Microsatellite loci for studies of wild and hatchery Australian Murray cod Maccullochella peelii peelii (Percichthyidae)

Murray cod is a species of conservation concern that is subject both to wild harvest and to aquaculture production. Six polymorphic microsatellite loci have been developed for this species, which will facilitate studies of wild-stock structure, will help the management of hatchery diversity, and will aid genetic improvement programmes. The markers exhibited nonindependence of genotypes between loci and deviations from Hardy–Weinberg expectations, although these most probably reflect practices at the hatchery from which the genotyped individuals were sourced.

Isolation and characterization of microsatellite loci to DNA fingerprint the powerful owl (Ninox Strenua)

An enriched microsatellite library was constructed for the Powerful Owl (Aves; Strigiformes: Ninox strenua) from which 14 polymorphic microsatellite markers were characterized. Forty individuals (32 unrelated and four pairs of siblings) were genotyped to determine the application of these markers for genetic profiling. The mean observed and expected heterozygosity for unrelated individuals was 0.53 and 0.59, respectively. We demonstrate that this suite of markers is sufficient to unequivocally identify individuals and will be beneficial in assessing the population genetics and reproductive ecology of this species.

Polymorphic microsatellite loci in the Australian tree frog, Litoria peronii

Eleven novel polymorphic microsatellite loci developed from a microsatellite enriched genomic library, are presented for the Australian tree frog <i>Litoria peroniii>. We screened 29 individuals from a single population and detected high levels of polymorphism for all 11 loci with the number of alleles/locus ranging from 9 to 24. Values of expected and observed heterozygosities ranged from 0.789–0.955 and 0.207–1.00, respectively. These microsatellite markers should prove useful in determining levels of genetic diversity, measuring gene flow and migration, assigning individuals to their most likely population of origin, and in the assignment of paternity.

Genome - wide association study identifies novel breast cancer susceptibility loci

Breast cancer exhibits familial aggregation, consistent with variation in genetic susceptibility to the disease. Known susceptibility genes account for less than 25% of the familial risk of breast cancer, and the residual genetic variance is likely to be due to variants conferring more moderate risks. To identify further susceptibility alleles, we conducted a two-stage genome-wide association study in 4,398 breast cancer cases and 4,316 controls, followed by a third stage in which 30 single nucleotide polymorphisms (SNPs) were tested for confirmation in 21,860 cases and 22,578 controls from 22 studies. We used 227,876 SNPs that were estimated to correlate with 77% of known common SNPs in Europeans at r² > 0.5. SNPs in five novel independent loci exhibited strong and consistent evidence of association with breast cancer (P < 10^-7). Four of these contain plausible causative genes (FGFR2, TNRC9, MAP3K1 and LSP1). At the second stage, 1,792 SNPs were significant at the P < 0.05 level compared with an estimated 1,343 that would be expected by chance, indicating that many additional common susceptibility alleles may be identifiable by this approach.

COMT Val158Met and 5HTTLPR functional loci interact to predict anxiety across adolescence : results from the Victorian Adolescent Health Cohort Study (1992-2006)

We investigated whether a composite genetic factor, based on the combined actions of catechol-O-methyltransferase (COMT) (Val158Met) and serotonin transporter (5HTTLPR) (Long-Short) functional loci, has a greater capacity to predict persistence of anxiety across adolescence than either locus in isolation. Analyses were performed on DNA collected from 962 young Australians participating in an eight-wave longitudinal study of mental health and well-being (Victorian Adolescent Health Cohort Study). When the effects of each locus were examined separately, small dose–response reductions in the odds of reporting persisting generalized (free-floating) anxiety across adolescence were observed for the COMT Met158 [odds ratio (OR) = 0.85, 95% confidence interval (CI) = 0.76–0.95, P = 0.004] and 5HTTLPR Short alleles (OR = 0.88, CI = 0.79–0.99, P = 0.033). There was no evidence for a dose–response interaction effect between loci. However, there was a double-recessive interaction effect in which the odds of reporting persisting generalized anxiety were more than twofold reduced (OR = 0.45, CI = 0.29–0.70, P < 0.001) among carriers homozygous for both the COMT Met158 and the 5HTTLPR Short alleles (Met158Met + Short-Short) compared with the remaining cohort. The double-recessive effect remained after multivariate adjustment for a range of psychosocial predictors of anxiety. Exploratory stratified analyses suggested that genetic protection may be more pronounced under conditions of high stress (insecure attachments and sexual abuse), although strata differences did not reach statistical significance. By describing the interaction between genetic loci, it may be possible to describe composite genetic factors that have a more substantial impact on psychosocial development than individual loci alone, and in doing so, enhance understanding of the contribution of constitutional processes in mental health outcomes.

