Measures Of Genetic Diversity Research Articles

Kernel density estimation of allele frequency including undetected alleles.

Whereas undetected species contribute to estimation of species diversity, undetected alleles have not been used to estimated genetic diversity. Although random sampling guarantees unbiased estimation of allele frequency and genetic diversity measures, using undetected alleles may provide biased but more precise estimators useful for conservation. We newly devised kernel density estimation (KDE) for allele frequency including undetected alleles and tested it in estimation of allele frequency and nucleotide diversity using population generated by coalescent simulation as well as well as real population data. Contrary to expectations, nucleotide diversity estimated by KDE had worse bias and accuracy. Allele frequency estimated by KDE was also worse except when the sample size was small. These might be due to finity of population and/or the curse of dimensionality. In conclusion, KDE of allele frequency does not contribute to genetic diversity estimation.

Estimates of heterozygosity from single nucleotide polymorphism markers are context-dependent and oftenwrong.

Genetic diversity is frequently described using heterozygosity, particularly in a conservation context. Often, it is estimated using single nucleotide polymorphisms (SNPs); however, it has been shown that heterozygosity values calculated from SNPs can be biased by both study design and filtering parameters. Though solutions have been proposed to address these issues, our own work has found them to be inadequate in some circumstances. Here, we aimed to improve the reliability and comparability of heterozygosity estimates, specifically by investigating how sample size and missing data thresholds influenced the calculation of autosomal heterozygosity (heterozygosity calculated from across the genome, i.e. fixed and variable sites). We also explored how the standard practice of tri- and tetra-allelic site exclusion could bias heterozygosity estimates and influence eventual conclusions relating to genetic diversity. Across three distinct taxa (a frog, Litoria rubella; a tree, Eucalyptus microcarpa; and a grasshopper, Keyacris scurra), we found heterozygosity estimates to be meaningfully affected by sample size and missing data thresholds, partly due to the exclusion of tri- and tetra-allelic sites. These biases were inconsistent both between species and populations, with more diverse populations tending to have their estimates more severely affected, thus having potential to dramatically alter interpretations of genetic diversity. We propose a modified framework for calculating heterozygosity that reduces bias and improves the utility of heterozygosity as a measure of genetic diversity, whilst also highlighting the need for existing population genetic pipelines to be adjusted such that tri- and tetra-allelic sites be included in calculations.

Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas

Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000–180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer’s gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer’s gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.

Exploring Genetic Diversity of Maize (<em>Zea mays</em> L.) Accessions in Sri Lanka by Employing SSR Markers on Photosynthetic, Canopy Architectural and Grain Yield Traits

Purpose: The favorable alleles identified in maize landraces are treasurable resources to enhance the genetic base of crop breeding efforts. Therefore, our pioneering research aimed to explore SSR markers related to maize canopy architectural, photosynthetic and yield traits and hence to study the genetic diversity of 19 local maize accessions compared with high-performing maize cultivar Bhadra, as standard variety. Research Method: Genomic DNA extraction was done from young leaves of maize seedlings using standard protocols. The SSR markers employed were phi065, phi116, umc1065, umc1066, umc1222, umc1231, umc1545, bnlg155, bnlg249 and bnlg1805. Data analysis was performed using GenAlex and DARwin software. Findings: Four of the used markers (umc1066, bnlg1805, phi116, and phi065) had PIC values higher than that of the overall mean (0.692), showing their potential in this genetic diversity study. These markers are mainly associated with leaf area index, plant height, leaf chlorophyll content and quantum efficiency of photosystem II. The highest genetic diversity measures were observed in SEU2, SEU17, SEU18 and SEU23, compared to Bhadra while the lowest were in SEU3. The level of inbreeding was higher in SEU8. Cluster analysis identified three major genetic groups and the landraces collected from various areas did not exhibit any geographical association. Research Limitations: Large number of SSR markers are need to explore biomass and grain yield traits. Original/Value: These results will explore the potential uses of Sri Lankan maize accessions to identify best genetic clusters of germplasm with enhanced plant canopy architectural, photosynthesis and grain yield to be utilized in maize breeding programs.

Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds

In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25–25.25 Mb region of SSC18, 123.25–124 Mb region of SSC15 and 118.75–119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.

