ORCID Profile
0000-0001-6121-4860
Current Organisations
The University of Canberra
,
University of Sydney
Does something not look right? The information on this page has been harvested from data sources that may not be up to date. We continue to work with information providers to improve coverage and quality. To report an issue, use the Feedback Form.
Publisher: Springer Science and Business Media LLC
Date: 03-11-2022
DOI: 10.1038/S42003-022-04038-9
Abstract: The evolutionarily unique platypus ( Ornithorhynchus anatinus ) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation ( F ST ) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers F ST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, F ST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
Publisher: Modelling and Simulation Society of Australia and New Zealand (MSSANZ), Inc.
Date: 03-12-2017
Publisher: Zenodo
Date: 2022
Publisher: Unpublished
Date: 2009
Publisher: Research Square Platform LLC
Date: 14-04-2022
DOI: 10.21203/RS.3.RS-1406456/V1
Abstract: Populations of the evolutionarily unique platypus ( Ornithorhynchus anatinus ) have experienced major declines and local extinctions from a range of historical and recent interacting threats, including fur trade, land clearing, water resource developments (dams and extractions), invasive species, fire, pollution, and urbanisation. Although spending most of their time in the water, platypuses can move over land. Nevertheless, significant uncertainties remain whether major dams across the platypus’ distribution pose barriers to movement, limiting gene flow and dispersal, which are essential evolutionary and ecological processes. Here we examined disruption of gene flow between platypus groups below and above major dams (wall height 10 m). Platypuses were surveyed above and below five major dams, matched to four adjacent rivers without major dams. Genetic differentiation ( F ST ) across dams was 4- to 20- fold higher than along similar stretches of adjacent undammed rivers F ST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent significant barriers for platypus movements. Furthermore, F ST between populations was significantly correlated with the year in which the dam was built, increasing by 0.011 every generation (7.9 years), reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when populations are fragmented by major dams. Alternatives to large dam construction, such as building of by-pass structures and translocation between upstream and downstream populations, should be considered in water conservation and management planning.
Publisher: Unpublished
Date: 2015
Publisher: Academic Journals
Date: 09-01-2013
DOI: 10.5897/AJB11.4209
Publisher: The Royal Society
Date: 03-2022
DOI: 10.1098/RSOS.210558
Abstract: The Arabian oryx was the first species to be rescued from extinction in the wild by the concerted efforts of captive programmes in zoos and private collections around the world. Reintroduction efforts have used two main sources: the ‘World Herd’, established at the Phoenix Zoo, and private collections in Saudi Arabia. The breeding programme at the Al-Wusta Wildlife Reserve (WWR) in Oman has played a central role in the rescue of the oryx. In iduals from the ‘World Herd’ and the United Arab Emirates have been the main source for the WWR programme. However, no breeding strategies accounting for genetic ersity have been implemented. To address this, we investigated the ersity of the WWR population and historical s les using mitochondrial DNA (mtDNA) and single nucleotide polymorphisms (SNPs). We found in iduals at WWR contain 58% of the total mtDNA ersity observed globally. Inference of ancestry and spatial patterns of SNP variation shows the presence of three ancestral sources and three different groups of in iduals. Similar levels of ersity and low inbreeding were observed between groups. We identified in iduals and groups that could most effectively contribute to maximizing genetic ersity. Our results will be valuable to guide breeding and reintroduction programmes at WWR.
