4477-0.9632) million years ago (Ma). Through spatial and demographic analyses, we show that while PAR-I underwent a mid-Pleistocene population expansion resulting in several closely related haplotypes with little geographic structure across much of its range, PAR-II remained at constant size and may even have declined slightly in the last 0.1 Ma. The higher genetic drift experienced within PAR-II drove a greater degree of structure with little haplotype sharing and unique haplotypes in central Africa, the Cape, KwaZulu-Natal and the South African Highveld. The phylogeographic structure of PAR-II, with its increasing frequency southward and its exclusive occurrence in south-eastern South Africa, suggests that this lineage may have been isolated in South Africa during the mid-Pleistocene. This hypothesis is supported by historical changes in paleoclimate that promoted intense aridification around the Limpopo Basin between 1.0-0.6 Ma, potentially reducing gene flow and promoting genetic drift. Interestingly, we ascertained that the two nuclear DNA populations identified by a previous study as East and West Mpumalanga correspond to PAR-I and PAR-II, respectively, and that they have come into secondary contact in the Lowveld region of South Africa. Our results suggest a subdivision of African leopard mtDNA into two clades, with one occurring almost exclusively in South Africa, and we identify the potential environmental drivers of this observed structure. We caution that our results are based on a single mtDNA locus, but it nevertheless provides a hypothesis that can be further tested with a dense sample of nuclear DNA data, preferably whole genomes. If our interpretation holds true, it would provide the first genetic explanation for the smaller observed size of leopards at the southernmost end of their range in Africa.
Collapse
Affiliation(s)
- Declan R. Morris
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Todd J. McWhorter
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Wayne S. J. Boardman
- School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Gregory Simpson
- Department of Wildlife Studies, Faculty of Veterinary of Science, University of Pretoria, Onderstepoort, Gauteng, South Africa
| | - Jeanette Wentzel
- Department of Wildlife Studies, Faculty of Veterinary of Science, University of Pretoria, Onderstepoort, Gauteng, South Africa
- Department of Veterinary Tropical Diseases, Hans Hoheisen Wildlife Research Station, University of Pretoria, Onderstepoort, Gauteng, South Africa
| | - Jannie Coetzee
- Mpumalanga Tourism and Parks Agency, Nelspruit, Mpumalanga, South Africa
| | - Yoshan Moodley
- Department of Biological Sciences, University of Venda, Thohoyandou, Limpopo, South Africa
| |
Collapse
|
3
|
Rodrigues NT, Saranholi BH, Inforzato AR, Silveira L, Desbiez ALJ, Galetti PM. Reduced gene flow and bottleneck in the threatened giant armadillo (Priodontes maximus): implications for its conservation. Genet Mol Biol 2024; 47:e20230252. [PMID: 38446984 PMCID: PMC10917080 DOI: 10.1590/1678-4685-gmb-2023-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/30/2023] [Indexed: 03/08/2024] Open
Abstract
The progressive fragmentation and loss of habitats represent the main threats for endangered species, causing genetic consequences that may have potential implications for a population's long-term persistence. Large mammals are the most affected species among vertebrates. The giant armadillo Priodontes maximus is a large South American mammal threatened species, showing nocturnal, solitary and fossorial behavior, occurring at low population densities, and its population dynamics are still poorly known. In this study, we carried out the first assessment of genetic variability and population genetic structure of the species, using a panel of 15 polymorphic microsatellites developed by high-throughput genome sequencing. The spatial Bayesian clustering, Fst and Dest results indicated the presence of two genetic clusters (K = 2) in the study area. These results suggest a reduction in gene flow between individuals inhabiting the Brazilian savanna (Cerrado) and the Pantanal wetlands, with the increased human-driven habitat modifications possibly contributing for this scenario. A bottleneck signal was detected in both populations, and a subpopulation structuring in the Cerrado may also be reflecting consequences of the extensive habitat modifications. Findings from this study provide important and useful information for the future maintenance of genetic diversity and long-term conservation of this flagship species.
