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opencc-by-4.0May 2022View details →

Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels

<pre>This repository contains data related to: Diverse environmental perturbations reveal the evolution and context-dependency of genetic effects on gene expression levels Amanda J. Lea, Julie Peng, Julien F. Ayroles A preprint of this work can be found here: https://www.biorxiv.org/content/10.1101/2021.11.04.467311v2 Specifically, the filtered, normalized, and batch corrected gene expression data file (31Mar21_all_runs_voom_resid.txt) is provided along with the metadata. We also provide the output from matrix eQTL that was used as input for mashR. Scripts used to generate and analyze these data are provided here: https://github.com/AmandaJLea/LCLs_gene_exp</pre>

Genetic architecture of alcohol consumption identified by a genotype-stratified GWAS, and impact on esophageal cancer risk in Japanese

An East Asian-specific variant on aldehyde dehydrogenase 2 (ALDH2 rs671, G>A) is the major genetic determinant of alcohol consumption. We performed an rs671 genotype-stratified genome-wide association study (GWAS) meta-analysis in up to 175,672 Japanese individuals to uncover additional loci associated with alcohol consumption in an rs671-dependent manner. Three loci (GCKR, KLB, and ADH1B) satisfied the genome-wide significance threshold in wild-type homozygotes (GG), whereas six loci (GCKR, ADH1B, ALDH1B1, ALDH1A1, ALDH2, and GOT2) did so in heterozygotes (GA). Of these, five loci showed genome-wide significant interaction with rs671. Genetic correlation analyses revealed ancestry-specific genetic architecture in heterozygotes. Subsequent polygenic risk scoring depicted interactions highlighted by stratified GWAS. Further, most discovered loci showed significant effects on risk of esophageal cancer, a representative alcohol-related disease, and multiple other phenotypes. Our results identify the genotype-specific genetic architecture of alcohol consumption and reveal its potential impact on alcohol-related disease risk.

opencc-by-4.0Oct 2023View details →

Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent - nuclear genomic genotypes

Genotype likelihood (GMR_minind40_mmaf0.05_glf2.beagle.gz) and pseudohaploid calls (GMR_minind40_mmaf0.05_glf2.haplo.gz) used for the nuclear genomic analyses in the manuscript "Topographic barriers drive the pronounced genetic subdivision of a range-limited fossorial rodent".The order of the individuals in each file is listed in Names.txt

Data for: Genetic and context-specific effects on individual inhibitory control performance in the guppy (Poecilia reticulata)

Among-individual variation in cognitive traits, widely assumed to have evolved under adaptive processes, is increasingly being demonstrated across animal taxa. As variation among individuals is required for natural selection, characterising individual differences and their heritability is important to understand how cognitive traits evolve. Here we use a quantitative genetic study of wild-type guppies repeatedly exposed to a 'detour task' to test for genetic variance in the cognitive trait of inhibitory control. We also test for genotype-by-environment interactions (GxE) by testing related fish under alternative experimental treatments (transparent vs. semi-transparent barrier in the detour-task). We find among-individual variation in detour task performance, consistent with differences in inhibitory control. However, analysis of GxE reveals that heritable factors only contribute to performance variation in one treatment. This suggests that the adaptive evolutionary potential of inhibitory control (and/or other latent variables contributing to task performance) may be highly sensitive to environmental conditions. The presence of GxE also implies that the plastic response of detour task performance to treatment environment is genetically variable. Our results are consistent with a scenario where variation in individual inhibitory control stems from complex interactions between heritable and plastic components.

Environmental, sex-specific, and genetic determinants of infant social behavior in a wild primate

Affiliative social bonds are linked to fitness components in many social mammals. However, despite their importance, little is known about how the tendency to form social bonds develops in young animals, or if the timing of development is heritable and thus can evolve. Using four decades of longitudinal observational data from a wild baboon population, we assessed the environmental determinants of an important social developmental milestone in baboons—the age at which a young animal first grooms a conspecific—and we assessed how the rates at which offspring groom their mothers develops during the juvenile period. We found that grooming development differs between the sexes: female infants groom at an earlier age and reach equal rates of grooming with their mother earlier than males. We also found that age at first grooming for both sexes is weakly heritable (h2 = 0.043, 95% CI: 0.002 – 0.110). These results show that sex differences in grooming emerge at a young age; that strong, equitable social relationships between mothers and daughters begin very early in life; and that age at first grooming is heritable and therefore can be shaped by natural selection.

Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever

Canine anterior cruciate ligament (ACL) rupture is a common complex disease. Prevalence of ACL rupture is breed-dependent. In an epidemiological study, yellow coat color was associated with increased risk of ACL rupture in the Labrador Retriever. ACL rupture risk variants may be linked to coat color through genetic selection or through linkage with coat color genes. To investigate these associations, Labrador Retrievers were phenotyped as ACL rupture cases or controls and for coat color and were single nucleotide polymorphism (SNP) genotyped. After filtering, ~697K SNPs were analyzed using GEMMA and mvBIMBAM for multivariate association. Functional annotation clustering analysis with DAVID was performed on candidate genes. A large 8Mb region on chromosome 5 that included ACSF3, as well as 32 additional SNPs, met genome-wide significance at P<6.07E-7 or Log10(BF) = 3.0 for GEMMA and mvBIMBAM, respectively. On chromosome 23, SNPs were located within or near PCCB and MSL2. On chromosome 30, a SNP was located within IGDCC3. SNPs associated with coat color were also located within ADAM9, FAM109B, SULT1C4,RTDR1, BCR, and RGS7. DZIP1L was associated with ACL rupture. Several significant SNPs on chromosomes 2, 3, 7, 24, and 26 were located within uncharacterized regions or long non-coding RNA sequences. This study validates associations with the previous ACL rupture candidate genes ACSF3 and DZIP1L and identifies novel candidate genes. These variants could act as targets for treatment or as factors in disease prediction modeling. The study highlighted the importance of regulatory SNPs in the disease, as several significant SNPs were located within non-coding regions.

Raw data for the association of genetic variants of ErbB4 gene and gestational diabetes mellitus

<div>Gestational diabetes (GDM) is one of the common complications of female pregnancy, which seriously affects the health of patients and their offspring. So far, the etiology has not yet been fully clarified. To clarify the relationship of Erb-b2 receptor tyrosine kinase 4 (ErbB4) genetic variants and GDM risk in a Chinese population, ErbB4 variants (rs1595064, rs1595065, rs1595066 and rs6719645) were selected and genotyped in 554 GDM cases and 641 healthy controls. The associations between variants and GDM risk were evaluated with the odds ratios (ORs) and their corresponding 95% confidence intervals (CIs). The false-positive reporting probability (FPRP), multi-factor dimension reduction (MDR) and bioinformatics analysis were adopted to confirm the significant associations. A nomogram model was constructed to predict the risk of GDM. Association analysis demonstrated that the rs1595066 genotype performed a protective effect on GDM risk among whole subjects. Meanwhile, stratified analysis showed that rs1595066 was significantly associated with GDM risk in various subgroups, such as age>30.09 years old, pre-pregnancy BMI>22.23 Kg/m2 ,SBP≤110.08 mmHg, etc. Further, interactions between rs1595066 and DBP (Pinteraction=0.01), FPG (Pinteraction<0.001) and HbA1c (Pinteraction< 0.001) were detected. The FPRP analysis confirmed that association of rs1595066 and GDM risk in subjects of FPG≤4.79 mmol/L (P=0.199) is true at a prior probability of 0.1. The MDR analysis suggested that rs1595066 was the best single locus model, while the 4-loci model was considered the best multiple factors model to predict GDM risk. Functional prediction revealed that rs1595066 may disturb the microRNA binding sites to influence the stability of miRNA-mRNA binding. The predictive nomogram model has a good consistency and acceptable discriminative ability with a diagnosed AUC of 0.813.ErbB4 rs1595066 was significantly associated with GDM risk and underlying mechanism causing GDM may be the interaction of gene-gene, gene-environment and the changes in the regulatory effects of miRNAs on ERBB4 expression. The nomogram model has a good prospect for GDM prediction.</div>

Data from: Genetic depletion does not prevent rapid evolution in island-introduced lizards

Experimental introductions of species have provided some of the most tractable examples of rapid phenotypic changes, which may reflect plasticity, the impact of stochastic processes, or the action of natural selection. Yet to date, very few studies have investigated the neutral and potentially adaptive genetic impacts of experimental introductions. We dissect the role of these processes in shaping the population differentiation of wall lizards in three Croatian islands (Sušac, Pod Kopište, Pod Mrčaru), including the islet of Pod Mrčaru where experimentally introduced lizards underwent rapid (~30 generations) phenotypic changes associated to a shift from an insectivorous to a plant-based diet. Using a genomic approach (~82,000 ddRAD loci), we confirmed a founder effect during introduction, and very low neutral genetic differentiation between the introduced population and its source. However, genetic depletion did not prevent rapid population growth, as the introduced lizards exhibited population genetic signals of expansion and are known to have reached a high density. Our genome-scan analysis identified just a handful of loci showing large allelic shifts between ecologically divergent populations. This low overall signal of selection suggests that the extreme phenotypic differences observed among populations are determined by a small number of large-effect loci, and/or that phenotypic plasticity plays a major role in phenotypic changes. Nonetheless, functional annotation of the outlier loci revealed some candidate genes relevant to diet-induced adaptation, in agreement with the hypothesis of directional selection. Our study provides important insights on the evolutionary potential of bottlenecked populations in response to new selective pressures on short ecological timescales.

