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Botswana Lion Genetics Project

Simon Dures

  • Botswana is one of only seven countries believed to have a lion population of over 1 000 individuals and, as such, has considerable responsibility in ensuring that it can effectively protect a stable and healthy population of these animals.

    Over the past century, the lion populations of Africa have undergone dramatic contraction in range due to human encroachment, as well as considerable population reduction from hunting, both as a pest and trophy species. This has affected the size of both the overall lion meta-population in Botswana and any individual isolated populations. The consequences of such changes in population structure, amongst other effects, results in modified community composition, smaller population sizes, and decreased population connectivity.

    The isolation of many populations as a result of anthropogenic barriers is highly likely to prevent individual dispersal and gene flow. Under this scenario there is a significant chance that lion populations will lose genetic diversity via increased genetic drift in small, isolated populations, increasing their susceptibility to the effects of stochastic events; in turn this can lead to the increased risk of localised extinction.

    The current global lion population is believed to be around 30 000 individuals and a recent population estimate for the Okavango Delta was estimated at 1 500 individuals. Estimates of the size that a population is required to maintain a viable long term population varies from 500 to 5 000 individuals. This, however, assumes the population is not influenced by overlapping generations, unequal sex ratios, fragmented habitat and other life history and biogeographic traits.

    Therefore the current population size, both locally and internationally, appears to be on the cusp of falling into unsustainable inbreeding, risking the long term sustainability of the population. If there is significant inbreeding and genetic mutation within the local populations already, as is likely, urgent conservation management will be required to sustain this charismatic population long in to the future.
     

    1.To determine current levels of genetic variation using measures of heterozygosity (i.e., gene differences), the effective population size, and the degree of inbreeding in the resident lion population. Genetic biopsy darting followed by laboratory analysis will be used to determine this.
    2.To analyse past genetic differences of the populations residing in the Delta to provide  some indication of past population size, how heterozygosity has changed with time and what goals conservationists should address in limiting the loss of regional genetic variation in  future lion conservation planning. Genetic sampling from historic lion tropies followed by laboratory analysis used. 
    3.To use biogeographic analysis to assess the relationship between genetic variation and current degree of lion population fragmentation, isolation / connectivity and human density through remote sensing and ground truthing of this data.
  •  

    The primary goal of this project is to develop a comprehensive understanding of the past and present genetic structure of the lion population centred in Botswana’s Okavango Delta. From this, hopefully, future genetic trends can be predicted and suitable management plans informed to mitigate any negative possible future scenarios.

    In addition, the project aims to identify possible genetic risks faced by the lion population in northern Botswana; these may have developed through reduced dispersal possibilities due to natural fragmentation, fragmentation through hunting barriers, and lack of dispersal due to reduced game movements across the entire system.

    Objectives
    1. To determine current levels of genetic variation using measures of heterozygosity (i.e., gene differences), the effective population size, and the degree of inbreeding in the resident lion population. Genetic biopsy darting followed by laboratory analysis will be used to determine this.

    2. To analyse past genetic differences of the populations residing in the Delta to provide  some indication of past population size, how heterozygosity has changed with time and what goals conservationists should address in limiting the loss of regional genetic variation in  future lion conservation planning. Genetic sampling from historic lion tropies followed by laboratory analysis used.

    3. To use biogeographic analysis to assess the relationship between genetic variation and current degree of lion population fragmentation, isolation / connectivity and human density through remote sensing and ground truthing of this data.

    Methodology
    Initially 100 to 150 samples from within the Delta will be collected using biopsy darts. Once sampling of this area has been completed the study will be extended to enable comparisons with lion prides in other areas.

    Each individual lion will be darted and photographed. Facial whisker patterns and scarring will be used to identify individual lions to reduce repeat sampling. Where age is not already known, each individual will be placed into a cohort category based upon the ‘pinkness’ of the nose.

    Historical data will be gathered from museum material (e.g. Natural History Museum of Zimbabwe, Bulawayo) and from the collections of hunters. Using hair samples and ancient DNA techniques, these individuals will be analysed at the same microsatellite loci as biopsy samples, providing a historic estimate of genetic diversity.

    To analyse biogeographic influences on heterozygosity we will use remote sensing and survey techniques to develop a series of independent variables that can be considered in describing lion movements and habitat (e.g. vegetation, proximity to water, prey population density, historical hunting activities, connectivity and isolation). A combination of correlation analysis and path analysis will be used to clarify those variables with the strongest influence on current levels of lion genetic differences.

    Initially 60 to 100 samples from within the Delta will be collected using biopsy darts. Once sampling of this area has been completed the study will be extended to enable comparisons with lion prides in other areas.
    Each individual lion will be darted and photographed. Facial whisker patterns and scarring will be used to identify individual lions to reduce repeat sampling. Where age is not already known, each individual will be placed into a cohort category based upon the ‘pinkness’ of the nose.
    Historical data will be gathered from museum material (e.g. Natural History Museum of Zimbabwe, Bulawayo) and from the collections of hunters. Using hair samples and ancient DNA techniques, these individuals will be analysed at the same microsatellite loci as biopsy samples, providing a historic estimate of genetic diversity.
    To analyse biogeographic influences on heterozygosity we will use remote sensing and survey techniques to develop a series of independent variables that can be considered in describing lion movements and habitat (e.g. vegetation, proximity to water, prey population density, historical hunting activities, connectivity and isolation). A combination of correlation analysis and path analysis will be used to clarify those variables with the strongest influence on current levels of lion genetic differences.