Collapse
Affiliation(s)
- Nayra T. Rodrigues
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | - Bruno H. Saranholi
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
- Imperial College London, Department of Life Sciences, Ascot, United Kingdom
| | - Alexandre R. Inforzato
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| | | | - Arnaud Leonard Jean Desbiez
- Instituto de Conservação de Animais Silvestres (ICAS), Campo Grande, Mato Grosso do Sul, Brazil
- Royal Zoological Society of Scotland (RZSS), Murrayfield, Edinburgh, United Kingdom
- Instituto de Pesquisas Ecológicas (IPE), Nazaré Paulista, São Paulo, Brazil
| | - Pedro M. Galetti
- Universidade Federal de São Carlos, Departamento de Genética e Evolução, São Carlos, SP, Brazil
| |
Collapse
|
4
|
McManus J, Faraut L, Couldridge V, van Deventer J, Samuels I, Cilliers D, Devens C, Vorster P, Smuts B. Assessment of leopard translocations in South Africa. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.943078] [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
Translocations are commonly employed to mitigate human–carnivore conflict but rarely evaluated, resulting in conflicting reports of success, particularly for leopards (Panthera pardus). We evaluate the status of available leopard translocation data, the factors driving the intentional removal of leopards, and the potential causal factors associated with successful and failed translocation events. We obtained data on 60 leopard translocation events across five provinces in South Africa between 1994 and 2021. We considered a successful translocation outcome when (1) the animal was moved outside of its original home range, (2) the animal established a new home range away from the capture site, (3) no substantive livestock losses were linked to the translocated animal in the post-release monitoring period, and (4) the animal survived at least 6 months post-translocation. If mortality occurred due to factors that were equally likely to impact resident individuals and were unrelated to the translocation event (e.g., poaching), the event was not considered a failed effort. Most translocations were the result of human–carnivore conflict (HCC; 82%, n = 49), stressing the high prevalence of HCC and the importance of advocating preventative conflict mitigation efforts to conserve leopards. The leopards were moved distances from 2.5 to 196.3 km (63.3 ± 51.7km). Forty (67%) translocation events had unknown outcomes, indicating the limited data available on translocation outcomes. This also indicates the disparity in the objectives of translocations by various entities involved with translocations and suggests that monitoring be a prerequisite for future translocations. Twenty events offered reliable outcomes by means of post-event monitoring, with seven (12%) considered successful, with three (5%) as failures, and with four (7%) not moved beyond their original home ranges, while six (8%) ended in unrelated deaths. The failed events were attributed to inter/intra-specific competition, and one animal returned to its original home range after a translocation distance of 68 km. Translocation success was strongly explained by translocation distance. We found that damage-causing leopards were successfully translocated under specific conditions, and longer translocation distances increase success. Translocations are commonly employed but are still poorly monitored. We discuss basic standardized protocols to improve future leopard translocations (including pre- and post-monitoring) while advocating alternative non-lethal practices to reduce the prevalence of human–carnivore conflict.
Collapse
|
5
|
Saranholi BH, Sanches A, Moreira-Ramírez JF, Carvalho CDS, Galetti M, Galetti Jr PM. Long-term persistence of the large mammal lowland tapir is at risk in the largest Atlantic forest corridor. Perspect Ecol Conserv 2022. [DOI: 10.1016/j.pecon.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
|
6
|
Delineating Functional Corridors Linking Leopard Habitat in the Eastern and Western Cape, South Africa. CONSERVATION 2022. [DOI: 10.3390/conservation2010009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Natural landscapes are increasingly fragmented due to human activity. This contributes to isolation and inadequate gene flow among wildlife populations. These threats intensify where populations are already low, and gene flow is compromised. Ensuring habitat connectivity despite transformed landscapes can mitigate these risks. Leopards are associated with high levels of biodiversity and are the last widely occurring, free-roaming apex predator in South Africa. Although highly adaptable, leopard survival is reduced by human-caused mortality and habitat destruction. We aimed to assess the connectivity of leopard habitat in the Eastern Cape and Western Cape, South Africa. We predicted leopard habitat by correlating GPS data from 31 leopards to environmental features that included human-associated and natural landscapes. We used circuit theory to delineate corridors linking known leopard populations. Finally, using camera traps, we tested whether five predicted corridors were used by leopards. Leopard habitat was strongly correlated to moderate slopes and areas of natural land-cover and plantations, highlighting mountainous areas as important habitat with high connectivity probability. While most habitat patches showed some level of connectivity, leopards avoided highly transformed landscapes, potentially isolating some populations. Where corridors are not functional, active conservation measures for species connectivity becomes important.
