Bayesian Inference for Retrospective Population Genetics Models Using Markov Chain Monte Carlo Methods

Genetics, the science of heredity and variation in living organisms, has a central role in medicine, in breeding crops and livestock, and in studying fundamental topics of biological sciences such as evolution and cell functioning. Currently the field of genetics is under a rapid development because of the recent advances in technologies by which molecular data can be obtained from living organisms. In order that most information from such data can be extracted, the analyses need to be carried out using statistical models that are tailored to take account of the particular genetic processes. In this thesis we formulate and analyze Bayesian models for genetic marker data of contemporary individuals. The major focus is on the modeling of the unobserved recent ancestry of the sampled individuals (say, for tens of generations or so), which is carried out by using explicit probabilistic reconstructions of the pedigree structures accompanied by the gene flows at the marker loci. For such a recent history, the recombination process is the major genetic force that shapes the genomes of the individuals, and it is included in the model by assuming that the recombination fractions between the adjacent markers are known. The posterior distribution of the unobserved history of the individuals is studied conditionally on the observed marker data by using a Markov chain Monte Carlo algorithm (MCMC). The example analyses consider estimation of the population structure, relatedness structure (both at the level of whole genomes as well as at each marker separately), and haplotype configurations. For situations where the pedigree structure is partially known, an algorithm to create an initial state for the MCMC algorithm is given. Furthermore, the thesis includes an extension of the model for the recent genetic history to situations where also a quantitative phenotype has been measured from the contemporary individuals. In that case the goal is to identify positions on the genome that affect the observed phenotypic values. This task is carried out within the Bayesian framework, where the number and the relative effects of the quantitative trait loci are treated as random variables whose posterior distribution is studied conditionally on the observed genetic and phenotypic data. In addition, the thesis contains an extension of a widely-used haplotyping method, the PHASE algorithm, to settings where genetic material from several individuals has been pooled together, and the allele frequencies of each pool are determined in a single genotyping.

Extremely Low Microsatellite Diversity but Distinct Population Structure in a Long-Lived Threatened Species, the Australian Lungfish Neoceratodus forsteri (Dipnoi)

The Australian lungfish is a unique living representative of an ancient dipnoan lineage, listed as ‘vulnerable’ to extinction under Australia’s Environment Protection and Biodiversity Conservation Act 1999. Historical accounts indicate this species occurred naturally in two adjacent river systems in Australia, the Burnett and Mary. Current day populations in other rivers are thought to have arisen by translocation from these source populations. Early genetic work detected very little variation and so had limited power to answer questions relevant for management including how genetic variation is partitioned within and among sub-populations. In this study, we use newly developed microsatellite markers to examine samples from the Burnett and Mary Rivers, as well as from two populations thought to be of translocated origin, Brisbane and North Pine. We test whether there is significant genetic structure among and within river drainages; assign putatively translocated populations to potential source populations; and estimate effective population sizes. Eleven polymorphic microsatellite loci genotyped in 218 individuals gave an average within-population heterozygosity of 0.39 which is low relative to other threatened taxa and for freshwater fishes in general. Based on F_ST values (average over loci = 0.11) and STRUCTURE analyses, we identify three distinct populations in the natural range, one in the Burnett and two distinct populations in the Mary. These analyses also support the hypothesis that the Mary River is the likely source of translocated populations in the Brisbane and North Pine rivers, which agrees with historical published records of a translocation event giving rise to these populations. We were unable to obtain bounded estimates of effective population size, as we have too few genotype combinations, although point estimates were low, ranging from 29 - 129. We recommend that, in order to preserve any local adaptation in the three distinct populations that they be managed separately.

Optimising initial population density, growth time and nitrogen nutrition for assessing resistance of wheat cultivars to root-lesion nematode (Pratylenchus thornei)

Pratylenchus thornei is a major pathogen of wheat in Australia. Two glasshouse experiments with four wheat cultivars that had different final populations (Pf) of P. thornei in the field were used to optimise conditions for assessing resistance. With different initial populations (Pi) ranging up to 5250 P. thornei/kg soil, Pf of P. thornei increased to 16 weeks after sowing, and then decreased at 20 weeks in some cultivar x Pi combinations. The population dynamics of P. thornei up to 16 weeks were best described by a modified exponential equation P f (t) = aP i e kt where P f (t) is the final population density at time t, P i is the initial population density, a is the proportion of P i that initiates population development, and k is the intrinsic rate of increase of the population. The cultivar GS50a had very low k values at Pi of 5250 and 1050 indicating its resistance, Suneca and Potam had high k values indicating susceptibility, whereas intolerant Gatcher had a low value at the higher Pi and a high value at the lower Pi. Nitrate fertiliser increased plant growth and Pf values of susceptible cultivars, but in unplanted soil it decreased Pf. Nematicide (aldicarb 5 mg/kg soil) killed P. thornei more effectively in planted than in unplanted soil and increased plant growth particularly in the presence of N fertiliser. In both experiments, the wheat cultivars Suneca and Potam were more susceptible than the cultivar GS50a reflecting field results. The method chosen to discriminate wheat cultivars was to assess Pf after growth for 16 weeks in soil with Pi ~1050–5250 P. thornei/kg soil and fertilised with 200 mg NO3–N/kg soil.

