Population Differentiation Research Articles

Inter‐population variations of saccular otolith of Walton's mudskipper (Periophthalmus waltoni) of the Persian Gulf and Gulf of Oman

AbstractUnderstanding population structure is crucial for predicting species' responses to environmental change and elucidating evolutionary history. This study investigated the population structure of Periophthalmus waltoni in the Persian Gulf and Gulf of Oman using landmark‐based geometric morphometrics (GMM) and discrete wavelet transform (DWT) methods on sagittal otoliths. The objectives were to (i) examine otolith shape variation across different populations and (ii) compare GMM and DWT methods for resolving population differences. Both methods distinguished populations based on general otolith shape, with DWT revealing finer details due to its high accuracy in detecting otolith margins. Interestingly, populations from Sistan‐Baluchestan and Hormozgan, despite geographical separation, showed minimal variation in shape, suggesting environmental factors may influence otolith morphology. Distinct otolith shapes in the Khuzestan population, likely due to geographic isolation, may be influenced by the mangrove forests near Qeshm Island acting as barriers to larval dispersal. This aligns with molecular data and indicates that the relatively young eastern Persian Gulf may also contribute to these differences. Our findings revealed distinct geographical patterns in otolith shape, highlighting the influence of local environmental factors and larval dispersal on population differentiation. These results provide valuable insights into P. waltoni's population structure and evolutionary history, advancing our understanding of its adaptation to the diverse environmental conditions of the Persian Gulf and Oman Sea.

Comparing microsatellites and single nucleotide polymorphisms to evaluate genetic structure and diversity in wolverines (Gulo gulo) across Alaska and western Canada

Abstract The Wolverine (Gulo gulo) is a cold-adapted species of conservation interest because it is sensitive to human development, disturbance, exploitation, and climate warming. Wolverine populations have been studied across much of their distributional range to evaluate patterns of genetic diversity, genetic structure, and gene flow. Little population structure has been detected in northwestern North America with microsatellite loci, but low genomic diversity in wolverines may limit detection of genetic differences in this highly vagile species. Here, we genotyped a relatively large sample of wolverines from across Alaska (US) and adjacent Yukon (Canada) with 12 microsatellite loci (n = 501) and 4,222 single nucleotide polymorphisms (SNPs; n = 201) identified using restriction-site associated DNA sequencing. We compared the relative ability of our microsatellite and SNP datasets to evaluate population genetic structure, genetic diversity, differentiation, and isolation by distance (IBD). We predicted that the SNP dataset would detect a higher degree of genetic structure and provide more significant support for IBD. We found evidence for multiple genetic clusters, including genetic distinctiveness of wolverines in southeast Alaska and on the Kenai Peninsula. The SNP dataset detected additional genetic clusters that align largely with ecoregions, and the SNP dataset showed stronger evidence of IBD, while the 2 datasets were generally consistent in estimates of genetic diversity and differentiation among regional groups. Our results highlight the importance of genomic methods to assess gene flow in wolverines. Identifying population genetic structure allows an assessment of the potential impacts of conservation threats and is an important precursor for designing population monitoring programs.

Genetic Mechanism Analysis Related to Cold Tolerance of Red Swamp Crayfish, Procambarus clarkii.

In China, the red swamp crayfish (Procambarus clarkii), a notorious invasive species, has become an important economic freshwater species. In order to compare the genetic diversity and population structure of crayfish from northern and southern China, we collected 60 crayfish individuals from 4 crayfish populations in northern China and 2 populations in southern China for sequencing using the 2b-RAD technique. Additionally, the whole genome sequence information obtained by 2b-RAD of 90 individuals from 2 populations in northern China and 7 populations in southern China were downloaded from NCBI. After quality control, a total of 25,371 SNPs were detected from approximately 54.22 billion raw reads. Based on these SNPs, high genetic diversity was observed in the 15 crayfish populations in China. The pairwise FST values indicated that there was a large genetic differentiation of crayfish populations in northern and southern China. Despite common genetic backgrounds, due to geographical barriers, genetic divergence has been observed in northern and southern China crayfishes. The principal component analysis in combination with Admixture and Neighbor-Joining tree analysis showed that the crayfish fell into two clusters corresponding to geographical regions. The integrated analysis of whole genome and transcriptome data showed that two genes (CETN4 and CPEB2) might play important roles during crayfish resistance to a cold environment. This study reveals the genetic differentiation of crayfish populations in northern and southern China and provides clues to the genetic mechanism related to cold adaptation.