Collapse
|
7
|
Population density estimate of leopards (Panthera pardus) in north-western Mpumalanga, South Africa, determined using spatially explicit capture–recapture methods. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00179-2] [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]
|
8
|
Singh VK, Singh SK, Joshi BD, Singh A, Kumar H, Chandra K, Sharma LK, Thakur M. Population genetic attributes of common leopard (Panthera pardus fusca) from Uttarkashi, Western Himalayas. Mol Biol Rep 2021; 49:1573-1579. [PMID: 34729672 DOI: 10.1007/s11033-021-06908-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The common leopard (Panthera pardus fusca), which persists in most of its historic range, is experiencing steady population decline due to habitat loss, anthrophonic disturbances, illegal poaching for their body parts, and retaliatory killings in response to the leopard-human conflicts. METHODS AND RESULTS We analysed 143 scats samples and identified 32 unique leopards following a selected panel of seven loci with cumulative PID sibs 5.30E-04. We observed moderate genetic diversity at nuclear (Ho = 0.600 ± 0.06) and mitochondrial markers (Hd = 0.569 ± 0.009; π = 0.001 ± 0.0002) and found sub-structuring in the leopard population at Uttarkashi, Western Himalayas. CONCLUSIONS The present study exhibits the utility of non-invasive genetics in monitoring the leopard population and paves the path to investigate population genetic parameters in further studies.
Collapse
Affiliation(s)
- Vinaya Kumar Singh
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India
| | - Sujeet Kumar Singh
- Amity Institute of Forestry and Wildlife, Amity University, Sector-125, Noida, 201 303, India
| | - Bheem Dutt Joshi
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India
| | - Abhishek Singh
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India
| | - Hemant Kumar
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Calcutta, West Bengal, 700053, India.
| |
Collapse
|
9
|
McManus J, Marshal JP, Keith M, Tshabalala T, Smuts B, Treves A. Factors predicting habitat use by leopards in human-altered landscapes. J Mammal 2021. [DOI: 10.1093/jmammal/gyab110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Transformed landscapes caused by human activity leave remnant patches of natural habitat for wildlife. The persistence of species in the face of such transformation depends on individuals’ ability to adapt to novel habitat, and to secure resources and reproductive opportunities despite habitat alterations. The leopard, Panthera pardus, is the last free-roaming top carnivore in South Africa whose high trophic status and wide-ranging movements make them an effective focal species in conservation planning. Using location data from leopards, we investigated key correlates of habitat selection in human-altered landscapes at two spatial scales. We compared sex-related differences and predicted how conspecific home range locations influenced habitat selection. Leopards avoided human-altered landscapes more strongly at the large spatial scale, where both sexes selected core areas near formally protected areas. Conspecific home range locations had a strong positive effect at both spatial scales for males, while for females, conspecifics explained fine-scale habitat selection by selecting areas near neighboring females. Spatial scale, sex-related differences, and conspecific location play roles in habitat selection for solitary felids and have implications for conservation planning and management. Excluding these factors may result in inappropriate species management policies.