     

  • November 2013
    The Trust funded laboratory equipment for the next part of this project. An update of the aims etc. from Simon:

    I have gathered around 200 samples from Northern Botswana and am collaborating with a number of other research teams who are donating samples that will form a total data set of over 500 samples from the Kavango Zambezi Transfontier area (KAZA).

    All individuals sampled are to be genotyped at 20 microsatellite loc. 100-year-old historical data will be gathered from museum material (Natural History Museum, London) and ancient DNA techniques; these individuals will be analysed at the same microsatellite loci as biopsy samples, providing a historic estimate of genetic diversity to compare to the present-day population.

    To analyse biogeographic influences on heterozygosity we will use remote sensing and survey techniques to develop a series of independent variables that could be considered predictive in describing lion movements and habitat (e.g. vegetation, proximity to water, prey population density, historical hunting activities, connectivity and isolation). A combination of correlation analysis and path analysis will be used to elucidate those variables with the strongest influence on current levels of lion heterozygosity.

    February 2013
    In February 2013 Simon Dures and Dr. Erik Verreynne led a team to dart and undertake the first-ever physical examination of a maned female lion. This individual is resident close to Mombo Camp in Moremi Game Reserve within a pride known as the ‘Western Pride’. The pride itself (at the time of the operation) consisted of a single male, five females, two cubs approximately three months old and the maned female. Within the region, three other such animals are known to exist, one other in another pride close to Mombo, and two much further south just outside the reserve. In addition there was another in the same pride who has since died of natural causes. 

    At exactly 14h16 Dr Verreynne darted the subject lion with a cocktail of sedatives and anaesthetics. After approximately three minutes she was on the ground asleep and we began to examine her. 
    Measurements of height, skull diameter, canine tooth length and a number of other measurements were taken. She appears to be slightly taller with a larger skull-diameter compared to other females, but this is by no means diagnostic. Blood for hormone and genetic analysis was collected and an examination of her reproductive physiology was performed confirming that she has full intact female genetalia with no evidence of a pseudopenis or anything that would otherwise suggest being a hermaphrodite. Her labia and clitoris are somewhat enlarged compared to a ‘normal’ female. At this stage and due to the nature of the examination we are unable to determine if she has undescended testicles. With regards to her behaviour, she appears to be showing both male and female behaviour traits, however this may warrant further observation. 
     
    Once export of the various blood, serum and genetic material has been completed and lab results returned, a more accurate diagnosis will be made and circulated. 
     
    Thanks to the Department of Wildlife and National Parks for permission to perform this examination and to Dr. Rick and Barbara Neilson for funding and assisting with the differential diagnostics; also to Wilderness Safaris for logistical support. 

    In February 2013 Simon Dures and Dr. Erik Verreynne led a team to dart and undertake the first-ever physical examination of a maned female lion. This individual is resident close to Mombo Camp in Moremi Game Reserve within a pride known as the ‘Western Pride’. The pride itself (at the time of the operation) consisted of a single male, five females, two cubs approximately three months old and the maned female. Within the region, three other such animals are known to exist, one other in another pride close to Mombo, and two much further south just outside the reserve. In addition there was another in the same pride who has since died of natural causes.

    At exactly 14h16 Dr Verreynne darted the subject lion with a cocktail of sedatives and anaesthetics. After approximately three minutes she was on the ground asleep and we began to examine her.

    Measurements of height, skull diameter, canine tooth length and a number of other measurements were taken. She appears to be slightly taller with a larger skull-diameter compared to other females, but this is by no means diagnostic. Blood for hormone and genetic analysis was collected and an examination of her reproductive physiology was performed confirming that she has full intact female genetalia with no evidence of a pseudopenis or anything that would otherwise suggest being a hermaphrodite. Her labia and clitoris are somewhat enlarged compared to a ‘normal’ female. At this stage and due to the nature of the examination we are unable to determine if she has undescended testicles. With regards to her behaviour, she appears to be showing both male and female behaviour traits, however this may warrant further observation.

    Once export of the various blood, serum and genetic material has been completed and lab results returned, a more accurate diagnosis will be made and circulated.

    Thanks to the Department of Wildlife and National Parks for permission to perform this examination and to Dr. Rick and Barbara Neilson for funding and assisting with the differential diagnostics; also to Wilderness Safaris for logistical support. 

     

    August 2012

    The Wilderness Wildlife Trust has provided funding for the dart gun and the DNA darts as well as accommodation and research facilities at various camps.

    The following work plan has been provided for 2012:

                           Activity

    Feb

    Mar

    Apr

    May

    Jun

    Jul

    Aug

    Sep

    Oct

    Nov

    Dec

    Jan

    Feb

     

     

     

     

     

     

     

     

     

     

     

     

     

     

    Biopsy darting of lion population – Northern Botswana

    X

    X

    X

    X

    X

    X

    X

    X

     

     

    X

    X

    X

    Photographic ID of sample lion population

    X

    X

    X

    X

    X

    X

    X

    X

     

     

    X

    X

    X

    Calling station surveys

    X

    X

    X

    X

    X

    X

    X

    X

     

     

    X

    X

    X

    Analysis of fragmentation using remote sensing

     

     

     

     

     

     

     

     

    X

    X

     

     

     

    Genetic Analysis at Imperial College London

     

     

     

     

     

     

     

     

    X

    X

     

     

     

    Interim Reports

     

     

     

    X

     

     

     

    X

     

     

     

     

    X

    Write up of initial findings and reporting

     

     

     

     

     

     

     

     

     

    X

    X

     

     

    Supplementary sampling

     

     

     

     

     

     

     

     

     

     

    X

    X

    X