Environmental Variation Influences Genome Evolution in Hispaniolan Trunk Anoles (Anolis distichus).

Environmental variation often drives evolutionary processes like population differentiation, local adaptation and speciation. We used genome-scale data to investigate the contribution of environmental variation to evolution of the North Caribbean bark anole (Anolis distichus), a widespread common lizard that exhibits impressive phenotypic variation across varying habitats on the island of Hispaniola. We obtained new double-digest restriction-associated DNA sequence data (ddRADseq) from nearly 200 individuals and used 53 GIS data layers representing a range of environmental variables. We first asked how environmental variation has contributed to genome-wide differentiation across Hispaniola. We found that Hispaniola's three major mountain ranges contribute to deep genome-wide divergence and patterns of migration, that some deeply genomically divergent populations occupy significantly different environments, and that environmental variation is broadly capable of explaining more range-wide genomic differentiation than geographic distance alone. We then asked whether specific loci exhibit evidence of local adaptation to environmental variation using genotype-environment association (GEA) methods. We initially identified hundreds of loci broadly distributed across the genome that are significantly correlated with one or more environmental variables, but ultimately found that fewer than 100 of these candidate loci are shared across different GEA methods applied to our entire dataset, and that only 10 candidate loci are shared by independent analyses of two regional subsets of our dataset, suggesting parallel evolution is infrequent. Our study shows that abiotic environmental variation has played a critical role in explaining the evolution and diversity of a widespread and phenotypically diverse Caribbean anole species.

Plastome data provides new insights into population differentiation and evolution of Ginkgo in the Sichuan Basin of China

BackgroundGinkgo biloba L., an iconic living fossil, challenges traditional views of evolutionary stasis. While nuclear genomic studies have revealed population structure across China, the evolutionary patterns reflected in maternally inherited plastomes remain unclear, particularly in the Sichuan Basin - a potential glacial refugium that may have played a crucial role in Ginkgo’s persistence.ResultsAnalysis of 227 complete plastomes, including 81 newly sampled individuals from the Sichuan Basin, revealed three distinct maternal lineages differing from known nuclear genome patterns. We identified 170 sequence variants and extensive RNA editing (235 sites) with a bias toward hydrophobic amino acid conversions, suggesting active molecular evolution. A previously undocumented haplotype (IIA2), predominant in western Sichuan Basin populations, showed close genetic affinity with rare refugial haplotypes. Western populations exhibited higher haplotypic diversity and distinctive genetic structure, supporting the basin’s role as both glacial refugium and corridor for population expansion. Ancient trees (314–784 years) provided evidence for interaction between natural processes and historical human dispersal in shaping current genetic patterns.ConclusionsOur findings demonstrate substantial genetic diversity within Sichuan Basin Ginkgo populations and reveal dynamic molecular evolution through plastome variation and RNA editing patterns, challenging the notion of evolutionary stasis in this living fossil. This study provides crucial genomic resources for understanding Ginkgo’s evolution and informs conservation strategies for this endangered species.

Human longevity and Alzheimer's disease variants act via microglia and oligodendrocyte gene networks.

