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Kyriazis CC, Serieys LE, Bishop JM, Drouilly M, Viljoen S, Wayne RK, Lohmueller KE. The influence of gene flow on population viability in an isolated urban caracal population. Mol Ecol 2024; 33:e17346. [PMID: 38581173 PMCID: PMC11035096 DOI: 10.1111/mec.17346] [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: 07/20/2023] [Revised: 01/23/2024] [Accepted: 03/26/2024] [Indexed: 04/08/2024]
Abstract
Wildlife populations are becoming increasingly fragmented by anthropogenic development. Small and isolated populations often face an elevated risk of extinction, in part due to inbreeding depression. Here, we examine the genomic consequences of urbanization in a caracal (Caracal caracal) population that has become isolated in the Cape Peninsula region of the City of Cape Town, South Africa, and is thought to number ~50 individuals. We document low levels of migration into the population over the past ~75 years, with an estimated rate of 1.3 effective migrants per generation. As a consequence of this isolation and small population size, levels of inbreeding are elevated in the contemporary Cape Peninsula population (mean FROH = 0.20). Inbreeding primarily manifests as long runs of homozygosity >10 Mb, consistent with the effects of isolation due to the rapid recent growth of Cape Town. To explore how reduced migration and elevated inbreeding may impact future population dynamics, we parameterized an eco-evolutionary simulation model. We find that if migration rates do not change in the future, the population is expected to decline, though with a low projected risk of extinction. However, if migration rates decline or anthropogenic mortality rates increase, the potential risk of extinction is greatly elevated. To avert a population decline, we suggest that translocating migrants into the Cape Peninsula to initiate a genetic rescue may be warranted in the near future. Our analysis highlights the utility of genomic datasets coupled with computational simulation models for investigating the influence of gene flow on population viability.
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Affiliation(s)
- Christopher C. Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Laurel E.K. Serieys
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Marine Drouilly
- Panthera, 8 W 40th St, 18th Floor, New York, NY 10018, USA
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
- Centre for Social Science Research, University of Cape Town, Rondebosch, 7701, South Africa
| | - Storme Viljoen
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, 7701, South Africa
| | - Robert K. Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
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Leighton GRM, Froneman PW, Serieys LEK, Bishop JM. Sustained use of marine subsidies promotes niche expansion in a wild felid. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169912. [PMID: 38184259 DOI: 10.1016/j.scitotenv.2024.169912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/08/2024]
Abstract
The use of marine subsidies by terrestrial predators can facilitate substantial transfer of nutrients between marine and terrestrial ecosystems. Marine resource subsidies may have profound effects on predator ecology, influencing population and niche dynamics. Expanding niches of top consumers can impact ecosystem resilience and interspecific interactions, affecting predator-prey dynamics and competition. We investigate the occurrence, importance, and impact of marine resources on trophic ecology and niche dynamics in a highly generalist predator, the caracal (Caracal caracal), on the Cape Peninsula, South Africa. Caracals have flexible diets, feeding across a wide range of terrestrial and aquatic prey. We use carbon and nitrogen stable isotope analysis of fur samples (n = 75) to understand trophic position and niche shifts in coastal and inland foragers, as well as the implications of a diet rich in marine resources. We found significant differences in isotope signatures between these groups, with higher δ13C (P < 0.05) and δ15N values (P < 0.01) in coastal foragers. Isotope mixing models reveal that these elevated signatures were due to non-terrestrial food subsidies, where approximately a third of coastal foraging caracal diet comprised marine prey. The addition of marine prey species to diet increased both the trophic level and isotope niche size of coastal foraging caracals, with potential impacts on prey populations and competition. Our results suggest that marine prey are an important dietary resource for coastal foraging caracals, where seabirds, including two endangered species, are a major component of their diet. However, there are likely risks associated with these resource benefits, as routine consumption of seabirds is linked with higher pollutant burdens, particularly metals. Increased encounters between this terrestrial predator and seabirds may be a result of increased mainland colonies due to changes in habitat availability and the highly opportunistic and generalist foraging behaviour of a native predator.
