School of BioSciences - Research Publications
Permanent URI for this collection
Search Results
1 - 8 of 8
-
ItemUnbiased population heterozygosity estimates from genome-wide sequence data(WILEY, 2021-10)Abstract Heterozygosity is a metric of genetic variability frequently used to inform the management of threatened taxa. Estimating observed and expected heterozygosities from genome‐wide sequence data has become increasingly common, and these estimates are often derived directly from genotypes at single nucleotide polymorphism (SNP) markers. While many SNP markers can provide precise estimates of genetic processes, the results of ‘downstream’ analysis with these markers may depend heavily on ‘upstream’ filtering decisions. Here we explore the downstream consequences of sample size, rare allele filtering, missing data thresholds and known population structure on estimates of observed and expected heterozygosity using two reduced‐representation sequencing datasets, one from the mosquito Aedes aegypti (ddRADseq) and the other from a threatened grasshopper, Keyacris scurra (DArTseq). We show that estimates based on polymorphic markers only (i.e. SNP heterozygosity) are always biased by global sample size (N), with smaller N producing larger estimates. By contrast, results are unbiased by sample size when calculations consider monomorphic as well as polymorphic sequence information (i.e. genome‐wide or autosomal heterozygosity). SNP heterozygosity is also biased when differentiated populations are analysed together while autosomal heterozygosity remains unbiased. We also show that when nucleotide sites with missing genotypes are included, observed and expected heterozygosity estimates diverge in proportion to the amount of missing data permitted at each site. We make three recommendations for estimating genome‐wide heterozygosity: (a) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (b) sites with any missing data should be omitted and (c) populations should be analysed in independent runs. This should facilitate comparisons within and across studies and between observed and expected measures of heterozygosity.
-
ItemConservation genetics as a management tool: The five best-supported paradigms to assist the management of threatened species(NATL ACAD SCIENCES, 2022-01-04)About 50 y ago, Crow and Kimura [An Introduction to Population Genetics Theory (1970)] and Ohta and Kimura [Genet. Res. 22, 201-204 (1973)] laid the foundations of conservation genetics by predicting the relationship between population size and genetic marker diversity. This work sparked an enormous research effort investigating the importance of population dynamics, in particular small population size, for population mean performance, population viability, and evolutionary potential. In light of a recent perspective [J. C. Teixeira, C. D. Huber, Proc. Natl. Acad. Sci. U.S.A. 118, 10 (2021)] that challenges some fundamental assumptions in conservation genetics, it is timely to summarize what the field has achieved, what robust patterns have emerged, and worthwhile future research directions. We consider theory and methodological breakthroughs that have helped management, and we outline some fundamental and applied challenges for conservation genetics.
-
Item
-
Item
-
ItemHeterogeneous genetic invasions of three insecticide resistance mutations in Indo-Pacific populations of Aedes aegypti (L.)(WILEY, 2020-05)Nations throughout the Indo-Pacific region use pyrethroid insecticides to control Aedes aegypti, the mosquito vector of dengue, often without knowledge of pyrethroid resistance status of the pest or origin of resistance. Two mutations (V1016G + F1534C) in the sodium channel gene (Vssc) of Ae. aegypti modify ion channel function and cause target-site resistance to pyrethroid insecticides, with a third mutation (S989P) having a potential additive effect. Of 27 possible genotypes involving these mutations, some allelic combinations are never seen whereas others predominate. Here, five allelic combinations common in Ae. aegypti from the Indo-Pacific region are described and their geographical distributions investigated using genome-wide SNP markers. We tested the hypothesis that resistance allele combinations evolved de novo in populations versus the alternative that dispersal of Ae. aegypti between populations facilitated genetic invasions of allele combinations. We used latent factor mixed-models to detect SNPs throughout the genome that showed structuring in line with resistance allele combinations and compared variation at SNPs within the Vssc gene with genome-wide variation. Mixed-models detected an array of SNPs linked to resistance allele combinations, all located within or in close proximity to the Vssc gene. Variation at SNPs within the Vssc gene was structured by resistance profile, whereas genome-wide SNPs were structured by population. These results demonstrate that alleles near to resistance mutations have been transferred between populations via linked selection. This indicates that genetic invasions have contributed to the widespread occurrence of Vssc allele combinations in Ae. aegypti in the Indo-Pacific region, pointing to undocumented mosquito invasions between countries.