Data from: Investigating the spatial, demographic, and genetic structures of Cylicodiscus gabunensis Harms, a light-demanding African timber species

Most Central African rainforest canopies consist of light-demanding tree species that hold high commercial value but also suffer locally from regeneration deficits, raising concerns about the sustainability of logging. Regeneration is influenced by factors such as past perturbations (including human activity), mating systems, and seed/pollen dispersal processes that impact demographic, spatial, and genetic structures within populations. To gain a better understanding of these interactions, we studied the spatial distribution and trunk diameter structure of Cylicodiscus gabunensis (Fabaceae) - a wind-dispersed, insect-pollinated, timber species - in three plots ranging from 400 to 839 ha situated in various environmental contexts (e.g. forest types and elephant densities) across Central Africa. We also genotyped adults and juveniles using microsatellite markers to analyze the spatial genetic structure of each population and infer the selfing rate, seed and pollen dispersal capacities and selection gradients using the 'neighborhood model'. The selfing rate was low (3 – 4 %), and seed dispersal distances (ds = 184 m) were much shorter than pollen dispersal distances (dp > 2 km). The three populations displayed contrasted spatial, demographic and genetic structures. One population showed no spatial aggregation or genetic structure, and a multimodal diameter structure indicating pulses of regeneration events. Two populations showed strong spatial aggregation and genetic structures. One exhibited a unimodal diameter structure indicating one ancient pulse of regeneration, while the other displayed a 'reverse J-shaped' diameter structure, typical of ongoing regeneration. In the latter, reproductive success appeared leptokurtic, three mother trees accounting for over 90 % of the regeneration and no tree below the minimum cutting diameter implemented by logging companies had offspring. The idiosyncratic nature of population characteristics observed in C. gabunensis suggests that, for sustainable management, a nuanced approach is needed. This involves protecting productive seed trees in areas where natural regeneration is occurring and actively supporting regeneration in areas exhibiting deficits, especially in contexts with low elephant densities.

Understudied regions and messy taxonomy: Geography, not taxonomy, is the best predictor for genetic divergence of the Poecilimon bosphoricus species group

The complex and dynamic history of the Anatolian Peninsula during the Pleistocene set the stage for species diversification. However, the evolutionary history of biodiversity in the region is shrouded by the challenges of studying species divergence in the recent, dynamic past. Here we study the Poecilimon bosphoricus (PB) species group to understand how the bush crickets' diversification and the region's complex history are coupled. Specifically, using sequences of two mitochondrial and two nuclear gene segments from over 500 individuals for a comprehensive set of taxa with extensive geographic sampling, we infer the phylogenetic and geographic setting of species divergence. In addition, we use the molecular data to examine hypothesized species boundaries that were defined morphologically. Our analyses of the timing of divergence confirm the recent origin of the PB complex, indicating its diversification coincided with the dynamic geology and climate of the Pleistocene. Moreover, the geography of divergence suggests a history of fragmentation followed by admixture of populations, suggestive of a ring species. However, the evolutionary history based on genetic divergence conflicts with morphologically defined species boundaries, raising the prospect that incipient species divergences may be relatively ephemeral. As such, the morphological differences observed in the PB complex may not be sufficient to have prevented homogenizing gene flow in the past. Alternatively, with the recent origin of the complex, the lack of time for lineage sorting may underlie the discord between morphological species boundaries and genetic differentiation. Under either hypothesis, geography – not taxonomy – is the best predictor of genetic divergence.

opencc-by-4.0Nov 2023View details →

Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery

Data Associated with Figures 1 and 2 in Communications Biology Matters Arising: Genetic differentiation at methylation array probe SNPs leads to spurious results in meQTL discovery.  Original data arising from B. Li et al. Communications Biology <a href="https://doi.org/10.1038/s42003-022-03353-5">https://doi.org/10.1038/s42003-022-03353-5</a> (2022)

Data from: Relict stands of Central European oaks: unravelling autochthony and genetic structure based on a multi-population study