Episodic population fragmentation and gene flow reveal a trade-off between heterozygosity and allelic richness.

In episodic environments like deserts, populations of some animal species exhibit irregular fluctuations such that populations are alternately large and connected or small and isolated. Such dynamics are typically driven by periodic resource pulses due, for example, to large but infrequent rainfall events. The repeated population bottlenecks resulting from fragmentation should lower genetic diversity over time, yet species undergoing these fluctuations appear to maintain high levels of genetic diversity. To resolve this apparent paradox, we simulated a metapopulation of constant size undergoing repeat episodes of fragmentation and change in gene flow to mimic outcomes experienced by mammals in an Australian desert. We show that episodic fragmentation and gene flow have contrasting effects on two measures of genetic diversity: heterozygosity and allelic richness. Specifically, fragmentation into many, small subpopulations, coupled with periods of infrequent gene flow, preserves allelic richness at the expense of heterozygosity. In contrast, fragmentation into a few, large subpopulations maintains heterozygosity at the expense of allelic richness. The strength of the trade-off between heterozygosity and allelic richness depends on the amount of gene flow and the frequency of gene flow events. Our results imply that the type of genetic diversity maintained among species living in strongly fluctuating environments will depend on the way populations fragment, with our results highlighting different mechanisms for maintaining allelic richness and heterozygosity in small, fragmented populations.

ShinyCore: An R/Shiny program for establishing core collection based on single nucleotide polymorphism data

BackgroundManaging and investigating all available genetic resources are challenging. As an alternative, breeders and researchers use core collection—a representative subset of the entire collection. A good core is characterized by high genetic diversity and low repetitiveness. Among the several available software, GenoCore uses a coverage criterion that does not require computationally expensive distance-based metrics.ResultsShinyCore is a new method to select a core collection through two phases. The first phase uses the coverage criterion to quickly attain a fixed coverage, and the second phase uses a newly devised score (referred to as the rarity score) to further enhance diversity. It can attain a fixed coverage faster than a currently available algorithm devised for the coverage criterion, so it will benefit users who have big data. ShinyCore attains the minimum coverage specified by a user faster than GenoCore, and it then seeks to add entries with the rarest allele for each marker. Therefore, measures of genetic diversity and distance can be improved.ConclusionAlthough GenoCore is a fast algorithm, its implementation is difficult for those unfamiliar with R, ShinyCore can be easily implemented in Shiny with RStudio and an interactive web applet is available for those who are not familiar with programming languages.

Spatial phenotypic variability is higher between island populations than between mainland populations worldwide

Spatial isolation is a key driver of population‐level variability in traits and genotypes worldwide. Geographical distance between populations typically increases isolation, but organisms face additional environmental barriers when dispersing between suitable habitat patches. Despite the predicted universal nature of the causes of isolation, global comparisons of isolation effects across taxa and geographic systems are few. We assessed the strength of isolation due to geographic and macroclimatic distance for paired marine island and paired mainland populations within the same species. Our meta‐analysis included published measurements of phenotypic traits and neutral genetic diversity from 1608 populations of 108 plant and animal species at a global scale. As expected, phenotypic differentiation was higher between marine islands than between populations on the mainland, but we found no consistent signal for differences in spatial patterns of neutral genetic diversity between the two systems. Geographic distance had comparatively weak effects on the spatial patterns of phenotypes and neutral genetic diversity. These results suggest that spatial patterns of phenotypic variation are determined by eco‐evolutionary pressures that differ more between islands than between mainland populations, while the spatial variability of neutral genetic diversity might be shaped by rather similar processes in the two systems. Our approach demonstrates that global biodiversity models that include island biology studies may progress our understanding of the interacting effects of spatial habitat structure, geographic‐ and environmental distances on biological processes underlying spatial population variability. We formulate future research directions for empirical tests and global syntheses in the field.

Robustness of genetic diversity measures under spatial sampling and a new frequency-independent measure.