Challenges in conserving indigenous culture in Minahasa : culture, Genius Loci and the Indonesian Environmental Planning system

Culture and spirit of land is integral to Indigenous community meaning and identity. With colonisation, transmigration and assimilation policies and practices over the last 200 years, many Indigenous communities, like the Minahasa, have witnessed their culture, curatorial responsibilities, and their mythological associations to their lands eroded. Minahasa, meaning 'becoming one united', encompasses some eight ethnic communities who reside in the Minahasa regencies in the North Sulawesi Province on Sulawesi Island in Indonesia. The region was first colonised by the Portuguese in the 16th century, and then by the Dutch VOC (Verenigde Oostindische Compagnie) in the 17th and 18th centuries bringing a strong Christian Protestant faith to the communities that appropriated many of the cultural symbols and mythological narratives of the Minahasa, and now compromises the largest concentration of Christian faith in the Indonesian archipelago being one of the reasons why there was considerable political requests for the region to formally become a province of The Netherlands in the lead up to Indonesian independence in 1945.

North Sulawesi never developed any large empire like on other islands in the archipelago. In 670, the leaders of the different tribes, who all spoke different languages, met by a stone known as Watu Pinawetengan. There they founded a community of independent states, who would form one unit and stay together and would fight any outside enemies if they were attacked, and the Dutch used this cultural ethos to help unite the linguistically diverse Minahasa confederacy under their colonial regime. Integral to the Minahasa is the Watu Pinawetengan and the series of narratives that enjoin the Minahasan communities to this place and around Lake Tondano. With Indonesian governance considerable angst has been launched by the Minahasa about loss of local autonomy, generic Indonesian policies, and a lack of respect of Indigenous culture and non-mainstream religions within this predominantly Moslem nation. This paper reviews the state of knowledge as to the cultural associations and genius loci meanings of the Minahasa, to their landscape and place, cast against contemporary Indonesian 10 year plans and policies that seek to generically manage the collective Indonesian archipelago as one community and landscape. It is a critique about the Minahasan Indigenous land use and planning philosophies, against top-down generic land use and environmental policies and plans written in Jakarta for generic application across the Indonesian archipelago.

The development of 20 microsatellite loci for the Australian marine mollusk, Donax deltoides, through next generation DNA sequencing

 Next Generation DNA sequencing was used to develop a suite of microsatellite markers for the marine mollusk, Donax deltoides. A total of 20 polymorphic loci were identified and 12 characterized using 30 individuals from a single population (Venus Bay) in south eastern Australia. We observed moderate to high genetic variation across most loci (mean number of alleles per locus = 7.3; mean heterozygosity = 0.633) with only a single locus (Ddel32) displaying significant deviation from Hardy–Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, however two loci were found to be influenced by null alleles. The 10 viable markers characterized in the present study provide a valuable resource for future population genetic assessments and fisheries management of D. deltoides in Australia.

Isolation and characterisation of polymorphic microsatellite loci for Noisy Miners Manorina melanocephala, with successful cross-amplification in Bell Miners M. melanophrys

We characterized 15 polymorphic microsatellite loci identified from a Noisy Miner (Manorina melanocephala) blood sample using 454 whole genome shotgun sequencing. Levels of polymorphism were assessed using 15 Noisy Miners. The average number of alleles per locus was 5.1. These loci were then cross-amplified to assess their suitability in a single population of Bell Miners (M. melanophrys). Given the landscape level impact that these species are having on the health of vegetation and biodiversity of a range of vertebrates throughout much of south-eastern Australia, these primers will help identify colony dispersal patterns and thus aid in modeling predictions of miner presence and tenure length in threatened ecosystems.

Isolation and characterization of 12 polymorphic tetranucleotide microsatellite loci in the apostlebird (Struthidea cinerea)

The apostlebird (Struthidea cinerea) is an Australian endemic passerine belonging to the Corcoracidae family. The species is highly gregarious throughout the year and the name of the species refers to the apparent prevalence of social groups of around 12 birds. The species is becoming a model system for the study of sociality in vertebrates, which will require the analysis of relatedness, paternity and maternity. We characterize 12 microsatellite loci tested for polymorphism on 25 individuals from a population in western New South Wales, Australia. The number of alleles ranged from 4 to 9 per locus. Expected heterozygosities ranged from 0.69 to 0.88. This microsatellite panel will facilitate future studies that will advance our understanding of dispersal processes, inbreeding avoidance and reproductive skew in social animals.