Ageing underlies functional decline of the brain and is the primary risk factor for several neurodegenerative conditions, including Alzheimer's disease (AD). However, the molecular mechanisms that cause functional decline of the brain during ageing, and how these contribute to AD pathogenesis, are not well understood. The objective of this study was to identify biological processes that are altered during ageing in the hippocampus and that modify Ad risk and lifespan, and then to identify putative gene drivers of these programmes. We integrated common human genetic variation associated with human lifespan or Ad from genome-wide association studies with co-expression transcriptome networks altered with age in the mouse and human hippocampus. Our work confirmed that genetic variation associated with Ad was enriched in gene networks expressed by microglia responding to ageing and revealed that they were also enriched in an oligodendrocytic gene network. Compellingly, longevity-associated genetic variation was enriched in a gene network expressed by homeostatic microglia whose expression declined with age. The genes driving this enrichment include CASP8 and STAT3, highlighting a potential role for these longevity-associated genes in the homeostatic functions of innate immune cells, and these genes might drive 'inflammageing'. Thus, we observed that gene variants contributing to ageing and AD balance different aspects of microglial and oligodendrocytic function. Furthermore, we also highlight putative Ad risk genes, such as LAPTM5, ITGAM and LILRB4, whose association with Ad falls below genome-wide significance but show strong co-expression with known Ad risk genes in these networks. Indeed, five of the putative risk genes highlighted by our analysis, ANKH, GRN, PLEKHA1, SNX1 and UNC5CL, have subsequently been identified as genome-wide significant risk genes in a subsequent genome-wide association study with larger sample size, validating our analysis. This work identifies new genes that influence ageing and AD pathogenesis, and highlights the importance of microglia and oligodendrocytes in the resilience of the brain against ageing and AD pathogenesis. Our findings have implications for developing markers indicating the physiological age of the brain and new targets for therapeutic intervention.

Maternal high-fat diet programs offspring airway hyperinnervation and hyperresponsiveness.

The impact of diet-induced maternal obesity on offspring airway hyperresponsiveness was studied in a diversity outbred mouse model that mirrors human genetic diversity. Female mice were started on high-fat or regular diet 8 weeks before breeding and throughout pregnancy and lactation. After weaning, all offspring were fed a regular diet. By 12 weeks, body weight and fat were increased in offspring of high-fat diet-fed dams, which was accompanied by metabolic dysfunction and hyperinsulinemia. This was followed by increased epithelial sensory innervation and increased bronchoconstriction to inhaled 5-hydroxytryptamine at 16 weeks. Bronchoconstriction was nerve mediated and blocked by vagotomy or atropine. A high-fat diet before pregnancy exerted the most influence on offspring airway physiology. Maternal obesity induced metabolic dysfunction and hyperinsulinemia, resulting in hyperinnervation and subsequent increased reflex-mediated hyperresponsiveness in their offspring. This is relevant to our understanding of asthma inheritance, considering the genetic diversity of humans.

A Post-Mortem Molecular Damage Profile in the Ancient Human Mitochondrial DNA.

Mitochondrial DNA (mtDNA) analysis is crucial for understanding human population structure and genetic diversity. However, post-mortem DNA damage poses challenges, that make analysis difficult. DNA preservation is affected by environmental conditions which, among other factors, complicates the differentiation of endogenous variants from artefacts in ancient mtDNA mix profiles. This study aims to develop a molecular damage profile for ancient mtDNA that can become a useful tool in analysing mtDNA from ancient remains. A dataset of 427 whole genomes or capture of mtDNA sequences from individuals representing different historical periods and climatic regions was compiled from the ENA database. Present-day and UDG-treated ancient samples were also included and used to establish levels of damaged reads. Results indicated that samples from cold regions exhibited the lowest percentage of damaged reads, followed by arid, cold, tropical and temperate regions, with significant differences observed between cold and temperate regions. A global damage profile was generated, identifying 2933 positions (25% of the positions considered) with damage in more than 23.8% of the samples analysed, deemed as damage hotspots. Notably, 2856 of these hotspots had never been reported as damage or mutational hotspots, or heteroplasmic positions. Damage hotspot frequency by position was slightly higher in the non-coding region compared with the coding region. In conclusion, this study provides a molecular damage profile for ancient mtDNA analysis that is expected to be a valuable tool in the interpretation of mtDNA variation in ancient samples.

The Impact of Administrative Districts and Urban Landscape on the Dispersal of Aedes aegypti via Genetic Differentiation.