Collapse
Affiliation(s)
- Jeannine McManus
- Research Department, Landmark Foundation, P.O. Box 22, Riversdale 6677, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Jason P Marshal
- School of Animals, Plants and Environmental Sciences, Witwatersrand University, Private Bag 3, Johannesburg 2050, South Africa
| | - Mark Keith
- Mammal Research Institute, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Thulani Tshabalala
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X 01, Pietermaritzberg 3201, South Africa
| | - Bool Smuts
- Research Department, Landmark Foundation, P.O. Box 22, Riversdale 6677, South Africa
- Department of Biodiversity and Conservation Biology, University of the Western Cape, Private Bag X17, Bellville 7535, South Africa
| | - Adrian Treves
- Nelson Institute for Environmental Studies, University of Wisconsin, 122 Science Hall, 550 North Park Street, Madison, Wisconsin, USA
| |
Collapse
|
10
|
Barragán-Ruiz CE, Silva-Santos R, Saranholi BH, Desbiez ALJ, Galetti PM. Moderate Genetic Diversity and Demographic Reduction in the Threatened Giant Anteater, Myrmecophaga tridactyla. Front Genet 2021; 12:669350. [PMID: 34276776 PMCID: PMC8280777 DOI: 10.3389/fgene.2021.669350] [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: 02/18/2021] [Accepted: 05/24/2021] [Indexed: 11/15/2022] Open
Abstract
In general, large mammal species with highly specialized feeding behavior and solitary habits are expected to suffer genetic consequences from habitat loss and fragmentation. To test this hypothesis, we analyzed the genetic diversity distribution of the threatened giant anteater inhabiting a human-modified landscape. We used 10 microsatellite loci to assess the genetic diversity and population structure of 107 giant anteaters sampled in the Brazilian Central-Western region. No genetic population structuring was observed in this region suggesting no gene flow restriction within the studied area. On the other hand, the moderate level of genetic diversity (Ho = 0.54), recent bottleneck detected and inbreeding (Fis, 0.13; p ≤ 0.001) signatures suggest potential impacts on the genetic variation of this Xenarthra. Additionally, a previous demographic reduction was suggested. Thus, considering the increased human-promoted impacts across the entire area of distribution of the giant anteater, our results can illustrate the potential effects of these disturbances on the genetic variation, allowing us to request the long-term conservation of this emblematic species.
Collapse
Affiliation(s)
| | - Rosane Silva-Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Bruno H Saranholi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Arnaud L J Desbiez
- Instituto de Conservação de Animais Silvestres, Campo Grande, Brazil.,Royal Zoological Society of Scotland, Edinburgh, United Kingdom.,Instituto de Pesquisas Ecológicas, Nazaré Paulista, Brazil
| | - Pedro Manoel Galetti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| |
Collapse
|
11
|
Anteyi WO, Rasche F. Population genetic structure and marker-trait associations in East and West African Striga hermonthica with varying phenotypic response to Fusarium oxysporum f. sp. strigae isolates Foxy-2 and FK3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:391-402. [PMID: 32654253 DOI: 10.1111/tpj.14930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 06/11/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
To examine the genetic basis for the variable susceptibility of Striga hermonthica from differing zones of sub-Saharan Africa to Fusarium oxysporum f. sp. strigae (Fos) isolates Foxy-2 and FK3, 10 S. hermonthica populations from Eastern and Western Africa were phenotyped for their susceptibility response to Foxy-2 and FK3, and then genotyped with 22 simple sequence repeat (SSR) markers. There is low genetic differentiation between East African and West African S. hermonthica populations (i.e. the proportion of the total genetic variance contained in the subpopulation relative to the total genetic variance, FST = 0.012, P < 0.05), but intermediate genetic differentiation (FST = 0.143, P < 0.01) underlies the S. hermonthica groups that are differentiated by their phenotypic responses to Fos isolates. An expressed sequence tag SSR (EST-SSR) marker Y53 (P < 0.01) and a genomic SSR marker E1009 (P < 0.05) were associated with the S. hermonthica class susceptible to Foxy-2 and FK3 (group A). A divergent S. hermonthica class, consisting of groups with intermediate susceptibility to Foxy-2 (group B) and susceptibility to either FK3 (group C) or Foxy-2 (group D), showed no marker-trait association, instead demonstrated linkage disequilibrium decay. Owing to point substitutions and insertion-deletion mutations, the unique, protein-coding nucleotide sequence at the E1009 locus in group A was partly dissimilar to group B, but was totally distinct from groups C and D. These findings implied that the inconsistent effectiveness of a Fos isolate is better explained by genomic variation in S. hermonthica, rather than by S. hermonthica sampling zones.