The genetic diversity of a taxon has often been estimated by genetic diversity measures. However, they assume random sampling of individuals which is often inapplicable. Except when the distribution of the taxon is limited, researchers conventionally choose several sampling locations from the known distribution and then collect individuals from each location. Spatial sampling is a formalized version of the conventional sampling, which objectively provides geographically even sampling locations to cover genetic variation in a taxon assuming isolation by distance. To evaluate the validity of the spatial sampling in estimating genetic diversity, we conducted coalescent simulation experiments. The sampling locations were selected by spatial sampling and one sample was collected from each location for the sake of theoretical simplicity. We also devised a new measure of genetic diversity, ς, which assumes spatial sampling and is independent of allele frequency. This new measure places an emphasis on rare and phylogenetically distant alleles which have relatively small effect on nucleotide diversity. Therefore, it can complementarily serve for conservation studies although it cannot be used to estimate population mutation rate. We compared ς with the other diversity measures in the experiments. Nucleotide diversity, expected heterozygosity and ς showed within 3% relative biases on average while Watterson's theta was 31% overestimation on average. Thus, genetic diversities other than Watterson's theta held good robustness under the spatial sampling.

Genetic diversity and income inequality: The case for Y-chromosome DNA diversity

This paper examines how patrilineal genetic diversity affects income inequality. We create a new measure of genetic diversity by implementing the notion of Y chromosome diversity. Using a cross section of more than 120 countries and controlling for other geographic and economic variations, we find that countries with higher genetic diversity also have higher income inequality. We show that this measure captures variations in income inequality that is unexplained by previous popular diversity indices and overcomes some of the empirical issues of those measures. Additionally, we find that countries with higher degree of genetic diversity have lower levels of social cooperation and government efficiency, which then leads to a decrease in redistribution and an increase in income inequality.

Genetic diversity of a flightless dung beetle appears unaffected by wildfire

The wildfires of Australia’s Black Summer in 2019/2020 caused a massive loss of wildlife and habitats, but the effects of the fire on invertebrate species post-burn are unknown. We hypothesised that the fires would negatively affect the genetic diversity of invertebrate species by impeding movement between populations due to habitat loss. We studied the genetic diversity of a flightless dung beetle, Amphistomus primonactus Matthews 1974, to determine the impact of the wildfires on this species. We examined 90 SNPs from 193 individuals across seven localities impacted by the wildfires in north-eastern New South Wales. We used STRUCTURE to determine the overall population structure of the seven localities. We calculated four within-locality genetic diversity measures (observed heterozygosity (Ho), unbiased expected heterozygosity (uHe), Shannon’s Information (1H), and the inbreeding coefficient (FIS). We calculated three between-locality genetic diversity measures (Fixation Index (FST), Hedrick’s G”ST, and Shannon’s Mutual Information (I). We used partial Mantel tests to compare the between-locality genetic diversity measures with the mean fire intensity along each pairwise linear transect, while accounting for genetic variation due to geographic distance. We compared the within-locality genetic diversity measures to the mean fire intensity at each site. STRUCTURE showed a large degree of intermixing between localities. We found no significant effect of fire on any within-locality genetic diversity measure, or on any between-locality genetic diversity measure. We suggest that the genetic diversity of A. primonactus was not significantly affected by the Black Summer wildfires.Implications for insect conservation: Our results show that the 2019/2020 wildfires had a negligible impact on the genetic structure of A. primonactus. This offers a promising outlook for the species in its recovery from the fires.

Historical land use patterns provide insight into contemporary insect diversity loss.

Healthy insect populations are vital for maintaining natural ecosystems and essential to global food security. The ongoing dramatic loss of insect species and biomass is thus a global cause for concern, with much focus on this topic in the media. Yet, determining the mechanism behind these declines remains difficult, particularly when attempting to differentiate between anthropogenic drivers of biodiversity loss and long-term natural fluctuations. In a From the Cover manuscript in this issue of Molecular Ecology, Crossley et al. (2022) examined the long-term impact of land use change on freshwater insects by estimating levels of genetic diversity with publicly available data for the cytochrome c oxidase subunit 1 (CO1) mitochondrial locus from >700 aquatic insect species across the United States. Contemporary genetic diversity measures reflect both current and past demography and therefore are related to both past and present habitat change. Crossley et al. found that environments with greater cropland extent over the last 200 years were associated with lower genetic diversity in contemporary aquatic insect populations. This indicates that historical land use is an important factor in contemporary population dynamics. Most critically, in regions of historical cropland cover that have been converted towards other uses (such as urban environments) more recently, aquatic insect populations exhibited higher levels of genetic diversity, indicating a possible rebound in insect populations after cessation of agricultural activity. This study highlights the power of using publicly available data to answer crucial questions regarding the current biospheric emergency.