Characterisation of 22 polymorphic microsatellite loci for the Broadbill Swordfish, Xiphias gladius

The Broadbill Swordfish is harvested by fisheries throughout the world. In order to devise more effective management strategies, we need a clear understanding of the population structure of the species. From a library of 29 tetranucleotide repeats, 22 microsatellite markers were characterised for 94 swordfish samples captured from eastern and western Australia. The number of alleles ranged from 2 to 26 and observed heterozygosity from 0.066 to 0.923. We have identified 18 microsatellites that will be valuable in the examination of swordfish population structure.

Development and characterisation of 20 microsatellite loci isolated from the large bent-wing bat, Miniopterus schreibersii (Chiroptera: Miniopteridae) and their cross-taxa utility in the family Miniopteridae

The large bent-wing bat, Miniopterus schreibersii (Kuhl 1819), has a long history of taxonomic uncertainty and many populations are known to be in a state of decline. Microsatellite loci were developed for the taxonomic and population genetic assessment of the Australian complex of this species. Of the 33 primer sets designed for this research, seven (21%) were deemed suitably polymorphic for population-level analyses of the Australian taxa, with five (71%) of these loci revealing moderate to high levels of polymorphism (PIC = 0.56 to 0.91). The cross-taxa utility of the M. schreibersii microsatellite markers was assessed in the microbat (Chiroptera) family Miniopteridae. Sub-species and species covering the Miniopteridae’s global distribution (with the exception of the Middle East) were selected, numbering 25 taxa in total. Amplification was successful for 26 loci, of which 20 (77%) were polymorphic. High cross-taxa utility of markers was observed with amplification achieved for all taxa for between four (20%) and 20 (100%) loci, and polymorphism was considered moderate to high (PIC = 0.47–0.91) for 12 (60%) of these loci. The high cross-taxa utility of the microsatellites reported herein reveal versatile and cost-effective molecular markers, contributing an important genetic resource for the research and conservation of Miniopteridae species worldwide.

Characterization of nine polymorphic microsatellite loci in the dyeing poison frog Dendrobates tinctorius (Dendrobatidae), and their cross-species utility in two other dendrobatoid species

While field and laboratory based studies have provided significant insights into the parental care and courtship behaviour of dendrobatoid frogs, a comprehensive assessment of their genetic mating systems and population genetic parameters has been precluded because ofthe lack of highly variable DNA markers. Here we document the development of nine novel polymorphic microsatellite markers for the dyeing poison frog Dendrobates tinct or ius (Dendrobatidae ). We found between three and 16 alleles per locus in 60 individuals (30 males, 30 females) from the field site Saut Parare, French Guiana, with an average observed heterozygosity of 0. 75. None of the loci deviated significantly from Hardy-Weinberg equilibrium or showed linkage disequilibrium. We also report successful cross-species amplification of the nine markers in two other dendrobatoid species (Allobates femora/is and Oophaga pumilio). These markers have the potential to aid in determining the genetic structure of local populations, identifying small-scale phylogenies such as parent-offspring relationships and will allow for cross-species comparisons within dendrobatoid species. Therefore, these markers can be applied to a wide range of scientific fields, such as conservation, behavioural ecology and evolutionary biology.

Variation of yield loci in finite element analysis by considering texture evolution for AA5042 aluminum sheets

 Yield function has various material parameters that describe how materials respond plastically in given conditions. However, a significant number of mechanical tests are required to identify the many material parameters for yield function. In this study, an effective method using crystal plasticity through a virtual experiment is introduced to develop the anisotropic yield function for AA5042. The crystal plasticity approach was used to predict the anisotropic response of the material in order to consider a number of stress or strain modes that would not otherwise be evident through mechanical testing. A rate-independent crystal plasticity model based on a smooth single crystal yield surface, which removes the innate ambiguity problem within the rate-independent model and Taylor model for polycrystalline deformation behavior were employed to predict the material’s response in the balanced biaxial stress, pure shear, and plane strain states to identify the parameters for the anisotropic yield function of AA5042.