Collapse
Affiliation(s)
- Williams Oyifioda Anteyi
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, 70593, Germany
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, 70593, Germany
| |
Collapse
|
12
|
Finnegan SP, Galvez‐Bravo L, Silveira L, Tôrres NM, Jácomo ATA, Alves GB, Dalerum F. Reserve size, dispersal and population viability in wide ranging carnivores: the case of jaguars in Emas National Park, Brazil. Anim Conserv 2020. [DOI: 10.1111/acv.12608] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- S. P. Finnegan
- Department of Environmental and Forest Biology College of Environmental Science and Forestry State University of New York New York NY USA
- School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK
- Jaguar Conservation Fund/Instituto Onça‐Pintada Mineiros Goias Brazil
| | - L. Galvez‐Bravo
- School of Biological and Environmental Sciences Liverpool John Moores University Liverpool UK
| | - L. Silveira
- Jaguar Conservation Fund/Instituto Onça‐Pintada Mineiros Goias Brazil
| | - N. M. Tôrres
- Jaguar Conservation Fund/Instituto Onça‐Pintada Mineiros Goias Brazil
- Federal University of Uberlândia Uberlândia Brazil
| | - A. T. A Jácomo
- Jaguar Conservation Fund/Instituto Onça‐Pintada Mineiros Goias Brazil
| | - G. B. Alves
- Jaguar Conservation Fund/Instituto Onça‐Pintada Mineiros Goias Brazil
- Federal University of Uberlândia Uberlândia Brazil
| | - F. Dalerum
- Mixed Unit of Biodiversity (UMIB) University of Oviedo Oviedo Spain
- Department of Zoology and Entomology Mammal Research Institute University of Pretoria Pretoria South Africa
- Department of Zoology Stockholm University Stockholm Sweden
| |
Collapse
|
13
|
Naude VN, Balme GA, O'Riain J, Hunter LT, Fattebert J, Dickerson T, Bishop JM. Unsustainable anthropogenic mortality disrupts natal dispersal and promotes inbreeding in leopards. Ecol Evol 2020; 10:3605-3619. [PMID: 32313621 PMCID: PMC7160178 DOI: 10.1002/ece3.6089] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 11/07/2022] Open
Abstract
Anthropogenic mortality of wildlife is typically inferred from measures of the absolute decline in population numbers. However, increasing evidence suggests that indirect demographic effects including changes to the age, sex, and social structure of populations, as well as the behavior of survivors, can profoundly impact population health and viability. Specifically, anthropogenic mortality of wildlife (especially when unsustainable) and fragmentation of the spatial distribution of individuals (home-ranges) could disrupt natal dispersal mechanisms, with long-term consequences to genetic structure, by compromising outbreeding behavior and gene flow. We investigate this threat in African leopards (Panthera pardus pardus), a polygynous felid with male-biased natal dispersal. Using a combination of spatial (home-range) and genetic (21 polymorphic microsatellites) data from 142 adult leopards, we contrast the structure of two South African populations with markedly different histories of anthropogenically linked mortality. Home-range overlap, parentage assignment, and spatio-genetic autocorrelation together show that historical exploitation of leopards in a recovering protected area has disrupted and reduced subadult male dispersal, thereby facilitating opportunistic male natal philopatry, with sons establishing territories closer to their mothers and sisters. The resultant kin-clustering in males of this historically exploited population is comparable to that of females in a well-protected reserve and has ultimately led to localized inbreeding. Our findings demonstrate novel evidence directly linking unsustainable anthropogenic mortality to inbreeding through disrupted dispersal in a large, solitary felid and expose the genetic consequences underlying this behavioral change. We therefore emphasize the importance of managing and mitigating the effects of unsustainable exploitation on local populations and increasing habitat fragmentation between contiguous protected areas by promoting in situ recovery and providing corridors of suitable habitat that maintain genetic connectivity.
Collapse
Affiliation(s)
- Vincent N. Naude
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
- PantheraNew YorkNYUSA
| | | | - Justin O'Riain
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| | - Luke T.B. Hunter
- Wildlife Conservation SocietyBronxNYUSA
- Centre for Functional BiodiversitySchool of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
| | - Julien Fattebert
- PantheraNew YorkNYUSA
- Centre for Functional BiodiversitySchool of Life SciencesUniversity of KwaZulu‐NatalDurbanSouth Africa
- Wyoming Cooperative Fish and Wildlife Research UnitDepartment of Zoology and PhysiologyUniversity of WyomingLaramieWYUSA
| | | | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in AfricaUniversity of Cape TownCape TownSouth Africa
| |
Collapse
|
14
|
Bhatt S, Biswas S, Karanth K, Pandav B, Mondol S. Genetic analyses reveal population structure and recent decline in leopards ( Panthera pardus fusca) across the Indian subcontinent. PeerJ 2020; 8:e8482. [PMID: 32117616 PMCID: PMC7006512 DOI: 10.7717/peerj.8482] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/29/2019] [Indexed: 11/21/2022] Open
Abstract
Background Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, Panthera pardus, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. Methods We collected faecal samples from the Terai-Arc landscape of northern India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. Results Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75–90% population decline between ∼120–200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. Conclusions Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.