Genetic footprints of a rapid and large-scale range expansion: the case of cyclic common vole in Spain.

In the Anthropocene, many species are rapidly shifting their ranges in response to human-driven habitat modifications. Studying patterns and genetic signatures of range shifts helps to understand how species cope with environmental disturbances and predict future shifts in the face of global environmental change. We investigated the genetic signature of a contemporary wide-range expansion observed in the Iberian common vole Microtus arvalis asturianus shortly after a colonization event. We used mtDNA and microsatellite data to investigate patterns of genetic diversity, structure, demography, and gene flow across 57 localities covering the historical range of the species and the newly colonized area. The results showed a genetic footprint more compatible with a true range expansion (i.e. the colonization of previously unoccupied areas), than with a model of "colonization from within" (i.e. local expansions from small, unnoticed populations). Genetic diversity measures indicated that the source population was likely located at the NE of the historical range, with a declining gradient of genetic diversity towards the more recently invaded areas. At the expansion front, we observed the greatest gene flow and smallest pairwise differences between nearby localities. Both natural landscape features (rivers) and recent anthropogenic barriers (roads, railways) explained a large proportion of genetic variance among populations and had a significant impact on the colonization pathways used by voles.

Differences in genetic diversity and reproductive performance of a moss, a leafy liverwort, and a thalloid liverwort from forests of contrasting ages

Two competing predictions regarding highly dispersible clonal plants, such as bryophytes, expect levels of genetic diversity to either increase or decrease over time following a disturbance that opens habitat for colonization. Following up on previous research that found higher levels of genetic variation in bryophytes from relatively undisturbed forest sites, we examined unisexual, haploid species of a moss (Plagiomnium ciliare), a leafy liverwort (Porella platyphylloidea), and a thalloid liverwort (Conocephalum conicum sensu lato) from the Mountains, Piedmont, and Coastal Plain of the southeastern United States. In terms of time since last disturbance, sites were ranked Mountains > Piedmont > Coastal Plain. Measures of genetic variation, including percentage of loci polymorphic, mean number of alleles per locus, mean expected heterozygosity, and number of multilocus genotypes, all fit the prediction that genetic diversity should increase over time. We also examined several components of reproductive success expected to influence levels of genetic variation, including colony size, colony mixing, sex expression, phenotypic sex ratio, and sporophyte production (percentage of females producing sporophytes). Most, but not all, of our predictions for populations of varying time since last disturbance were fulfilled, although other ecological differences related to soil, climate, and vegetation are also likely to influence reproductive success.

When Theory Meets Practice: Balancing Genetic Diversity and Behaviour When Choosing Founders for a Recently Reintroduced Bison (Bison bison) Herd in Banff National Park, Canada

The tragic decline of plains bison (Bison bison bison) in North America is well known. By the turn of the 20th century, plains bison, once numbering in the tens of millions, were extirpated from the wild in Canada. Banff National Park, AB, Canada, is within the original range of bison in North America, and still contains suitable habitat for the species. In 2017, we used measures of genetic diversity, as well as age and reproductive status, to select 16 plains bison for reintroduction to an unoccupied corner of their former historic range in Banff National Park. However, five of the preferred founders from this genetically diverse group needed to be substituted for less ideal candidates when aggressive behavior was observed, which could have compromised animal welfare during translocation. The level of genetic diversity in the founding population was therefore lower than if all proposed founders had been used, although the difference was not substantial. As expected, adults in this small, reintroduced herd had lower observed heterozygosity and number of alleles than the larger source herd, but expected heterozygosity was higher, likely a result of preferentially choosing individuals with rare alleles. Another substantial contribution to genetic diversity was in unborn fetuses: sired by males that were not translocated, the calves born a few months later provided a boost to the genetic diversity of this small founder herd. Where opportunities allow, the inclusion of pregnant females can significantly increase the genetic diversity of small founder populations. When compared to other founded herds of bison, the techniques described here have ensured that the newly established Banff NP herd is one of the most diverse bison herds in Canada, despite its relatively small number of founders.

