Conservation and population genetics of African and Asian rhinoceros

Brandt, Jessica R

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Description

Title

Conservation and population genetics of African and Asian rhinoceros

Author(s)

Brandt, Jessica R

Issue Date

2016-06-13

Director of Research (if dissertation) or Advisor (if thesis)

Roca, Alfred L.

Doctoral Committee Chair(s)

Roca, Alfred L.

Committee Member(s)

• Fischer, Amy E.
• Malhi, Ripan S.
• Kukekova, Anna

Department of Study

Animal Sciences

Discipline

Animal Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

Ph.D.

Degree Level

Dissertation

Keyword(s)

• Conservation ecology
• Rhinoceros
• Population genetics
• Immunogenetics

Abstract

There are five living species of rhinoceros inhabiting Africa and Asia: black rhinoceros (Diceros bicornis), white rhinoceros (Ceratotherium simum), Indian rhinoceros (Rhinoceros unicornis), Javan rhinoceros (Rhinoceros sondaicus) and Sumatran rhinoceros (Dicerorhinus sumatrensis). Anthropogenic activities, such as poaching and habitat disruption, have led to steep declines in the population size of all rhinoceros species, placing them in danger of extinction. The development of genetic markers for assessment of diversity at neutral and adaptive loci can be used to address a number of questions that will aid in the conservation of rhinoceros populations both ex situ and in the wild. In order to evaluate genetic diversity in rhinoceros populations, I investigated three research questions that will contribute substantially to the conservation and management of rhinoceros species. (1) Accurate estimates of population size are often difficult to obtain for rhinoceros species that are elusive or prefer dense habitat. Knowing the precise number of individuals in an area is essential for managers to develop and implement conservation plans that address the issues facing a particular population. To enable the use of molecular methods for censusing of rhinoceros populations 29 novel Sumatran rhinoceros microsatellites and 17 novel black rhinoceros microsatellites were characterized from next generation sequencing data for use with low quality DNA extracted from non-invasively collected fecal samples. A subset of these markers is sufficient for identification of individuals based on PID and PID(sib) values. Through a series of optimization steps I was able to show that these markers can be successfully used to obtain genotypes from fecal samples. These markers are of particularly importance for Sumatran rhinoceros populations since the reported number of individual has been difficult to accurately estimate and drastically overstated. Studies aimed at implementing these markers for estimating census size in wild rhinoceros populations are ongoing. (2) The Sumatran rhinoceros, once widespread across Southeast Asia, now consists of ca. 100 individuals primarily found in three isolated populations on the island of Sumatra. No studies have examined the population genetic structure of Sumatran rhinoceros using techniques beyond mitochondrial restriction mapping analysis. Given the requirement for substantial management of the remaining Sumatran rhino populations in the wild and in ex situ breeding facilities, more information regarding their genetic status needs to be available. I used mitochondrial DNA sequences from modern and archival museum samples to assess genetic diversity and structure. Among all samples, haplotype diversity was high; samples identified as being members of the subspecies D. s. sumatrensis formed a cluster containing ten haplotypes. The number of haplotypes and the haplotype diversity among the museum samples of D. s. sumatrensis were higher than in the modern samples even after rarefaction, suggesting that genetic diversity has been lost as the population has declined. Microsatellite data from the modern samples indicated low diversity and showed the presence of three distinct genetic clusters associated with geographic barriers to gene flow within the modern population. Continual isolation of the extant populations without management intervention will likely result in further loss of genetic diversity. (3) Adaptive loci within the immune system possess crucial information about the ability of a population to resist infectious pathogens. Toll-like receptors (TLR) bind pathogen-specific molecules and initiate both innate and adaptive immune responses, and thus may be of particular relevance to conservation geneticists and management authorities. I sequenced gene regions coding for the extracellular domain of eight TLR loci in eastern black (D. b. michaeli), south-central black (D. b. minor), and southern white (C. s. simum) rhinos from North American zoos and ex situ breeding facilities. Additionally, mitochondrial control region haplotypes were sequenced for all individuals and multi-locus genotypes were obtained for the black rhinos. Overall, diversity was very low at TLR and mitochondrial loci among white rhinos. Black rhinos exhibited higher levels of diversity at the TLR loci than white rhinos. Between subspecies, the south-central black rhino was less diverse than the eastern black rhino at the TLR genes; however, they share some haplotypes at all TLR loci. Mitochondrial haplotypes and microsatellite genotypes support strong differentiation between the two studied subspecies. Unique TLR haplotypes and differentiation at mitochondrial and microsatellite loci between the black rhinoceros subspecies were identified, supporting the continued management of the taxa as two separate conservation units. Limited variation in the TLR genes of the African rhinos, especially the white rhinoceros, suggests that the evolutionary potential of the immune system is limited. Future management efforts and breeding programs for rhinoceros species should seek to preserve immune system diversity.

Graduation Semester

2016-08

Type of Resource

text

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http://hdl.handle.net/2142/92892

Copyright and License Information

Copyright 2016 Jessica Brandt

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