Collapse
Affiliation(s)
- Supriya Bhatt
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| | - Suvankar Biswas
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| | - Krithi Karanth
- Centre for Wildlife Studies, Bengaluru, India.,Nicholas School of Environment, Duke University, Durham, United States of America
| | - Bivash Pandav
- Endangered Species Management, Wildlife Institute of India, Dehradun, India
| | - Samrat Mondol
- Animal Ecology and Conservation Biology, Wildlife Institute of India, Dehradun, India
| |
Collapse
|
15
|
Dures SG, Carbone C, Savolainen V, Maude G, Gottelli D. Ecology rather than people restrict gene flow in Okavango‐Kalahari lions. Anim Conserv 2020. [DOI: 10.1111/acv.12562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- S. G. Dures
- Institute of Zoology Zoological Society of London London UK
- Department of Life Sciences Imperial College London Ascot UK
| | - C. Carbone
- Institute of Zoology Zoological Society of London London UK
| | - V. Savolainen
- Department of Life Sciences Imperial College London Ascot UK
| | - G. Maude
- Kalahari Research and Conservation Maun Botswana
| | - D. Gottelli
- Institute of Zoology Zoological Society of London London UK
| |
Collapse
|
16
|
Deng JY, van Noort S, Compton SG, Chen Y, Greeff JM. The genetic consequences of habitat specificity for fig trees in southern African fragmented forests. ACTA OECOLOGICA 2020. [DOI: 10.1016/j.actao.2019.103506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
17
|
Estimating leopard density across the highly modified human-dominated landscape of the Western Cape, South Africa. ORYX 2019. [DOI: 10.1017/s0030605318001473] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
AbstractApex predators play a critical role in maintaining the health of ecosystems but are highly susceptible to habitat degradation and loss caused by land-use changes, and to anthropogenic mortality. The leopard Panthera pardus is the last free-roaming large carnivore in the Western Cape province, South Africa. During 2011–2015, we carried out a camera-trap survey across three regions covering c. 30,000 km2 of the Western Cape. Our survey comprised 151 camera sites sampling nearly 14,000 camera-trap nights, resulting in the identification of 71 individuals. We used two spatially explicit capture–recapture methods (R programmes secr and SPACECAP) to provide a comprehensive density analysis capable of incorporating environmental and anthropogenic factors. Leopard density was estimated to be 0.35 and 1.18 leopards/100 km2, using secr and SPACECAP, respectively. Leopard population size was predicted to be 102–345 individuals for our three study regions. With these estimates and the predicted available leopard habitat for the province, we extrapolated that the Western Cape supports an estimated 175–588 individuals. Providing a comprehensive baseline population density estimate is critical to understanding population dynamics across a mixed landscape and helping to determine the most appropriate conservation actions. Spatially explicit capture–recapture methods are unbiased by edge effects and superior to traditional capture–mark–recapture methods when estimating animal densities. We therefore recommend further utilization of robust spatial methods as they continue to be advanced.
Collapse
|
18
|
Eurasian lynx fitness shows little variation across Scandinavian human-dominated landscapes. Sci Rep 2019; 9:8903. [PMID: 31222101 PMCID: PMC6586631 DOI: 10.1038/s41598-019-45569-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/11/2019] [Indexed: 11/08/2022] Open
Abstract
Despite extensive research on the ecology and behavioural adaptations of large carnivores in human-dominated landscapes, information about the fitness consequences of sharing landscapes is still limited. We assessed the variation in three consecutive components of female fitness: the probability of reproduction, litter size and juvenile survival in relation to environmental and human factors in a solitary carnivore, the Eurasian lynx (Lynx lynx), occurring in human-dominated landscapes in Scandinavia. We used demographic data from 57 radio-collared adult females between 1995-2011 (126 radio-years). Overall, the yearly probability of female reproduction was 0.80, mean litter size was 2.34 (range 1-4) and the probability to find a female that reproduced in the spring being accompanied by at least one offspring during the subsequent winter was 0.70. We did not find evidence that food availability was a key factor influencing female fitness. Female lynx may adapt to food availability when establishing their home ranges by adopting an obstinate strategy, ensuring a minimum amount of prey necessary for survival and reproduction even during periods of prey scarcity. In human-dominated landscapes, where sufficient prey are available for lynx, mortality risk may have a larger influence on lynx population dynamics compared to food availability. Our results suggest that lynx population dynamics in human-dominated landscapes may be mainly driven by human impacts on survival.
