Biology subjects

Schmidt, T. L.

Publications and source records attributed to Schmidt, T. L..

24 records · Page 2Linked to original sources

bioRxiv2020

Unbiased population heterozygosity estimates from genome-wide sequence data

O_LIHeterozygosity 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. C_LIO_LIHere 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). C_LIO_LIWe 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. C_LIO_LIWe make three recommendations for estimating genome-wide heterozygosity: (i) autosomal heterozygosity should be reported instead of (or in addition to) SNP heterozygosity; (ii) sites with any missing data should be omitted; (iii) populations should be analysed in independent runs. This should facilitate comparisons within and across studies and between observed and expected measures of heterozygosity. C_LI

genomics↗

bioRxiv2020

Spatial population genomics of a recent mosquito invasion

Population genomic approaches can characterise dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally-restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG), and 4 incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232-577. Close kin dyads revealed recent movement between islands 31-203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and non-adjacent islands. Private alleles and a coancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

genomics↗

bioRxiv2020

Comparative genomics of two invasive mosquitoes (Aedes aegypti and Aedes albopictus) from the Indo-Pacific

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. Author SummaryThe mosquitoes Ae. aegypti and Ae. albopictus are highly invasive and transmit dengue and other arboviruses. This study investigates the genetics of these mosquitoes in the Indo-Pacific region, where 70% of global dengue transmission occurs and where both species have established widespread invasions by hitch-hiking on human transport vessels. We compared patterns of genetic differentiation to determine the pathways these species have taken while spreading through the Indo-Pacific, and to better understand how they disperse. We sequenced DNA from 480 mosquitoes sampled from 27 locations in the Indo-Pacific, and found many genetic differences between the two species. Populations of Ae. aegypti, which is not native to the region, tended to be genetically different from each other, and populations in the Pacific Ocean were particularly divergent. Aedes albopictus populations were generally more similar to each other, though genetically different populations in Sri Lanka and Indonesia point to these having a different history to other populations. Genetic differences between Ae. aegypti populations were larger when populations were geographically distant, while differences between Ae. albopictus populations were larger when populations likely had limited access to human transportation. These results will help improve strategies for controlling these species and stopping their spread around the world.

genomics↗

bioRxiv2019

Heterogeneous genetic invasions of three insecticide resistance mutations in Indo-Pacific populations of Aedes aegypti (L.)

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 while 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, while 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.

evolutionary biology↗

bioRxiv2017

Genome-Wide SNPs Reveal the Drivers of Gene Flow In An Urban Population of the Asian Tiger Mosquito, Aedes albopictus

Aedes albopictus is a highly invasive disease vector with an expanding worldwide distribution. Genetic assays using low to medium resolution markers have found little evidence of spatial genetic structure even at broad geographic scales, suggesting frequent passive movement along human transportation networks. Here we analysed genetic structure of Ae. albopictus collected from 12 sample sites in Guangzhou, China, using thousands of genome-wide single nucleotide polymorphisms (SNPs). We found evidence for passive gene flow, with distance from shipping terminals being the strongest predictor of genetic distance among mosquitoes. As further evidence of passive dispersal, we found multiple pairs of full-siblings distributed between two sample sites 3.7 km apart. After accounting for geographical variability, we also found evidence for isolation by distance, previously undetectable in Ae. albopictus. These findings demonstrate how large SNP datasets and spatially-explicit hypothesis testing can be used to decipher processes at finer geographic scales than formerly possible. Our approach can be used to help predict new invasion pathways of Ae. albopictus and to refine strategies for vector control that involve the transformation or suppression of mosquito populations.\n\nAuthor SummaryAedes albopictus, the Asian Tiger Mosquito, is a highly invasive disease vector with a growing global distribution. Designing strategies to prevent invasion and to control Ae. albopictus populations in invaded regions requires knowledge of how Ae. albopictus disperses. Studies comparing Ae. albopictus populations have found little evidence of genetic structure even between distant populations, suggesting that dispersal along human transportation networks is common. However, a more specific understanding of dispersal processes has been unavailable due to an absence of studies using high-resolution genetic markers. Here we present a study using high-resolution markers, which investigates genetic structure among 152 Ae. albopictus from Guangzhou, China. We found that human transportation networks, particularly shipping terminals, had an influence on genetic structure. We also found genetic distance was correlated with geographical distance, the first such observation in this species. This study demonstrates how high-resolution markers can be used to investigate ecological processes that may otherwise escape detection. We conclude that strategies for controlling Ae. albopictus will have to consider both passive reinvasion along human transportation networks and active reinvasion from neighbouring regions.

ecology↗

bioRxiv2017

Fine-scale landscape genomics of Aedes aegypti reveals loss of Wolbachia transinfection, dispersal barrier and potential for occasional long distance movement

The endosymbiotic bacterium Wolbachia suppresses the capacity for arboviral transmission in the mosquito Aedes aegypti, and can spread through wild mosquito populations following local introductions. Recent introductions in Cairns, Australia have demonstrated slower than expected spread, that could be due to: i) barriers to Ae. aegypti dispersal; ii) leptokurtically distributed dispersal distances; and iii) intergenerational loss of Wolbachia. We investigated these three potential causes using genome-wide single-nucleotide polymorphisms (SNPs) and an assay for the Wolbachia infection wMel in 161 Ae. aegypti collected from Cairns in 2015. We observed a significant barrier effect of Cairns highways on Ae. aegypti dispersal using distance-based redundancy analysis and patch-based simulation analysis. We detected putative full-siblings in ovitraps 1312m apart, suggesting long-distance female movement likely mediated by human transport. Finally, we found a pair of full-siblings of different infection status, suggesting loss of Wolbachia in the field. While the long-distance movement and Wolbachia loss currently represent single observations, these findings together with the identified dispersal barriers can contribute to the slow spread of Wolbachia through the Ae. aegypti population in Cairns. Our landscape genomics approach can be extended to other host/symbiont systems that are being considered for biocontrol.

ecology↗