Mosquito-borne diseases affect millions and cause numerous deaths annually. Effective vector control, which hinges on understanding their dispersal, is vital for reducing infection rates. Given the variability in study results, likely due to environmental and human factors, gathering local dispersal data is critical for targeted disease control. To analyse the spread and differentiation of Aedes aegypti in southern Taiwan, we established a dengue vector monitoring network in Southern Taiwan's cities. This network employed GPS-equipped ovitraps to gather eggs that were subsequently hatched in the laboratory and genotyped using genome-wide SNP markers. From 168 individuals, we identified 757,238 SNPs for detailed analysis. The estimated effective dispersal distance was 154 m (95% CI: 126-180 m), consistent with prior mark-release-recapture (MRR) estimates. We discovered that geographic isolation significantly influences genetic differentiation at larger scales, such as between cities, whereas its correlation with genetic distances is considerably weaker at smaller scales, like within cities. This is likely due to the urban landscape in Taiwan, characterised by narrow roads and densely packed buildings, which facilitates extensive dispersal of Ae. aegypti. In evaluating potential barriers to Ae. aegypti dispersal, we found that roads had no significant impact, whereas administrative districts accounted for 4.8% of the population differentiation (p < 10-4). Surprisingly, this variation aligns with the effects of district-specific mosquito control measures implemented at the municipal level. These findings highlight the complex interplay between urban landscapes, administrative measures and Ae. aegypti dispersal, emphasising the need for implementing targeted control strategies that consider these local dynamics.

Genetic diversity and population structure of grewia nervosa (lour.) Panigrahi from Gazipur and Cumilla sal forests, Bangladesh

The study was carried out to determine the genetic diversity and population structure of a medicinal plant Grewia nervosa (Lour.) Panigrahi from two different regions of Sal forest, one from Cumilla showed more abundance than Sal plant and Gazipur showed relatively less abundance of it. Interest was taken to find out the best genotypes for breeding and conservation program. With these purposes 10 RAPD and 7 ISSR loci were used in the present investigation. Populations from Cumilla Sal forest showed significantly higher polymorphism and comparatively higher heterozygosity than that of Gazipur. Very low gene flow and high differentiation among the populations was noticed in Gazipur Sal forest whereas moderate gene flow and less differentiation of populations of Cumilla. Bangladesh J. Bot. 53(4): 991-999, 2024 (December)

GeniePool 2.0: advancing variant analysis through CHM13-T2T, AlphaMissense, gnomAD V4 integration, and variant co-occurrence queries.

Originally developed to meet the challenges of genomic data deluge, GeniePool emerged as a pioneering platform, enabling efficient storage, accessibility, and analysis of vast genomic datasets, enabled due to its data lake architecture. Building on this foundation, GeniePool 2.0 advances genomic analysis through the integration of cutting-edge variant databases, such as CHM13-T2T, AlphaMissense, and gnomAD V4, coupled with the capability for variant co-occurrence queries. This evolution offers an unprecedented level of granularity and scope in genomic analyses, from enhancing our understanding of variant pathogenicity and phenotypic associations to facilitating research collaborations. The introduction of CHM13-T2T provides a more accurate reference for human genetic variation, AlphaMissense enriches the platform with protein-level impact predictions of missense mutations, and gnomAD V4 offers a comprehensive view of human genetic diversity. Additionally, the innovative feature for variant co-occurrence analysis is pivotal for exploring the combined effects of genetic variations, advancing our comprehension of compound heterozygosity, epistasis, and polygenic risk factors in disease pathogenesis. GeniePool 2.0 is a comprehensive and scalable platform, which aims to enhance genomic data analysis and contribute to genomic research, potentially supporting new discoveries and clinical innovations. Database URL: https://GeniePool.link.

Increasing IQ Test Scores and Decreasing g: The Flynn Effect and Decreasing Positive Manifold Strengths in Austria (2005-2018).