Collapse
|
19
|
Shaffer AA, Dowler RC, Perkins JC, Ferguson AW, McDonough MM, Ammerman LK. Genetic variation in the eastern spotted skunk (Spilogale putorius) with emphasis on the plains spotted skunk (S. p. interrupta). J Mammal 2018. [DOI: 10.1093/jmammal/gyy098] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
| | - Robert C Dowler
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - J Clint Perkins
- Department of Biology, Angelo State University, San Angelo, TX, USA
| | - Adam W Ferguson
- Gantz Family Collection Center, Field Museum of Natural History, Chicago, IL, USA
| | - Molly M McDonough
- Center for Conservation Genomics, Smithsonian Conservation Biology Institute, National Zoo, Washington, DC, USA
- Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA
| | - Loren K Ammerman
- Department of Biology, Angelo State University, San Angelo, TX, USA
| |
Collapse
|
20
|
Devens C, Tshabalala T, McManus J, Smuts B. Counting the spots: The use of a spatially explicit capture-recapture technique and GPS data to estimate leopard (Panthera pardus) density in the Eastern and Western Cape, South Africa. Afr J Ecol 2018. [DOI: 10.1111/aje.12512] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carolyn Devens
- Centre for Wildlife Management; University of Pretoria; Pretoria South Africa
| | | | - Jeannine McManus
- Research Department; Landmark Foundation; Riversdale South Africa
- Animal Plants and Environmental Sciences; University of the Witwatersrand; Johannesburg South Africa
| | - Bool Smuts
- Research Department; Landmark Foundation; Riversdale South Africa
| |
Collapse
|
21
|
Boeckman KR, Whiteman HH. Predators Lack Complementarity in a Degraded Stream. COPEIA 2017. [DOI: 10.1643/ce-16-574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
22
|
Evidence of Recent Fine-Scale Population Structuring in South American Puma concolor. DIVERSITY 2017. [DOI: 10.3390/d9040044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
23
|
Thapa K, Wikramanayake E, Malla S, Acharya KP, Lamichhane BR, Subedi N, Pokharel CP, Thapa GJ, Dhakal M, Bista A, Borah J, Gupta M, Maurya KK, Gurung GS, Jnawali SR, Pradhan NMB, Bhata SR, Koirala S, Ghose D, Vattakaven J. Tigers in the Terai: Strong evidence for meta-population dynamics contributing to tiger recovery and conservation in the Terai Arc Landscape. PLoS One 2017; 12:e0177548. [PMID: 28591175 PMCID: PMC5462344 DOI: 10.1371/journal.pone.0177548] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 04/28/2017] [Indexed: 11/18/2022] Open
Abstract
The source populations of tigers are mostly confined to protected areas, which are now becoming isolated. A landscape scale conservation strategy should strive to facilitate dispersal and survival of dispersing tigers by managing habitat corridors that enable tigers to traverse the matrix with minimal conflict. We present evidence for tiger dispersal along transboundary protected areas complexes in the Terai Arc Landscape, a priority tiger landscape in Nepal and India, by comparing camera trap data, and through population models applied to the long term camera trap data sets. The former showed that 11 individual tigers used the corridors that connected the transboundary protected areas. The estimated population growth rates using the minimum observed population size in two protected areas in Nepal, Bardia National Park and Suklaphanta National Park showed that the increases were higher than expected from growth rates due to in situ reproduction alone. These lines of evidence suggests that tigers are recolonizing Nepal's protected areas from India, after a period of population decline, and that the tiger populations in the transboundary protected areas complexes may be maintained as meta-population. Our results demonstrate the importance of adopting a landscape-scale approach to tiger conservation, especially to improve population recovery and long term population persistence.
