Harrisson K.A.,Monash University |
Pavlova A.,Monash University |
Goncalves Da Silva A.,Monash University |
Goncalves Da Silva A.,University of Melbourne |
And 8 more authors.
Molecular Ecology | Year: 2016
Genetic diversity is positively linked to the viability and evolutionary potential of species but is often compromised in threatened taxa. Genetic rescue by gene flow from a more diverse or differentiated source population of the same species can be an effective strategy for alleviating inbreeding depression and boosting evolutionary potential. The helmeted honeyeater Lichenostomus melanops cassidix is a critically endangered subspecies of the common yellow-tufted honeyeater. Cassidix has declined to a single wild population of ~130 birds, despite being subject to intensive population management over recent decades. We assessed changes in microsatellite diversity in cassidix over the last four decades and used population viability analysis to explore whether genetic rescue through hybridization with the neighbouring Lichenostomus melanops gippslandicus subspecies constitutes a viable conservation strategy. The contemporary cassidix population is characterized by low genetic diversity and effective population size (Ne < 50), suggesting it is vulnerable to inbreeding depression and will have limited capacity to evolve to changing environments. We find that gene flow from gippslandicus to cassidix has declined substantially relative to pre-1990 levels and argue that natural levels of gene flow between the two subspecies should be restored. Allowing gene flow (~4 migrants per generation) from gippslandicus into cassidix (i.e. genetic rescue), in combination with continued annual release of captive-bred cassidix (i.e. demographic rescue), should lead to positive demographic and genetic outcomes. Although we consider the risk of outbreeding depression to be low, we recommend that genetic rescue be managed within the context of the captive breeding programme, with monitoring of outcomes. © 2016 John Wiley & Sons Ltd.
Hogg C.J.,Zoo and Aquarium Association Australasia |
Ivy J.A.,San Diego Zoo Global |
Srb C.,Healesville Sanctuary |
Hockley J.,Australian Department of Primary Industries and Fisheries |
And 3 more authors.
Conservation Genetics | Year: 2015
An insurance population for the critically endangered Tasmanian devil was established in 2006. Due to successful captive breeding, the population has reached its carrying capacity of 600 devils and retains 99.95 % of founding gene diversity. Although reproduction has been quite successful, possible relatedness among founding individuals, influences of genetic provenance and pairing success on female productivity were evaluated to further refine insurance population management. Ten polymorphic microsatellite markers were used to assess the founders. Although the data were ultimately insufficient for determining specific founder relationships, a STRUCTURE analysis determined founders to be of eastern or western provenance. Western provenance animals had an observed heterozygosity of 0.38; while eastern provenance was 0.41. Allelic frequencies between the two provenances were similar. Although differences in pairing success of eastern and western provenance animals were noted, there was no difference in overall productivity (number of joeys/female). Cross-provenance pairings were not as successful as W–W but had similar productivity, and produced viable offspring. Birth origin (wild-born vs. zoo-born) had no influence on pairing success but wild-born females produce significantly more joeys/female. For zoo-born females, the number of joeys produced per female had a downward trend between respective generations in captivity. Current and future population managers should be aware of potential reductions in productivity across captive generations and adjust breeding recommendations accordingly. The ability to recruit founders from diseased females, along with a better understanding of the influence of genetic provenance and birth origin on productivity, has led to changes in acquisition of future founders for this insurance population. © 2015, Springer Science+Business Media Dordrecht.
Sarker S.,Charles Sturt University |
Patterson E.I.,Charles Sturt University |
Peters A.,Charles Sturt University |
Baker G.B.,University of Tasmania |
And 6 more authors.
PLoS ONE | Year: 2014
Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV) infection in the orange-bellied parrot (Neophema chrysogaster). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and Rep gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap) gene with a high evolutionary rate (3.41×10-3 subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another. © 2014 Sarker et al.
Pacioni C.,Murdoch University |
Eden P.,Healesville Sanctuary |
Reiss A.,Murdoch University |
Knowles G.,Murdoch University |
And 2 more authors.
Ecological Management and Restoration | Year: 2015
Disease is increasingly being recognised as a risk factor in declining wildlife populations around the globe. However, there are limited protocols to assess disease risks in declining wildlife. Using epidemiological principles, we define a step-by-step framework to complete this complex and critical task. As an example, we assessed the potential role of diseases in relation to the decline of the woylie or brush-tailed bettong (Bettongia penicillata ogilbyi) in Western Australia. Between 1999 and 2006, woylie populations declined by 90%. The wildlife disease risk assessment began with a list of all known or suspected diseases to which the woylie, a species of macropod, is susceptible. This list was assessed against the spatial, temporal and demographic characteristics of the decline. Diseases causing widespread and high mortalities or debilitation leading to predation received high scores. Based on this assessment, priority diseases or pathogens for investigation identified were haemoparasites, gastrointestinal helminths, Neospora caninum, Toxoplasmosis (Toxoplasma gondii), Encephalomyocarditis virus, Macropod Orbiviruses (Wallal virus and Warrego virus), Macropod Herpesviruses (Macropodid herpesvirus 1 and 2) and Salmonella spp. © 2015 Ecological Society of Australia and Wiley Publishing Asia Pty Ltd.
Microsatellite loci and the complete mitochondrial DNA sequence characterized through next generation sequencing and de novo genome assembly for the critically endangered orange-bellied parrot, Neophema chrysogaster
Miller A.D.,Cesar |
Miller A.D.,University of Melbourne |
Good R.T.,University of Melbourne |
Coleman R.A.,University of Melbourne |
And 4 more authors.
Molecular Biology Reports | Year: 2013
A suite of polymorphic microsatellite markers and the complete mitochondrial genome sequence was developed by next generation sequencing (NGS) for the critically endangered orange-bellied parrot, Neophema chrysogaster. A total of 14 polymorphic loci were identified and characterized using DNA extractions representing 40 individuals from Melaleuca, Tasmania, sampled in 2002. We observed moderate genetic variation across most loci (mean number of alleles per locus=2.79; mean expected heterozygosity=0.53) with no evidence of individual loci deviating significantly from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, and analyses indicated no evidence of null alleles across loci. De novo and reference-based genome assemblies performed using MIRA were used to assemble the N. chrysogaster mitochondrial genome sequence with mean coverage of 116-fold (range 89 to 142-fold). The mitochondrial genome consists of 18,034 base pairs, and a typical metazoan mitochondrial gene content consisting of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a single large non-coding region (control region). The arrangement of mitochondrial genes is also typical of Avian taxa. The annotation of the mitochondrial genome and the characterization of 14 microsatellite markers provide a valuable resource for future genetic monitoring of wild and captive N. chrysogaster populations. As found previously, NGS provides a rapid, low cost and reliable method for polymorphic nuclear genetic marker development and determining complete mitochondrial genome sequences when only a fraction of a genome is sequenced. © 2012 Springer Science+Business Media Dordrecht.