Population genetics of the koala (Phascolarctos cinereus)

Ruiz-Rodriguez, Christina

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Description

Title

Population genetics of the koala (Phascolarctos cinereus)

Author(s)

Ruiz-Rodriguez, Christina

Issue Date

2015-01-21

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

Roca, Al

Department of Study

Animal Sciences

Discipline

Animal Sciences

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• Population genetics
• koala
• microsatellites
• mtDNA
• bottleneck
• founder effect
• zoo
• animal sciences
• genetic diversity

Abstract

The koala (Phascolarctos cinereus) is an arboreal marsupial native to Australia. Koalas can be found in eastern Australia in the states of Queensland, New South Wales, Victoria and South Australia. The koala is listed as ‘vulnerable’ in Queensland and New South Wales, while in South Australia the koala’s status is ‘rare’. In the United States, the species is listed as ‘threatened’ under the U.S Endangered Species Act. In the early 1900s, koala fur was a valuable commodity, and the high demand for their pelts resulted in the slaughter of millions of koalas across Australia. In an effort to reintroduce koalas to their former range, Victoria was gradually restocked with animals from French Island, which were descended from a small number of individuals. Because the koalas from French Island descended from a small number of founders this resulted in a widespread translocation of koalas with low genetic diversity. Koalas are currently threatened by loss of habitat and urbanization due to increasing growth of the human population. The goals of this study were: 1) to assess genetic diversity of the koala and 2) to determine the genetic structure of the koala. To achieve these goals, we sequenced 648 base pairs (bp) of the mitochondrial control region and developed 14 microsatellite markers. Queensland koala samples (N = 27) were collected from various United States zoos and are designated here as Queensland (zoo). Samples from wild koalas were collected from different localities in southern Australia, including: (BR) Brisbane Ranges (N = 23), (SR) Stony Rises (N = 24), (FI) French Island (N =1) and (KI) Kangaroo Island (N = 9). Mitochondrial control region haplotype diversity was extremely low in koalas from southern Australia. Koalas from BR, SR, FI and KI carried only haplotype (KCR1), compared to koalas from Queensland (zoo), which carried 8 haplotypes. We compared our 648 bp of koala mtDNA control region with previously published koala haplotypes from Houlden et al., (1999), and found one novel haplotype (KCR10) in our Queensland (zoo) koalas, all other mtDNA sequences matched haplotypes described by Houlden et al., (1999). Genotyping of 14 microsatellite markers showed low allelic diversity in koalas from BR and SR. Allelic diversity in koalas from BR and SR ranged from 2-5 alleles per locus. Three microsatellite markers (Phci21, Phci23 and Phci27) were monomorphic in BR, while two were monomorphic (Phci23 and Phci27) in SR. Allelic diversity for Queensland (zoo) koalas was much higher than for BR and SR koalas, with a range of 3-11 alleles per locus, and an average of 5 private alleles per locus. Observed heterozygosity ranged from a low Ho = 0.39 in koalas from BR to a high of Ho = 0.72 in the Queensland (zoo) koalas. One microsatellite marker (Phci17) deviated from Hardy-Weinberg equilibrium after Bonferroni correction (P < 0.0005). Linkage disequilibrium was detected after Bonferroni correction (P < 0.0005) in one marker Phci15. Modified Garza-Williamson values were low, and ranged from 0.11 to 0.62 in the BR and SR koalas, which suggested past population size reductions and loss of alleles after a bottleneck or founder effect. Population pairwise FST estimates showed significant genetic differentiation between the Queensland (zoo) koalas and the BR (FST = 0.32) and SR koalas (FST = 0.29). A low FST value was estimated between BR and SR koalas (FST = 0.02). Bayesian clustering analysis performed using STRUCTURE suggested the presence of two genetically distinct clusters: 1) Queensland (zoo) cluster, and 2) BR and SR cluster. Ad hoc methods to determine the number of partitions provided support for K = 2 for all models. Multivariate principal coordinate analysis (PCoA) implemented in GenAlEx was used to demonstrate genetic distinctiveness between koala populations. The PCoA determined two major groups based on the patterns found within a distance matrix generated by pairwise individual-by-individual comparisons. The first group was defined by koalas from Brisbane Ranges and Stony Rises, which overlapped on the first principal component. The second group consisted of koalas from Queensland (zoo), which were distinct from the southern koala group. The major patterns found by PCoA mirror the same clustering pattern as the one suggested in the STRUCTURE analysis. The PCoA analysis demonstrated the distinctiveness between Queensland (zoo) koalas and southern koalas. Our results showed that genetic diversity in koalas from southern Australia is low compared to koalas from Queensland (zoo). Limited haplotype and allelic diversity were revealed in koalas from BR, SR, FI and KI. Koalas in southern Australia have experienced severe population decline, which may have caused the loss of alleles from their gene pool. The translocation of koalas into BR and SR did not add any substantial genetic variation to the populations. The findings of this study may have implications for koala management in Australia and zoos in the US.

Graduation Semester

2014-12

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http://hdl.handle.net/2142/73012

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Copyright 2015 Christina T.Ruiz-Rodriguez

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