Integrating pest population models with biophysical crop models to better represent the farming system

Farming systems frameworks such as the Agricultural Production Systems simulator (APSIM) represent fluxes through the soil, plant and atmosphere of the system well, but do not generally consider the biotic constraints that function within the system. We designed a method that allowed population models built in DYMEX to interact with APSIM. The simulator engine component of the DYMEX population-modelling platform was wrapped within an APSIM module allowing it to get and set variable values in other APSIM models running in the simulation. A rust model developed in DYMEX is used to demonstrate how the developing rust population reduces the crop's green leaf area. The success of the linking process is seen in the interaction of the two models and how changes in rust population on the crop's leaves feedback to the APSIM crop modifying the growth and development of the crop's leaf area. This linking of population models to simulate pest populations and biophysical models to simulate crop growth and development increases the complexity of the simulation, but provides a tool to investigate biotic constraints within farming systems and further moves APSIM towards being an agro-ecological framework.

The study of genetic diversity and population structure of the Korean fleshy shrimp, Fenneropenaeus chinensis, using newly developed microsatellite markers

The fleshy shrimp, Fenneropenaeus chinensis, is the family of Penaeidae and one of the most economically important marine culture species in Korea. However, its genetic characteristics have never been studied. In this study, a total of 240 wild F. chinensis individuals were collected from four locations as follows: Narodo (NRD, n = 60), Beopseongpo (BSP, n = 60), Chaesukpo (CSP, n = 60), and Cheonsuman (CSM, n = 60). Genetic variability and the relationships among four wild F. chinensis populations were analyzed using 13 newly developed microsatellite loci. Relatively high levels of genetic variability (mean allelic richness = 16.87; mean heterozygosity = 0.845) were found among localities. Among the 52 population loci, 13 showed significant deviation from the Hardy–Weinberg equilibrium. Neighbor-joining, principal coordinate, and molecular variance analyses revealed the presence of three subpopulations (NRD, CSM, BSP and CSP), which was consistent with clustering based on genetic distance. The mean observed heterozygosity values of the NRD, CSM, BSP, and CSP populations were 0.724, 0.821, 0.814, and 0.785 over all loci, respectively. These genetic variability and differentiation results of the four wild populations can be applied for future genetic improvement using selective breeding and to design suitable management guidelines for Korean F. chinensis culture.

Editorial of "International Journal of Critical Indigenous Studies Volume 1, Number 1, 2008"

We perceive the epistemological boundaries of Critical Indigenous Studies as marked by analyses of contemporary colonising power in its multiple forms in different contexts. This first issue brings together a diverse group of international Indigenous scholars who are politically and intellectually engaged in theorising from their respective standpoints as well as spatial and geographic locations. As such these essays enable dialogue across and within different colonial power contexts addressing epistemological ethical and methodological concerns within the broad field of Indigenous studies. In each essay a connecting theme is the need for intercultural and comparative work and to import Indigenous agency in the writing of history...

Editorial of "International Journal of Critical Indigenous Studies Volume 2, Number 1, 2009"

Over the past two decades neo liberalism has shaped global economic activity. The international reach of the current economic crisis propelled by the subprime mortgage meltdown in the United States has affected Indigenous communities in different ways to those whose investments were depleted by the Wall Street activities of an unregulated corporate and banking sector. Throughout this roller coaster economic ride the low socio-economic position of Indigenous peoples continued in Canada, the United States of America, New Zealand, Hawaii and Australia. The logic, or illogic of capital, failed to extend the boom of the economic upturn to Indigenous peoples, but is poised to extend the repercussions of the current downturn deep into Indigenous lives. The consistency of the Indigenous socio-economic position across these countries, even where treaties exist, indicates that the phenomenon is based on a shared Indigenous reality. In this special edition, the commonality in the way in which Indigenous people are engaged in and positioned by market forces and regulation by their respective nation states is proposed as one of the foundation plates of that Indigenous positioning...

Editorial of "International Journal of Critical Indigenous Studies Volume 2, Number 2, 2009"

This edition of the International Critical Indigenous Studies Journal, our second for 2009 takes alternative understandings as its theme. All four articles in this edition attend to citizenship and Indigenous sovereignty though in different ways...

Editorial of "International Journal of Critical Indigenous Studies Volume 3, Number 1, 2010"

The articles in this edition of the International Journal of Critical Indigenous Studies engage collectively with how different epistemologies and cultural values inform power relations in different locations, situations and contemporary contexts. As a group, these articles demonstrate, over varying facets, how meaning, communicative intent and interpretive effect are constitutive of power relations between Indigenous people and non Indigenous people. Jackie Grey discusses the labour of belonging as played out in a dispute over Indigenous fishing rights in a small New England town of Aquinnah, located on Noepe Island the traditional lands of the Wampanoag in the United States of America. She reveals the ways in which the jurisdiction of non Indigenous belonging operates discursively and materially to preclude Indigenous rights and self determination. Grey's analysis highlights the incommensurability of Indigenous and non Indigenous belonging that are played out in power relations born of colonisation.