Publisher: Cold Spring Harbor Laboratory
Date: 24-03-2023
DOI: 10.1101/2023.03.22.533737
Abstract: Distance measures are widely used for examining genetic structure in datasets that comprise many in iduals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci. We examine the application of distance measures to SNP data (both genotypes and sequence tag presence-absence) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization. Missing values arise from ascertainment issues in the SNP discovery process (null alleles in the case of SNP genotyping true missing data in the case of sequence tag presence-absence data). Missing values can cause displacement of affected in iduals from their natural groupings and artificial inflation of confidence envelopes, leading to potential misinterpretation. Failure of a distance measure to conform to metric and Euclidean properties is important but only likely to create unacceptable outcomes in extreme cases. Lack of randomness in the selection of in iduals (e.g. inclusion of sibs) and lack of independence of both in iduals and loci (e.g. polymorphic haploblocks), can lead to substantial and otherwise inexplicable distortions of the visual representations and again, potential misinterpretation. Euclidean Distance is the metric of choice in many distance studies. However, other measures may be preferable because of underlying models of ergence, population demographic history, linkage disequilibrium, because it is desirable to down-weight joint absences, or because of other characteristics specific to the data or analyses. Distance measures for SNP genotype data that depend on the arbitrary choice of reference and alternate alleles (e.g. Bray-Curtis distance) should be avoided. Careful consideration should be given to which state is scored zero when applying binary distance measures to fragment presence-absence data (e.g. Jaccard distance). Filtering on missing values then imputing those that remain avoids distortion in visual representations. Presence of closely related in iduals or polymorphic haploblocks in the genomes of target species with limited genomic information occasionally emerge as challenges.
Publisher: Wiley
Date: 24-11-2015
DOI: 10.1111/MEC.12995
Abstract: Ecological restoration of degraded ecosystems has emerged as a critical tool in the fight to reverse and ameliorate the current loss of bio ersity and ecosystem services. Approaches derived from different genetic disciplines are extending the theoretical and applied frameworks on which ecological restoration is based. We performed a search of scientific articles and identified 160 articles that employed a genetic approach within a restoration context to shed light on the links between genetics and restoration. These articles were then classified on whether they examined association between genetics and fitness or the application of genetics in demographic studies, and on the way the studies informed restoration practice. Although genetic research in restoration is rapidly growing, we found that studies could make better use of the extensive toolbox developed by applied fields in genetics. Overall, 41% of reviewed studies used genetic information to evaluate or monitor restoration, and 59% provided genetic information to guide prerestoration decision-making processes. Reviewed studies suggest that restoration practitioners often overlook the importance of including genetic aspects within their restoration goals. Even though there is a genetic basis influencing the provision of ecosystem services, few studies explored this relationship. We provide a view of research gaps, future directions and challenges in the genetics of restoration.
Publisher: Wiley
Date: 16-01-2017
DOI: 10.1111/REC.12493
Publisher: Cold Spring Harbor Laboratory
Date: 04-2022
DOI: 10.1101/2022.03.30.486475
Abstract: Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of lified sequence tags) by providing user-friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR. In this iteration, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy-to-navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
Publisher: Wiley
Date: 11-07-2022
Abstract: Innumerable approaches to analyse genetic data are now available to guide conservation, ecological and agricultural projects. However, streamlined and accessible tools are needed to bring these approaches within the reach of a broader user base. dartR was released in 2018 to lessen the intrinsic complexity of analysing single nucleotide polymorphisms (SNPs) and dominant markers (presence/absence of lified sequence tags) by providing user‐friendly data quality control and marker selection functions. dartR users have grown steadily since its release and provided valuable feedback on their interaction with the package allowing us to enhance dartR capabilities. Here, we present Version 2 of dartR . In this version, we substantially increased the number of available functions from 45 to 144. In addition to improved functionality, we focused on enhancing the user experience by extending plot customisation, function standardisation, increasing user support and function speed. dartR provides functions for various stages in analysing genetic data, from data manipulation to reporting. dartR provides many functions for importing, exporting and linking to other packages, to provide an easy‐to‐navigate conduit between data generation and analysis options already available via other packages. We also implemented simulation functions whose results can be analysed seamlessly with several other dartR functions. As more methods and approaches mature to inform conservation, we envision that accessible platforms to analyse genetic data will play a crucial role in translating science into practice.
No related grants have been discovered for Jose Luis Mijangos Araujo.