After almost a century of global generational IQ test score gains, the Flynn effect has, in the past decades, been observed to show stagnation and reversals in several countries. Tentative evidence from academic achievement data has suggested that these trajectory changes may be rooted in a decreasing strength of the positive manifold of intelligence due to increasing ability differentiation and specialization in the general population. Here, we provide direct evidence for generational IQ test score and positive manifold strength changes based on IQ test standardization data from 1392 Austrian residents between 2005 and 2018. Our analyses revealed positive Flynn effects across all domains of the IQ test (Cohen's d from 0.21 to 0.91) but a trend toward decreasing strength in the positive manifold of intelligence (R2 from .908 to .892), though these changes were not statistically significant. Our results are consistent with the idea that increasingly inconsistent Flynn effect trajectories may be attributed to increasing ability differentiation and specialization in the general population over time.

Human disease-causing missense genetic variants are enriched in the evolutionarily ancient domains of the cytosolic aminoacyl-tRNA synthetase proteins.

All life depends on accurate and efficient protein synthesis. The aminoacyl-tRNA synthetases (aaRSs) are a family of proteins that play an essential role in protein translation, as they catalyze the esterification reaction that charges a transfer RNA (tRNA) with its cognate amino acid. However, new domains added to the aaRSs over the course of evolution in eukaryotes confer novel functions unrelated to protein translation. To date, damaging variants that affect aaRS-encoding genes have been linked to over 50 human diseases. In this study, we leverage the evolutionary history of the aaRS proteins to better understand the distribution of disease-causing missense variants in human cytosolic aaRSs. We hypothesized that disease-causing missense variants in human aaRSs were more likely to be located in the ancient domains of the aaRS, essential for the aminoacylation reaction, rather than in the evolutionarily more recent domains found in eukaryotes. We determined the locations of the modern and ancient domains in each aaRS protein found in humans. We then statistically assessed the positional conservation across each domain and examined the distribution of pathogenic and benign/unknown missense human genetic variants across these domains. We establish that pathogenic missense variants in the human aaRS proteins are enriched in the evolutionarily ancient domains while benign/unknown missense variants are enriched in the modern domains. In addition to defining the evolutionary history of human aaRS proteins through domain identification, we anticipate that this work will improve the ability to diagnose patients affected by damaging genetic variants in the aaRS protein family.

Trans-differentiation of Jdp2-depleted Gaba-receptor-positive cerebellar granule cells to Purkinje cells

The Jun dimerization protein (Jdp2) gene is active in mouse cerebellar granule cells and its protein product plays a crucial role in the formation of the cerebellum lobes through programmed cell death. However, the role of Jdp2 in cellular differentiation and pluripotency in the cerebellum, and the effect of the antioxidation reaction on cell plasticity, remain unknown. N-acetyl-l-cysteine (NAC) induced the early commitment of the differentiation of granule cell precursors (GCPs) to neurons, especially Purkinje cells, via the γ-aminobutyric acid type A receptor α6 subunit (Gabra6) axis; moreover, Jdp2 depletion enhanced this differentiation program of GCPs. The antioxidative effect of NAC was the main driving force of this decision toward the neural differentiation of the GCP population in the presence of Gabra6 in vitro. This implies that antioxidative drugs are effective agents for rescuing oxidative-stress-induced GCP damages in the cerebellum and commit this Gabra6-positive cell population toward differentiation into Purkinje cells.

Genetic Structural Changes While Maintaining Effective Population Size of Bighead Catfish in Nong Han Lake: Implications of Metapopulation Dynamics or Release Activities

ABSTRACTThe Bighead Catfish (Clarias macrocephalus) plays crucial roles in the ecosystem and as a protein source for humans in Nong Han Lake, Thailand, but their ecological and population dynamics, along with their genetic diversity and structure, are poorly understood. Therefore, the dynamics of genetic diversity and differentiation of bighead catfish populations in Nong Han Lake were investigated during 2018–2023 to provide essential insights into preserving biodiversity and maintaining ecological balance. Microsatellite genotyping was used to assess the genetic diversity of one bighead catfish population in 2018, two populations in 2023, and one hatchery population. Potentially stable, effective population sizes and distinct genetic clusters of these populations were identified, which represented the resilience of populations and the complexity of their genetic dynamics. Genetic differentiation between sample dates and among populations suggested that limited recent and historical genetic exchanges could potentially influence genetic structure. The impact of ecological factors, including flooding, metapopulation dynamics, and human interventions, was indicated by unique and shared gene pools among populations and subpopulations in different years. Ongoing assessment of genetic diversity and structure of bighead populations is essential for developing conservation strategies and ensuring sustainable management.