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Affiliation(s)
- Gabriella R M Leighton
- Department of Zoology and Entomology, Rhodes University, PO Box 94, Grahamstown 6140, South Africa; Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa.
| | - P William Froneman
- Department of Zoology and Entomology, Rhodes University, PO Box 94, Grahamstown 6140, South Africa
| | - Laurel E K Serieys
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa; Panthera, NY, New York, USA; Cape Leopard Trust, Cape Town, South Africa
| | - Jacqueline M Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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Leighton GRM, Froneman W, Serieys LEK, Bishop JM. Trophic downgrading of an adaptable carnivore in an urbanising landscape. Sci Rep 2023; 13:21582. [PMID: 38062237 PMCID: PMC10703923 DOI: 10.1038/s41598-023-48868-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Urbanisation critically alters wildlife habitat and resource distribution, leading to shifts in trophic dynamics. The loss of apex predators in human-transformed landscapes can result in changes in the ecological roles of the remaining mesocarnivores. Decreased top-down control together with increased bottom-up forcing through greater availability of anthropogenic foods can result in a predation paradox. Understanding these changes is important for conserving ecological function and biodiversity in rapidly urbanising systems. Here, we use stable isotope analysis to provide insight into longer term changes in trophic position, niche width and overlap of an elusive, medium-sized urban adapter, the caracal (Caracal caracal) in and around the city of Cape Town, South Africa. Using fur samples (n = 168) from individuals along a gradient of urbanisation we find that overall caracals have a broad isotopic dietary niche that reflects their large variation in resource use. When accounting for underlying environmental differences, the intensity of anthropogenic pressure, measured using the Human Footprint Index (HFI), explained variation in both food subsidy use (δ13C values) and trophic status (δ15N values). The significantly higher δ13C values (P < 0.01) and lower δ15N values (P < 0.001) of caracals in more urbanised areas suggest that predator subsidy consumption occurs via predictable, anthropogenic resource subsidies to synanthropic prey. These prey species are predominantly primary consumers, resulting in shifts in diet composition towards lower trophic levels. Further, caracals using areas with higher HFI had narrower isotope niches than those in less impacted areas, likely due to their hyperfocus on a few lower trophic level prey species. This pattern of niche contraction in urban areas is retained when accounting for caracal demographics, including sex and age. The removal of apex predators in human-transformed landscapes together with reliable resource availability, including abundant prey, may paradoxically limit the ecological influence of the remaining predators, and bring about a degree of predator trophic downgrading. The dampening of top-down control, and thus ecosystem regulation, likely points to widespread disruption of trophic dynamics in rapidly developing areas globally.
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Affiliation(s)
- Gabriella R M Leighton
- SARChI Chair in Marine Ecology, Department of Zoology and Entomology, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa.
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa.
| | - William Froneman
- SARChI Chair in Marine Ecology, Department of Zoology and Entomology, Rhodes University, PO Box 94, Grahamstown, 6140, South Africa
| | - Laurel E K Serieys
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
- Panthera, 8 W 40th St, New York, NY, 10018, USA
- Cape Leopard Trust, Cape Town, South Africa
| | - Jacqueline M Bishop
- Institute for Communities and Wildlife in Africa, Department of Biological Sciences, University of Cape Town, Rondebosch, Cape Town, 7701, South Africa
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Hinde K, Wilkinson A, Tokota S, Amin R, O’Riain MJ, Williams KS. Leopard density and the ecological and anthropogenic factors influencing density in a mixed-use landscape in the Western Cape, South Africa. PLoS One 2023; 18:e0293445. [PMID: 37889916 PMCID: PMC10610481 DOI: 10.1371/journal.pone.0293445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Large carnivores face numerous threats, including habitat loss and fragmentation, direct killing, and prey depletion, leading to significant global range and population declines. Despite such threats, leopards (Panthera pardus) persist outside protected areas throughout most of their range, occupying diverse habitat types and land uses, including peri-urban and rural areas. Understanding of leopard population dynamics in mixed-use landscapes is limited, especially in South Africa, where the majority of leopard research has focused on protected areas. We use spatially explicit capture-recapture models to estimate leopard density across a mixed-use landscape of protected areas, farmland, and urban areas in the Overberg region of the Western Cape, South Africa. Data from 86 paired camera stations provided 221 independent captures of 25 leopards at 50 camera trap stations with a population density estimate of 0.64 leopards per 100 km2 (95% CI: 0.55-0.73). Elevation, terrain ruggedness, and vegetation productivity were important drivers of leopard density in the landscape, being highest on elevated remnants of natural land outside of protected areas. These results are similar to previous research findings in other parts of the Western Cape, where high-lying natural vegetation was shown to serve as both a refuge and a corridor for leopard movement in otherwise transformed landscapes. Given the low leopard density and the prevalence of transformed land intermixed with patches of more suitable leopard habitat, prioritising and preserving connectivity for leopards is vital in this shared landscape. Ecological corridors should be developed in partnership with private landowners through an inclusive and multifaceted conservation strategy which also incorporates monitoring of and rapid mitigation of emerging threats to leopards.