Genetic diversity and principal component analysis in cultivated rice (Oryza sativa) varieties of Assam

Rice (Oryza sativa L.) is the pre-eminent cereal crop of Assam in term of production and cultivable area. The measurement of genetic diversity is crucial to pick up the appropriate genotypes in a crop improvement programme. Identification of traits contributing towards genetic diversity in a given population can help in formulating effective selection criteria. This study was carried out in 64 indigenous rice genotypes collected from North Bank Plains and Upper Brahmaputra valley zones of Assam during rainy (kharif) seasons of 2021 and 2022. Based on the yield attributing characters, the cultivars were categorized into 8 clusters. Cluster evaluation showed that cluster II and V had farthest distance from cluster V (431.18), followed by cluster I and II (377.62). The study on the Principal component analysis showed the traits, days to 50% flowering (DF), days to maturity (DM), filled grains per panicle (FG), biological yield (BY) and harvest index (HI) had maximum contribution towards the total variability. The genotypes from the diverse clusters having desirable per se performance could be selected for inclusion as parents in hybridization programme. Identification of component traits through the principal component analysis will help in formulating efficient selection criteria for further genetic improvement of rice.

Does genetic diversity on corporate boards lead to improved environmental performance?

We study the effects of boards’ genetic diversity on corporate environmental performance. Using a multidimensional information set for 3690 US firms during the period from 2005 to 2019, and three different measures of genetic diversity, we find that, pursuant to the diversity theory, which posits that diversity improves the quality of management decisions and business ethics, genetic diversity leads to improved environmental performance. We also find that genetic diversity improves carbon and governance performance, and ESG disclosure. Particularly, a one percentage point increase in boards’ genetic diversity will increase the carbon performance, measured by the inverse of the carbon emissions to total assets ratio, and environmental performance by 3.54% and 5.57%, respectively. Our results remain robust to different model specifications, while also controlling for endogeneity. In terms of policy implications, results suggest that the key to tackling climate challenges is to promote boards’ genetic diversity.

Genetic Diversity and Trends of Ancestral and New Inbreeding in German Sheep Breeds by Pedigree Data.

In Germany, many autochthonous sheep breeds have developed, adapted to mountain, heath, moorland, or other marginal sites, but breeds imported from other countries have also contributed to the domestic breeds, particularly improving wool and meat quality. Selective breeding and the intense use of rams may risk losing genetic diversity and increasing rates of inbreeding. On the other hand, breeds with a low number of founder animals and only regional popularity may not leave their endangered status, as the number of breeders interested in the breed is limited. The objective of the present study was to determine demographic measures of genetic diversity and recent as well as ancestral trends of inbreeding in all autochthonous German sheep breeds and sheep of all breeding directions, including wool, meat, and milk. We used pedigree data from 1,435,562 sheep of 35 different breeds and a reference population of 981,093 sheep, born from 2010 to 2020. The mean number of equivalent generations, founders, effective founders, effective ancestors, and effective founder genomes were 5.77, 1669, 123.2, 63.5, and 33.0, respectively. Genetic drift accounted for 69% of the loss of genetic diversity, while loss due to unequal founder contributions was 31%. The mean inbreeding coefficient, individual rate of inbreeding (∆Fi), and realized effective population size across breeds were 0.031, 0.0074, and 91.4, respectively, with a significantly decreasing trend in ∆Fi in 11/35 breeds. New inbreeding, according to Kalinowski, contributed to 71.8% of individual inbreeding, but ancestral inbreeding coefficients showed an increasing trend in all breeds. In conclusion, in our study, all but one of the mountain-stone sheep breeds and the country sheep breed Wald were the most vulnerable populations, with Ne < 50. The next most endangered breeds are exotic, country, and heath breeds, with average Ne of 66, 83, and 89, respectively. The wool, meat, and milk breeds showed the highest genetic diversity, with average Ne of 158, 120, and 111, respectively. The results of our study should help strengthen conservation program efforts for the most endangered sheep breeds and maintain a high genetic diversity in all sheep breeds.

