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Title:African elephant conservation and population genetics
Author(s):Brandt, Adam
Director of Research:Roca, Alfred L.
Doctoral Committee Chair(s):Roca, Alfred L.
Doctoral Committee Member(s):Fischer, Amy E.; Malhi, Ripan S.; Swanson, Kelly S.
Department / Program:Animal Sciences
Discipline:Animal Sciences
Degree Granting Institution:University of Illinois at Urbana-Champaign
Degree:Ph.D.
Genre:Dissertation
Subject(s):Proboscidea
savanna elephant
forest elephant
fecal DNA
Loxodonta
microsatellites
mitochondrial DNA
single nucleotide polymorphism
Abstract:Despite advances in technology and management practices, countless species of wildlife continue to decline and become threatened with extinction, largely due to human activities such as poaching and habitat destruction. The field of conservation genetics aims to reduce the rate and severity of species decline by better understanding their genetics and making relevant information available to conservation and management entities. African elephants are in decline and the research here aims to answer important questions relevant to conservation efforts. (1) Phylogeographic patterns between nuclear and mitochondrial DNA in African elephants are often incongruent, which has been attributed to sex-biased dispersal and variance in reproductive success. To examine this, we sequenced the mitochondrial genome of two African forest elephants and examined the coalescent dates within the elephantid lineage. Comparing mitochondrial and nuclear coalescence dates, we found the ratio to be much greater than 0.25, which is consistent with the expectation that sex differences in dispersal and in variance of reproductive success would have increased the effective population size of mtDNA relative to nuclear markers in elephantids, thus contributing to the persistence of incongruent mtDNA phylogeographic patterns. (2) Past research on African elephant genetics has focused heavily on the phylogenetic relationship of forest and savanna elephants. Few studies have examined savanna elephant population genetics exclusively; those that have were limited in geographic scope or relied on mitochondrial DNA which has been shown to be a poor indicator of nuclear population structure. In this study we determined the extent of range wide, intra-species genetic variation for the African savanna elephant using multilocus genotype data. Our findings indicated that African savanna elephants have not undergone a population bottleneck within the last 2 to 4 NE generations. Additionally, there was strong support for isolation by distance at the continental scale and there was evidence that localities in north-central Africa are distinct. (3) Many elephant populations in Africa are isolated within fragmented habitat and persist in low numbers. The elephants of Gash-Barka, Eritrea have become completely isolated, lacking any gene flow from other elephant populations. Using DNA isolated from dung, we examined nuclear and mitochondrial markers to better understand genetic variation and affinities to elephants elsewhere on the continent for conservation purposes. Elephants in Eritrea have low genetic diversity and a close affinity to savanna elephants in Eastern Africa. Conservation efforts should aim to protect Eritrean elephants and their habitat in the short run, with restoration of habitat connectivity and genetic diversity as long-term goals. (4) While conservation genetics aims to reduce species decline, research is often limited by the availability of high quality DNA samples like blood or tissue. Obtaining these samples requires direct contact and handling that may be stressful and dangerous for the animals involved. Non-invasively collected samples such as feces have become increasingly preferred, but due to the presence of PCR inhibitors and non-target or fragmented DNA, the quality and quantity of information that can be obtained from these samples is severely limited. Advances in sequencing technology and enrichment techniques may prove useful in overcoming these limitations. We describe methods of capture hybridization to enrich low quality DNA samples, such as dung and ivory, for use with next-generation sequencing technology with African elephants serving as a model.
Issue Date:2015-01-21
URI:http://hdl.handle.net/2142/72995
Rights Information:Copyright 2014 Adam Brandt
Date Available in IDEALS:2015-01-21
Date Deposited:2014-12


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