Pharmacogenomic associations with HIV-1 virologic suppression in TB/HIV patients.

Human genetic variants can affect TB and HIV drug metabolism, which may lead to toxicity or treatment failure. We evaluated associations between genetic variants of antiretroviral therapy (ART) and HIV-1 outcomes among TB/HIV patients. We included RePORT-Brazil participants with TB/HIV who initiated standard TB treatment [2 months of isoniazid/rifampicin (or rifabutin)/pyrazinamide/ethambutol, then 4 months or more of isoniazid/rifampicin (or rifabutin)], and ART. The endpoint was HIV-1 virologic suppression (defined as <1,000 HIV-1 RNA copies/mL, for primary analysis, and <50 HIV-1 RNA copies/mL, for secondary analysis) after at least 2 weeks of ART. We compared non-nucleoside reverse transcriptase inhibitor (NNRTI)-based and integrase strand transfer inhibitor (INSTI)-based ART regimens. We genotyped CYP2B6 (rs3745274, rs28399499, rs4803419; affects efavirenz metabolism) and UGT1A1 (rs887829; affects dolutegravir and raltegravir metabolism); all have defined normal, intermediate, and slow genotypes. Genotyping was performed by MassARRAY iPLEX Gold. We compared outcome proportions (Fisher's test) and time-to-virologic suppression (survival analysis, Wilcoxon-Gehan test). Among 194 TB/HIV participants included, efavirenz was the most frequent NNRTI ([n=76], one participant received etravirine), and raltegravir was the most frequent INSTI (n=88). The overall virologic suppression was suboptimal, with 32% (n=62) of participants not achieving HIV-1 virologic suppression. Among them, 36% (n=28) used efavirenz-based ART and were more likely to be CYP2B6 normal metabolizers (n=8, 44%); and 30% (n=30) used INSTI-based ART and the UGT1A1 normal genotype was also the most common (n=13, 50%). The median time to virologic suppression for efavirenz-based ART was 184 days (95% Confidence Interval (CI)160-207), and for INSTI-based ART, 188 days (95% CI 144-231) (p=0.84). No significant associations were found comparing the proportions and time to virologic suppression among CYP2B6 and UGT1A1genotypes. In this observational cohort of patients treated for TB/HIV, the proportion of participants achieving virologic suppression was low, and genetic variants affecting ART metabolism were not significantly associated with the likelihood of virologic suppression.

The multi-scale complexity of human genetic variation beyond continental groups.

Traditional clustering and visualization approaches in human genetics often operate under frameworks that assume inherent, discrete groupings1,2. These methods can inadvertently simplify multifaceted relationships, functioning to entrench the idea of typological groups3. We introduce a network-based pipeline and visualization tool grounded in relational thinking4, which constructs networks from a variety of genetic similarity metrics. We identify communities at multiple resolutions, departing from typological models of analysis and interpretation that categorize individuals into a (predefined) number of sets. We applied our pipeline to a dataset merged from the 1000 Genomes and Human Genome Diversity Project5, revealing the limitations of traditional groupings and capturing the complexities introduced by demographic events and evolutionary processes. This method embraces the context-specificity of genetic similarities that are salient depending on the question, markers of interest, and study individuals. Different numbers of communities are revealed depending on the resolution chosen and metric used, underscoring a fluid spectrum of genetic relationships and challenging the notion of universal categorization. We provide a web application (https://sohail-lab.shinyapps.io/GG-NC/) for interactive visualization and engagement with these intricate genetic landscapes.

Delimitation of Endangered Telmatobius Species (Anura: Telmatobiidae) of the Chilean Salt Puna.