RNA-Seq-Pop: Exploiting the sequence in RNA sequencing-A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae.

We provide a reproducible and scalable Snakemake workflow, called RNA-Seq-Pop, which provides end-to-end analysis of RNA sequencing data sets. The workflow allows the user to perform quality control, perform differential expression analyses and call genomic variants. Additional options include the calculation of allele frequencies of variants of interest, summaries of genetic variation and population structure, and genome-wide selection scans, together with clear visualizations. RNA-Seq-Pop is applicable to any organism, and we demonstrate the utility of the workflow by investigating pyrethroid resistance in selected strains of the major malaria mosquito, Anopheles gambiae. The workflow provides additional modules specifically for An.gambiae, including estimating recent ancestry and determining the karyotype of common chromosomal inversions. The Busia laboratory colony used for selections was collected in Busia, Uganda, in November 2018. We performed a comparative analysis of three groups: a parental G24 Busia strain; its deltamethrin-selected G28 offspring; and the susceptible reference strain Kisumu. Measures of genetic diversity reveal patterns consistent with that of laboratory colonization and selection, with the parental Busia strain exhibiting the highest nucleotide diversity, followed by the selected Busia offspring, and finally, Kisumu. Differential expression and variant analyses reveal that the selected Busia colony exhibits a number of distinct mechanisms of pyrethroid resistance, including the Vgsc-995S target-site mutation, upregulation of SAP genes, P450s and a cluster of carboxylesterases. During deltamethrin selections, the 2La chromosomal inversion rose in frequency (from 33% to 86%), supporting a previous link with pyrethroid resistance. RNA-Seq-Pop is hosted at: github.com/sanjaynagi/rna-seq-pop. We anticipate that the workflow will provide a useful tool to facilitate reproducible, transcriptomic studies in An.gambiae and other taxa.

Abstract 151: Genetic Factors And Outcomes After Stroke: A Preliminary Analysis Of The Strong Study

Introduction: Measures of genetic variation have provided insight into underlying biology and treatment approaches in a number of medical sciences. The STRONG (“The Stroke, sTress, RehabilitatiON, and Genetics Study”) Study evaluated genetic polymorphisms in relation to stroke recovery. Methods: The STRONG Study recruited patients with a new stroke from 28 U.S. stroke centers. Entry criteria included age ≥18 years and new ischemic stroke or intracerebral hemorrhage. Visit 1 was during acute admission; Visit 2, 90 days post-stroke; Visit 3, 6 mo post-stroke; and Visit 4, 12 mo post-stroke. Linear regression examined specific genotypes in relation to 2 primary outcomes (change in grip force from V1-V2 and global function (SIS-ADL) at V2) and 2 secondary outcomes (depression (PHQ-8) at V2 and cognitive function (t-MoCA) at V4). No correction for multiple comparisons is made below. Results: There were 763 patients enrolled from 2016-2020, with mean age 63.1±14.9 years, 41.1% female, median NIHSS score 4 [2-9]. Data were available in 510 patients at Visit 2 and 482 at Visit 4. The BDNF val66met polymorphism (rs6265) was related to poorer V4 MoCA score (p=0.01). Presence of ApoE4 was not related to any endpoint. For the dopamine polygene score, a relationship with lower score (reduced dopamine neurotransmission) and greater depression (higher V2 PHQ-8 score) was suggested (p=0.1). A polymorphism (rs1842681) associated with chronic mRS score in a prior GWAS study (Neurology. 2019;92:e1271) was related to STRONG Study d90 mRS score (p=0.05). Three polymorphisms (rs76221407, rs150862264, rs182008837) associated with 3-mo mRS score in a separate GWAS study (Circ Res. 2019;124:114) were not related to STRONG Study d90 mRS score (p=.71-.78). ConclusionS: The STRONG Study collected genotypes and detailed longitudinal behavioral data during the year following stroke. Data do not support several hypotheses. However, presence of the BDNF val66met polymorphism may be related to poorer cognitive outcome. Lower dopamine gene score showed a trend with greater depression, consistent with a prior publication. Current findings support a prior GWAS finding for chronic mRS score. Genetics studies provide insights into inter-subject differences in recovery after stroke.