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Affiliation(s)
- Kyle Hinde
- Institute for Communities and Wildlife in Africa (iCWild), University of Cape Town, Cape Town, South Africa
| | | | | | - Rajan Amin
- The Cape Leopard Trust, Cape Town, South Africa
- Conservation Programmes, Zoological Society of London, London, United Kingdom
| | - M. Justin O’Riain
- Institute for Communities and Wildlife in Africa (iCWild), University of Cape Town, Cape Town, South Africa
| | - Kathryn S. Williams
- The Cape Leopard Trust, Cape Town, South Africa
- Department of Anthropology, Durham University, Durham, United Kingdom
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Serieys LE, Bishop JM, Rogan MS, Smith JA, Suraci JP, O’Riain MJ, Wilmers CC. Anthropogenic activities and age class mediate carnivore habitat selection in a human-dominated landscape. iScience 2023; 26:107050. [PMID: 37534145 PMCID: PMC10391726 DOI: 10.1016/j.isci.2023.107050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 04/23/2023] [Accepted: 06/01/2023] [Indexed: 08/04/2023] Open
Abstract
Human activities increasingly challenge wild animal populations by disrupting ecological connectivity and population persistence. Yet, human-modified habitats can provide resources, resulting in selection of disturbed areas by generalist species. To investigate spatial and temporal responses of a generalist carnivore to human disturbance, we investigated habitat selection and diel activity patterns in caracals (Caracal caracal). We GPS-collared 25 adults and subadults in urban and wildland-dominated subregions in Cape Town, South Africa. Selection responses for landscape variables were dependent on subregion, animal age class, and diel period. Contrary to expectations, caracals did not become more nocturnal in urban areas. Caracals increased their selection for proximity to urban areas as the proportion of urban area increased. Differences in habitat selection between urban and wildland caracals suggest that individuals of this generalist species exhibit high behavioral flexibility in response to anthropogenic disturbances that emerge as a function of habitat context.
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Affiliation(s)
- Laurel E.K. Serieys
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town 7701, South Africa
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Panthera, New York, NY 10018, USA
- Cape Leopard Trust, Cape Town 7966, South Africa
| | - Jacqueline M. Bishop
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town 7701, South Africa
| | - Matthew S. Rogan
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town 7701, South Africa
- Natural State, Nanyuki, Kenya
| | - Justine A. Smith
- Department of Wildlife, Fish, and Conservation Biology, University of California, Davis, Davis, CA 95616, USA
| | - Justin P. Suraci
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
- Conservation Science Partners, Inc. Truckee, CA 96161, USA
| | - M. Justin O’Riain
- Institute for Communities and Wildlife in Africa, University of Cape Town, Cape Town 7701, South Africa
| | - Christopher C. Wilmers
- Environmental Studies Department, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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Parker KH, Bishop JM, Serieys LEK, Mateo R, Camarero PR, Leighton GRM. A heavy burden: Metal exposure across the land-ocean continuum in an adaptable carnivore. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 327:121585. [PMID: 37040831 DOI: 10.1016/j.envpol.2023.121585] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Urbanisation and associated anthropogenic activities release large quantities of toxic metals and metalloids into the environment, where they may bioaccumulate and threaten both wildlife and human health. In highly transformed landscapes, terrestrial carnivores may be at increased risk of exposure through biomagnification. We quantified metallic element and metalloid exposure in blood of caracals (Caracal caracal), an adaptable felid inhabiting the rapidly urbanising, coastal metropole of Cape Town, South Africa. Using redundancy analysis and mixed-effect models, we explored the influence of demography, landscape use, and diet on the concentration of 11 metals and metalloids. Although species-specific toxic thresholds are lacking, arsenic (As) and chromium (Cr) were present at potentially sublethal levels in several individuals. Increased use of human-transformed landscapes, particularly urban areas, roads, and vineyards, was significantly associated with increased exposure to aluminium (Al), cobalt (Co) and lead (Pb). Foraging closer to the coast and within aquatic food webs was associated with increased levels of mercury (Hg), selenium (Se) and arsenic, where regular predation on seabirds and waterbirds likely facilitates transfer of metals from aquatic to terrestrial food webs. Further, several elements were linked to lower haemoglobin levels (chromium, mercury, manganese, and zinc) and elevated levels of infection-fighting cells (mercury and selenium). Our results highlight the importance of anthropogenic activities as major environmental sources of metal contamination in terrestrial wildlife, including exposure across the land-ocean continuum. These findings contribute towards the growing evidence suggesting cities are particularly toxic areas for wildlife. Co-exposure to a suite of metal pollutants may threaten the long-term health and persistence of Cape Town's caracal population in unexpected ways, particularly when interacting with additional known pollutant and pathogen exposure. The caracal is a valuable sentinel for assessing metal exposure and can be used in pollution monitoring programmes to mitigate exposure and promote biodiversity conservation in human-dominated landscapes.