Clarifying the taxonomic status and distribution of endangered species is crucial to their conservation. In this study, we contrasted different lines of evidence (morphology, mtDNA, and nucDNA: microsatellites and SNP) to clarify the taxonomic status of endangered Telmatobius water frog species and unidentified populations that inhabit the Salt Puna in Chile. We studied population differentiation and species divergence by performing morphometric, population genetic and species delimitation analyses. The results confirmed the species status of Telmatobius fronteriensis and T. philippii, as they exhibited morphometric, mitochondrial and genomic SNP divergence. Although Bayes factor delimitation analysis indicated that the Telmatobius populations of Ascotán and Carcote could represent a new species, their few mitochondrial differences and similar morphology with respect to T. philippii suggested otherwise. Instead, they can be considered an evolutionarily significant unit of T. philippii that has differentiated from the type locality. These results extend the geographic distribution of T. philippii, which is categorized as critically endangered by the IUCN.

Analyses of Human Genetic Data to Identify Clinically Relevant Domains of Neuroligins

Background/Objectives: Neuroligins (NLGNs) are postsynaptic adhesion molecules critical for neuronal development that are highly associated with autism spectrum disorder (ASD). Here, we provide an overview of the literature on NLGN rare variants. In addition, we introduce a new approach to analyze human variation within NLGN genes to identify sensitive regions that have an increased frequency of ASD-associated variants to better understand NLGN function. Methods: To identify critical protein subdomains within the NLGN gene family, we developed an algorithm that assesses tolerance to missense mutations in human genetic variation by comparing clinical variants from ClinVar to reference variants from gnomAD. This approach provides tolerance values to subdomains within the protein. Results: Our algorithm identified several critical regions that were conserved across multiple NLGN isoforms. Importantly, this approach also identified a previously reported cluster of pathogenic variants in NLGN4X (also conserved in NLGN1 and NLGN3) as well as a region around the highly characterized NLGN3 R451C ASD-associated mutation. Additionally, we highlighted other, as of yet, uncharacterized regions enriched with mutations. Conclusions: The systematic analysis of NLGN ASD-associated variants compared to variants identified in the unaffected population (gnomAD) reveals conserved domains in NLGN isoforms that are tolerant to variation or are enriched in clinically relevant variants. Examination of databases also allows for predictions of the presumed tolerance to loss of an allele. The use of the algorithm we developed effectively allowed the evaluation of subdomains of NLGNs and can be used to examine other ASD-associated genes.

Human genetic variation reveals FCRL3 is a lymphocyte receptor for Yersinia pestis.

Yersinia pestis is the gram-negative bacterium responsible for plague, one of the deadliest and most feared diseases in human history. This bacterium is known to infect phagocytic cells, such as dendritic cells and macrophages, but interactions with non-phagocytic cells of the adaptive immune system are frequently overlooked despite the importance they likely hold for human infection. To discover human genetic determinants of Y. pestis infection, we utilized nearly a thousand genetically diverse lymphoblastoid cell lines in a cellular genome-wide association study method called Hi-HOST (High-throughput Human in-vitrO Susceptibility Testing). We identified a nonsynonymous SNP, rs2282284, in Fc receptor like 3 (FCRL3) associated with bacterial invasion of host cells (p=9×10-8). FCRL3 belongs to the immunoglobulin superfamily and is primarily expressed in lymphocytes. rs2282284 is within a tyrosine-based signaling motif, causing an asparagine-to-serine mutation (N721S) in the most common FCRL3 isoform. Overexpression of FCRL3 facilitated attachment and invasion of non-opsonized Y. pestis. Additionally, FCRL3 colocalized with Y. pestis at sites of cellular attachment, suggesting FCRL3 is a receptor for Y. pestis. These properties were variably conserved across the FCRL family, revealing molecular requirements of attachment and invasion, including an Ig-like C2 domain and a SYK interaction motif. Direct binding was confirmed with purified FCRL5 extracellular domain. Following attachment, invasion of Y. pestis was dependent on SYK and decreased with the N721S mutation. Unexpectedly, this same variant is associated with risk of chronic hepatitis C virus infection in BioBank Japan. Thus, Y. pestis hijacks FCRL proteins, possibly taking advantage of an immune receptor to create a lymphocyte niche during infection.