-
ItemGenetic mixing for population management: From genetic rescue to provenancing(WILEY, 2021-03)Animal and plant species around the world are being challenged by the deleterious effects of inbreeding, loss of genetic diversity, and maladaptation due to widespread habitat destruction and rapid climate change. In many cases, interventions will likely be needed to safeguard populations and species and to maintain functioning ecosystems. Strategies aimed at initiating, reinstating, or enhancing patterns of gene flow via the deliberate movement of genotypes around the environment are generating growing interest with broad applications in conservation and environmental management. These diverse strategies go by various names ranging from genetic or evolutionary rescue to provenancing and genetic resurrection. Our aim here is to provide some clarification around terminology and to how these strategies are connected and linked to underlying genetic processes. We draw on case studies from the literature and outline mechanisms that underlie how the various strategies aim to increase species fitness and impact the wider community. We argue that understanding mechanisms leading to species decline and community impact is a key to successful implementation of these strategies. We emphasize the need to consider the nature of source and recipient populations, as well as associated risks and trade-offs for the various strategies. This overview highlights where strategies are likely to have potential at population, species, and ecosystem scales, but also where they should probably not be attempted depending on the overall aims of the intervention. We advocate an approach where short- and long-term strategies are integrated into a decision framework that also considers nongenetic aspects of management.
-
ItemPopulation genomics of two invasive mosquitoes (Aedes aegypti and Aedes albopictus) from the Indo-Pacific(PUBLIC LIBRARY SCIENCE, 2020-07-01)The arbovirus vectors Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are both common throughout the Indo-Pacific region, where 70% of global dengue transmission occurs. For Ae. aegypti all Indo-Pacific populations are invasive, having spread from an initial native range of Africa, while for Ae. albopictus the Indo-Pacific includes invasive populations and those from the native range: putatively, India to Japan to Southeast Asia. This study analyses the population genomics of 480 of these mosquitoes sampled from 27 locations in the Indo-Pacific. We investigated patterns of genome-wide genetic differentiation to compare pathways of invasion and ongoing gene flow in both species, and to compare invasive and native-range populations of Ae. albopictus. We also tested landscape genomic hypotheses that genetic differentiation would increase with geographical distance and be lower between locations with high connectivity to human transportation routes, the primary means of dispersal at these scales. We found that genetic distances were generally higher in Ae. aegypti, with Pacific populations the most highly differentiated. The most differentiated Ae. albopictus populations were in Vanuatu, Indonesia and Sri Lanka, the latter two representing potential native-range populations and potential cryptic subspeciation respectively. Genetic distances in Ae. aegypti increased with geographical distance, while in Ae. albopictus they decreased with higher connectivity to human transportation routes. Contrary to the situation in Ae. aegypti, we found evidence of long-distance Ae. albopictus colonisation events, including colonisation of Mauritius from East Asia and of Fiji from Southeast Asia. These direct genomic comparisons indicate likely differences in dispersal ecology in these species, despite their broadly sympatric distributions and similar use of human transport to disperse. Our findings will assist biosecurity operations to trace the source of invasive material and for biocontrol operations that benefit from matching genetic backgrounds of released and local populations.
-
ItemDistribution of Culicoides biting midges (Diptera: Ceratopogonidae) in southern Australia and insight into the Culicoides victoriae morpho-variants(WILEY, 2021-08)Abstract Certain Culicoides species (biting midges) are important vectors globally of a range of viruses, protozoa and filarial parasites, imposing a significant economic and health burden. In a changing climate, understanding which Culicoides species occur in a region is important for biosecurity risk management. We examined the occurrence of predominant Culicoides species in south‐east Australia and provide insight into five Culicoides victoriae morpho‐variants. Culicoides were surveyed using Centre for Disease Control light traps and Yellow Sticky traps, with identification performed morphologically and molecularly. Two polymerase chain reaction – restriction fragment length polymorphism (PCR‐RFLP) assays based on mitochondrial cytochrome c oxidase subunit I were developed to differentiate morphologically similar C. victoriae, with a subset sequenced for nuclear carbomoylphosphate synthase. The structure of the five C. victoriae morpho‐variants was investigated through phylogenetic trees, haplotype networks and the Barcode Index Number system (BINs) in the Barcode of Life Data (BOLD) database. Twenty‐five different Culicoides species were identified in the sampled region with Culicoides austropalpalis, C. victoriae, C. marksi and C. molestus Gp sp No 2 being the most common. Two PCR‐RFLP assays were developed using either one or three enzymes, with a 90% or 99% success rate, respectively, of being able to differentiate the five C. victoriae morpho‐variants. Mitochondrial and nuclear sequence divergence supported by wing patterning allowed the recognition of multiple potentially new species of C. victoriae and identified species in uncharacterised regions.