Collapse
Affiliation(s)
| | | | | | | | | | - Naresh Subedi
- National Trust for Nature Conservation, Lalitpur, Nepal
| | | | | | - Maheshwar Dhakal
- Department of National Park and Wildlife Conservation, Babarmahal, Kathmandu, Nepal
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Singh SK, Aspi J, Kvist L, Sharma R, Pandey P, Mishra S, Singh R, Agrawal M, Goyal SP. Fine-scale population genetic structure of the Bengal tiger (Panthera tigris tigris) in a human-dominated western Terai Arc Landscape, India. PLoS One 2017; 12:e0174371. [PMID: 28445499 PMCID: PMC5405937 DOI: 10.1371/journal.pone.0174371] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 03/02/2017] [Indexed: 11/23/2022] Open
Abstract
Despite massive global conservation strategies, tiger populations continued to decline until recently, mainly due to habitat loss, human-animal conflicts, and poaching. These factors are known to affect the genetic characteristics of tiger populations and decrease local effective population sizes. The Terai Arc Landscape (TAL) at the foothills of the Himalaya is one of the 42 source sites of tigers around the globe. Therefore, information on how landscape features and anthropogenic factors affect the fine-scale spatial genetic structure and variation of tigers in TAL is needed to develop proper management strategies for achieving long-term conservation goals. We document, for the first time, the genetic characteristics of this tiger population by genotyping 71 tiger samples using 13 microsatellite markers from the western region of TAL (WTAL) of 1800 km2. Specifically, we aimed to estimate the genetic variability, population structure, and gene flow. The microsatellite markers indicated that the levels of allelic diversity (MNA = 6.6) and genetic variation (Ho = 0.50, HE = 0.64) were slightly lower than those reported previously in other Bengal tiger populations. We observed moderate gene flow and significant genetic differentiation (FST= 0.060) and identified the presence of cryptic genetic structure using Bayesian and non-Bayesian approaches. There was low and significantly asymmetric migration between the two main subpopulations of the Rajaji Tiger Reserve and the Corbett Tiger Reserve in WTAL. Sibship relationships indicated that the functionality of the corridor between these subpopulations may be retained if the quality of the habitat does not deteriorate. However, we found that gene flow is not adequate in view of changing land use matrices. We discuss the need to maintain connectivity by implementing the measures that have been suggested previously to minimize the level of human disturbance, including relocation of villages and industries, prevention of encroachment, and banning sand and boulder mining in the corridors.
Collapse
Affiliation(s)
- Sujeet Kumar Singh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | - Jouni Aspi
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Laura Kvist
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Reeta Sharma
- Population and Conservation Genetics, Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Puneet Pandey
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | | - Randeep Singh
- Department of Wildlife Sciences, Amity University, Noida, India
| | - Manoj Agrawal
- Wildlife Institute of India, Chandrabani, Dehradun, India
| | | |
Collapse
|
25
|
Matthee CA, Ropiquet A. The importance of correctly identifying the process responsible for spatial genetic structure in Leopard: A response to McManus and Smuts (2016). C R Biol 2016; 339:439-441. [PMID: 27720729 DOI: 10.1016/j.crvi.2016.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/08/2016] [Indexed: 11/16/2022]
Abstract
Microsatellite analyses suggest that spatial genetic structure among six leopard-sampling sites in southern Africa is the result of isolation by distance.
Collapse
Affiliation(s)
- Conrad A Matthee
- Department of Botany and Zoology, Evolutionary Genomics Group, Stellenbosch University, Private Bag X1, Matieland Natural Science Building, 7602 Stellenbosch, Western Cape, South Africa.
| | - Anne Ropiquet
- Department of Natural Sciences, School of Science and Technology, Middlesex University, The Burroughs-Hendon, NW4 4 BT London, United Kingdom
| |
Collapse
|
26
|
Low microsatellites used to investigate leopard genetic structure severely restricts the results by Ropiquet et al. (2015) to infer population structure for managers. C R Biol 2016; 339:378-9. [PMID: 27550729 DOI: 10.1016/j.crvi.2016.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/02/2016] [Indexed: 11/22/2022]
Abstract
Low microsatellites used to investigate leopard genetic structure severely restricts the results by Ropiquet et al. (2015) to infer population structure for managers.
Collapse
|