Phylogeography of the Koala, (Phascolarctos cinereus), and Harmonising Data to Inform Conservation

Abstract

The Australian continent exhibits complex biogeographic patterns but studies of the impacts of Pleistocene climatic oscillation on the mesic environments of the Southern Hemisphere are limited. The koala (Phascolarctos cinereus), one of Australia’s most iconic species, was historically widely distributed throughout much of eastern Australia but currently represents a complex conservation challenge. To better understand the challenges to koala genetic health, we assessed the phylogeographic history of the koala. Variation in the maternally inherited mitochondrial DNA (mtDNA) Control Region (CR) was examined in 662 koalas sampled throughout their distribution. In addition, koala CR haplotypes accessioned to Genbank were evaluated and consolidated. A total of 53 unique CR haplotypes have been isolated from koalas to date (including 15 haplotypes novel to this study). The relationships among koala CR haplotypes were indicative of a single Evolutionary Significant Unit and do not support the recognition of subspecies, but were separated into four weakly differentiated lineages which correspond to three geographic clusters: a central lineage, a southern lineage and two northern lineages co-occurring north of Brisbane. The three geographic clusters were separated by known Pleistocene biogeographic barriers: the Brisbane River Valley and Clarence River Valley, although there was evidence of mixing amongst clusters. While there is evidence for historical connectivity, current koala populations exhibit greater structure, suggesting habitat fragmentation may have restricted female-mediated gene flow. Since mtDNA data informs conservation planning, we provide a summary of existing CR haplotypes, standardise nomenclature and make recommendations for future studies to harmonise existing datasets. This holistic approach is critical to ensuring management is effective and small scale local population studies can be integrated into a wider species context.

Differential and defective expression of Koala Retrovirus indicate complexity of host and virus evolution

“…During this time, small refuge populations were established on offshore Victorian islands and these koalas have been subsequently used to restock most of their former southern range. This southern population is genetically distinct from the northern animals 5 . The mainland Mount Lofty Ranges koala population in South Australia originates from koalas from both the Kangaroo Island population 6 as well as koalas from Queensland and New South Wales 5,7 .…”

Validating the use of non-invasively sourced DNA for population genetic studies using pedigree data

“…The probability of identity and probability of identity between siblings were calculated using GenAlEx (Peakall and Smouse, 2012). The similarity between genotypes of pairs of individuals was also considered by examining the number of loci with different genotypes as described by Paetkau (2003).…”

“…Two individuals with identical genotypes at all 12 loci (no mismatches) are referred to as a 0MM pair; a 1MM pair describes a pair of individuals with a single mismatching locus, i.e. a unique genotype at one locus and identical genotypes at all other loci; and a 12MM pair has a unique genotype at every locus (Paetkau, 2003). To count the number of mismatched loci between each pair of individuals in the KCC population, the R package allelematch (Galpern et al, 2012;R Core Team, 2014) was used.…”

“…Examination of pairs of individuals with a small number of mismatched alleles (Paetkau, 2003) can be a very useful method for checking errors in samples collected from wild populations. Within the captive KCC population, no 0MM (same 12-marker genotype), 1MM or 2MM pairs were observed, while a 3MM pair was observed once between a pair of full siblings.…”

“…Consensus genotypes constructed from replicates were, however, not validated. The availability of empirical data permits the presence of errors in consensus genotypes to be examined and allows the likelihood that genotypes from two different individuals are the same or similar to be estimated (Paetkau, 2003).…”