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Affiliation(s)
- Kim H Parker
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, South Africa
| | - Jacqueline M Bishop
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, South Africa
| | - Laurel E K Serieys
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, South Africa; Panthera, New York, NY, USA; Cape Leopard Trust, Cape Town, South Africa
| | - Rafael Mateo
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Pablo R Camarero
- Instituto de Investigación en Recursos Cinegéticos (IREC-CSIC, UCLM, JCCM), Ciudad Real, Spain
| | - Gabriella R M Leighton
- Institute for Communities and Wildlife in Africa (iCWild), Department of Biological Sciences, University of Cape Town, South Africa; Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa.
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Seasonal Movement Patterns of Urban Domestic Cats Living on the Edge in an African City. Animals (Basel) 2023; 13:ani13061013. [PMID: 36978554 PMCID: PMC10044403 DOI: 10.3390/ani13061013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/27/2023] [Accepted: 03/03/2023] [Indexed: 03/16/2023] Open
Abstract
Domestic cats (Felis catus) are amongst the most destructive invasive vertebrates globally, depredating billions of native animals annually. The size and seasonal variation of their geographical “footprint” is key to understanding their effects on wildlife, particularly if they live near conservation areas. Here we report the first GPS-tracking studies of free-roaming owned cats in the city of Cape Town, South Africa. A total of 23 cats was tracked (14 cats in summer, 9 in winter) using miniature (22 g) GPS locators in 2010–2011. In summer, all cats living on the urban-edge (UE: n = 7) made extensive use of protected areas, while only one of seven urban (U) cats (>150 m from the edge) did so. In winter two of four UE and two of five U cats entered protected areas. Home ranges (95% kernel density estimates) were significantly larger in summer (3.00 ± 1.23 ha) than winter (0.87 ± 0.25 ha) and cats ventured further from their homes in summer (maximum 849 m) than in winter (max 298 m). The predation risk posed by caracal (Caracal caracal) may limit the time cats spend in protected areas, but our results suggest that cat buffers around conservation areas should be at least ~600 m wide to reduce impacts to native fauna.
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Osugi S, Baek S, Naganuma T, Tochigi K, Allen ML, Koike S. The effect of decreasing human activity from COVID-19 on the foraging of fallen fruit by omnivores. Ecol Evol 2022; 12:e9657. [PMID: 36582777 PMCID: PMC9790803 DOI: 10.1002/ece3.9657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/27/2022] Open
Abstract
In 2020, a lockdown was implemented in many cities around the world to contain the COVID-19 pandemic, resulting in a significant cessation of human activity which have had a variety of impacts on wildlife. But in many cases, due to limited pre-lockdown information, and there are limited studies of how lockdowns have specifically affected behaviors. Foraging behavior is inherently linked to fitness and survival, is particularly affected by changes in temporal activity, and the influence of human disturbance on foraging behavior can be assessed quantitatively based on foraging duration and quantity. The purpose of this study was to determine whether and how the fruit-foraging behaviors of two omnivores, the Japanese badger (Meles anakuma) and the raccoon dog (Nyctereutes procyonoides), were influenced by the decrease of human activity associated with lockdowns. Specifically, by comparing to a previous study in 2019-2020, we attempted to determine (1) whether foraging behavior increases during the daytime? (2) whether the duration of foraging per visit increases? and (3) what factors animals select for in fruiting trees? The results of the initial investigation showed that the foraging behavior of both species in 2019 was almost exclusively restricted to the nighttime. But as opportunities for foraging behavior without human interference increased in 2020 due to the lockdown, both species (but especially raccoon dogs) showed substantial changes in their activity patterns to be more diurnal. The duration of foraging per visit also increased in 2020 for both species, and the selection during foraging for both species shifted from selecting trees that provided greater cover in 2019 to trees with high fruit production in 2020. Our results show how human activity directly affects the foraging behavior of wildlife in an urban landscape.
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Affiliation(s)
- Shigeru Osugi
- United Graduate School of Agricultural ScienceTokyo University of Agriculture and TechnologyFuchu, TokyoJapan
| | - Seungyun Baek
- United Graduate School of Agricultural ScienceTokyo University of Agriculture and TechnologyFuchu, TokyoJapan
| | - Tomoko Naganuma
- Institute of Global Innovation ResearchTokyo University of Agriculture and TechnologyFuchu, TokyoJapan
| | - Kahoko Tochigi
- United Graduate School of Agricultural ScienceTokyo University of Agriculture and TechnologyFuchu, TokyoJapan
| | | | - Shinsuke Koike
- Institute of Global Innovation ResearchTokyo University of Agriculture and TechnologyFuchu, TokyoJapan
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Urban habitat use and home ranges of fishing cats in Colombo, Sri Lanka. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00198-z] [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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