Editorial of "International Journal of Critical Indigenous Studies Volume 3, Number 2, 2010"

In this of the International Journal of Critical Indigenous Studies, the articles reveal how competing economies of knowledge, capital and values are operationalised through colonising power within inter-subjective relations. Writing in the Australian context, Greg Blyton demonstrates how tobacco was used by colonists as a means of control and exchange in their relations with Indigenous people. He focuses on the Hunter region of New South Wales, Australia, in the early to mid-nineteenth century to reveal how colonists exchanged tobacco for food, safe passage and Indigenous services. Blyton suggests that these colonial practices enabled tobacco addiction to spread throughout the region, passing from one generation of Indigenous people to another. He asks us to consider the link between the colonial generation of Indigenous tobacco consumption and addiction, and Indigenous mortality rates today whereby twenty percent of deaths are attributed to smoking.

Editorial of "International Journal of Critical Indigenous Studies Volume 4, Number 1, 2011"

This special edition of the International Journal of Critical Indigenous Studies highlights the work of emerging scholars in the field of Indigenous Studies. The five featured authors were all finalists for the prize awarded by the Native American and Indigenous Studies Association (NAISA) to the best post-graduate student paper at the NAISA meeting held in 2010 in Tucson, Arizona. While the breadth of scholarship encompassed by the term ‘Indigenous Studies’ and the global representation of Indigenous peoples at NAISA mean that the topics and approaches vary widely, a common thematic of fraught post-colonial relations can be discerned within all five articles.

Editorial of "International Journal of Critical Indigenous Studies Volume 5, Number 1, 2012"

The first two articles of this edition of the journal testify to the lengthening reach of the discipline of Critical Indigenous Studies that is, remarkably, still in its nascence. Emiel Martens examines the development of Maori filmmaking since the 1980s and takes the opportunity to explore this Indigenous cinema in the context of developments in the New Zealand film industry generally. Shifting from cultural production to renewable energy, Steven M. Hoffman and Thibault Martin remind us that in the effort to satiate the demands for energy, it is often Indigenous peoples who bear adverse consequences. Using a social capital framework, the authors examine the impact of the development of hydroelectric power upon a displaced Aboriginal community and conclude that displacement has resulted in an erosion of cohesive social bonds that once ensured a sustainable way of life.

Editorial of "International Journal of Critical Indigenous Studies, Volume 5, Number 2, 2012"

This edition is marked by a strong Antipodean focus. The first three articles bring a critical Indigenous perspective to areas previously cosseted by Western understandings. Robyn Moore, using critical discourse analysis, takes Australian Prime Minister Julia Gillard’s 2011 ‘Closing the Gap’ speech to task for naturalising Indigenous Australia’s position on the wrong side of the social and economic ‘gap’. She argues that, far from accepting white culpability, Gillard instead polishes cultural deficit understandings of Indigenous disadvantage by framing the social and economic divide in meritocratic terms. In so doing, Moore further argues, Gillard casts a benevolent light upon white Australia.

Editorial of "International Journal of Critical Indigenous Studies, Volume 6, Number 1, 2013"

This edition of the International Journal of Critical Indigenous Studies marks the tenth since the journal’s launch in 2008. During that time, over forty articles and eleven book reviews have been published, which is testament to the continuing upward trajectory of Critical Indigenous Studies. Although there continues to be an increasing range of areas of Indigenous research to which a critical focus is brought to bear, a consistent issue for many of the journal’s contributors has been the delineation and application of Indigenous methods and methodologies in social research. The present edition is no exception, with two articles focussing on Indigenous-centred research. The first, by Krystal Summers, reflexively explores the author’s experiences as an undergraduate student undertaking Indigenous-centred research in Peru. As an Indigenous First Nations woman, Summers was mindful that her research practice was faithful to the ethics and protocols outlined in her original project proposal. Her subsequent ‘journey of critical reflexive understanding and storytelling’ supports the proposition of current literature in Indigenous research methodologies that a properly critical Indigenous ethnography will naturally enjoin with Indigenous epistemologies and methodologies.

Editorial of "International Journal of Critical Indigenous Studies Volume 6, Number 2, 2013"

The International Journal of Critical Indigenous Studies (IJCIS) now complements the recently launched National Indigenous Research and Knowledges Network (NIRAKN) in its efforts to build Indigenous research capacity. In this context the journal provides a platform for the research of Indigenous postgraduates, early- to mid-career researchers, and senior scholars. Indigenous scholars are therefore encouraged to submit their articles to future editions of the IJCIS, an ‘Excellence in Research for Australia’ (ERA) ranked journal.