Martin S Elphinstone

Population structure, timing of divergence and contact between lineages in the endangered Hastings River mouse (Pseudomys oralis)

Karen MC Rowe et al. — Tue, 04 Dec 2012 00:10:05 PST

Management of threatened species requires understanding their genetic structure, particularly when the potential for cryptic lineages exists for species with a broad geographic range. The Hastings River mouse (Pseudomys oralis) is an endangered species found along the eastern coast of Australia. Previous genetic investigation revealed two mitochondrial lineages, separated by an unsampled gap in northern New South Wales. Using new samples from within this gap and from throughout the species’ range, we recovered two evolutionary lineages in agreement with previous studies. Importantly, we identified Washpool National Park as the area of lineage overlap, located at the northern limit of the Macleay–McPherson Overlap Zone. We confirmed limited haplotype sharing between localities, suggesting low levels of gene flow. Historical demography suggested recent population expansion and decline for Lineages I and II, respectively. Our dating estimates placed lineage divergence at 300 000–900 000 years ago, at the lower limit of percentage divergence between other sister species in Pseudomys. While these results support separate management consideration for each lineage, nuclear markers are needed to evaluate whether these lineages represent separate species. In addition, comparative phylogeographic analyses of divergence times among lineages of other species distributed across the Macleay–McPherson Overlap Zone are needed to determine the significance of this biogeographic contact zone for ecological communities in the region generally.

Phylogenetics and revised taxonomy of the Australian freshwater cod genus, Maccullochella (Percichthyidae)

Catherine J. Nock et al. — Tue, 05 Oct 2010 22:02:36 PDT

Determining the phylogenetic and taxonomic relationships among allopatric populations can be difficult, especially when divergence is recent and morphology is conserved. We used mitochondrial sequence data from the control region and three protein-coding genes (1253 bp in total) and genotypes determined at 13 microsatellite loci to examine the evolutionary relationships among Australia’s largest freshwater fish, the Murray cod, Maccullochella peelii peelii, from the inland Murray–Darling Basin, and its allopatric sister taxa from coastal drainages, the eastern freshwater cod, M. ikei, and Mary River cod, M. peelii mariensis. Phylogenetic analyses provided strong support for taxon-specific clades, with a clade containing both of the eastern taxa reciprocally monophyletic to M. peelii peelii, suggesting a more recent common ancestry between M. ikei and M. peelii mariensis than between the M. peelii subspecies. This finding conflicts with the existing taxonomy and suggests that ancestral Maccullochella crossed the Great Dividing Range in the Pleistocene and subsequently diverged in eastern coastal drainages. Evidence from the present study, in combination with previous morphological and allozymatic data, demonstrates that all extant taxa are genetically and morphologically distinct. The taxonomy of Maccullochella is revised, with Mary River cod now recognised as a species, Maccullochella mariensis, a sister species to eastern freshwater cod, M. ikei. As a result of the taxonomic revision, Murray cod is M. peelii.

An inexpensive and high-throughput procedure to extract and purify total genomic DNA for population studies

Martin S. Elphinstone et al. — Tue, 23 Feb 2010 22:00:47 PST

We describe here a procedure for the purification of high molecular weight genomic DNA that combines the economies of ‘do-it-yourself’, single-tube protocols with the sample throughput and DNA quality of microplate-based DNA extraction and purification kits from commercial suppliers. The procedure allows the preparation of genomic DNA of a quality suitable for polymerase chain reaction-based studies of large populations at around one-tenth of the cost of commercially available kits. Furthermore, 96 samples can be purified from crude tissue digests in around 30 min and are produced in microtitre plate format to allow efficient downstream processing of samples.

Detecting mitochondrial genotypes by temperature gradient gel electrophoresis and heteroduplex analysis

Martin S. Elphinstone et al. — Tue, 23 Feb 2010 22:00:46 PST

Conservation implications of distinct genetic structuring in the endangered freshwater fish Nannoperca oxleyana (Percichthyidae)

James T. Knight et al. — Thu, 11 Feb 2010 02:09:40 PST

The maintenance of genetic diversity and gene flow in threatened species is a vital consideration for recovery programs. The endangered Oxleyan pygmy perch Nannoperca oxleyana has a fragmented distribution within coastal freshwater drainages of southern Queensland and northern New South Wales, Australia. In the present study, mitochondrial DNA control region variation was used to assess genetic diversity and structure across the geographical range of this species. Haplotypic diversity was highest in a small NSW subcatchment south of Evans Head (h = 0.594) followed by Marcus Creek in Queensland (h = 0.475). Distinct genetic differentiation was evident among the Queensland localities and the NSW subcatchments, implying restricted gene flow between coastal river systems. One of the nine haplotypes detected was distributed over 83.4% of the species’ range, suggesting historical connectivity among the now fragmented populations. These patterns were concordant with eustatic changes associated with the last glacial maximum. High barrier sand dunes may also act as barriers to gene flow and dispersal between adjacent NSW subcatchments. Conservation efforts should focus on the preservation of genetic diversity by maintaining as many genetically differentiated populations as possible. The relatively diverse populations inhabiting the South Evans Head subcatchment and Marcus Creek require special management consideration.