Central European white oaks expanded rapidly after the last glacial period and reached their current distribution range during the early Holocene. They have been an important resource of timber, fuelwood and animal feed for humans, who actively promoted their presence in forests and other landscape types at least since the early historical times. Besides stands with intensive management, putatively relict populations of three native oak species can be found on unproductive sites with restricted accessibility. Here, we apply chloroplast and nuclear microsatellite markers in order to address the autochthony of relict and managed stands and compare the spatial distribution of genetic variation between them. Based on data from more than 150 populations, we demonstrate that oak autochthony was preserved throughout historical times which is likely the result of traditional silvicultural treatment. This is supported by the fact that the spatial pattern of chloroplast haplotype distribution still reflects the post-glacial recolonization in both relict and old managed stands. We observed significant admixture of haplotypes only in stands established after the Second World War, which is attributable to the transfer of reproductive material used for afforestation. In terms of nuclear genetic variation, we observed marked differences among species. Quercus pubescens exhibited a pronounced genetic structure. Genetic drift and limited gene flow among its small and isolated populations in our study area might have contributed to this pattern. Varying extent of genetic introgression with other sympatric oak species could offer an additional explanation. On the contrary, the gene pools of Q. petraea and Q. robur are highly homogenous, displaying only weak isolation-by-distance. We found no significant differences of genetic diversity and differentiation between relict and managed stands. This suggests that seed transfer mostly occurred within our study area, even in those stands established in post-war times, verifying previous findings that point out limited human interference. We recommend consideration of population genetic structure for gene conservation, with a finer resolution of gene conservation units needed for Q. pubescens due to its spatial genetic structure. Both relict and old managed stands, species-pure or mixed, are suitable for conservation, as they host autochthonous gene pools. Coppice-with-standard management could contribute to preservation of autochthony. In the face of climate change, it is also important to maintain the evolutionary potential of the stands, by facilitating generative reproduction and allowing for hybridization in mixed stands.

opencc-by-4.0Nov 2023View details →

Clinical and genetic findings in an Italian cohort of individuals with congenital cataract

List of variants and associated clinical phenotypes identified in a cohort of individuals affected by congenital cataract (syndromic and non-syndromic forms) that have been submitted to the public ClinVar repository (https://www.ncbi.nlm.nih.gov/clinvar/) with their corresponding accession numbers.

Data for: The suppression of a selfish genetic element increases a male's mating success in a fly

X chromosome meiotic drive (XCMD) kills Y-bearing sperm during spermatogenesis, leading to the biased transmission of the selfish X chromosome. Despite this strong transmission, some natural XCMD systems remain at low and stable frequencies, rather than rapidly spreading through populations. The reason may be that male carriers can have reduced fitness, as they lose half of their sperm, only produce daughters, and may carry deleterious alleles associated with XCMD. Thus, females may benefit from avoiding mating with male carriers, yielding a further reduction in fitness. Genetic suppressors of XCMD, which block the killing of Y sperm and restore fair Mendelian inheritance, are also common and could prevent the spread of XCMD. However, whether suppressed males are as fit as a wild-type male remains an open question, and the effect that genetic suppressors may have on a male's mating success is rarely considered. Here, we investigate the mating ability of XCMD males and suppressed XCMD males in comparison to wild-type males in the fruit fly Drosophila subobscura, where drive remains at a stable frequency of 20% in wild populations where it occurs. We use both competitive and non-competitive mating trials to evaluate male mating success in this system. We found no evidence that unsuppressed XCMD males were discriminated against. Remarkably, however, their suppressed XCMD counterparts had a higher male mating success compared to wild-type controls. Unsuppressed XCMD males suffered 12% lower offspring production in comparison to wild-type males. This cost appears too weak to counter the transmission advantage of XCMD, and thus the factors preventing the spread of XCMD remain unclear.

Data from: Conservation genetics of Notelaea lloydii (Oleaceae) in south-eastern Queensland, Australia

Habitat fragmentation can increase the chance of population bottlenecks and inbreeding, and may ultimately lead to reduced fitness and local extinction. Notelaea lloydii is a native olive species endemic to Australia and listed as vulnerable due to its restricted distribution. A recent molecular systematics study has revealed there might be some geographic structuring among the N. lloydii populations. Therefore, we undertook a genome wide Single Nucleotide Polymorphism (SNP) analysis to determine levels and patterns of genetic diversity, inbreeding and gene flow within and among N. lloydii populations in south-eastern Queensland (SE-QLD). Furthermore, as the reproductive phase of a plant's life history has a profound influence on genetic diversity, life history reproductive traits were also studied. Our SNP analysis revealed low genetic diversity, inbreeding and significant genetic structuring even among proximate populations. Results of a flower and fruit bagging experiment in two consecutive seasons revealed that N. lloydii produced many flowers but only a few fruits survived to maturity. There were no differences in bagged and un-bagged flowering and fruiting rates and therefore, we conclude that the high fruit abortion rate was probably due to inbreeding depression and/or suboptimal conditions, rather than pollinator availability and insect attack. Overall, results of this study indicate that the populations of N. lloydii are small, inbred and genetically isolated and represent unique management units that require local conservation management due to ongoing threats associated with urbanisation.

opencc-by-4.0Nov 2023View details →

Phenotypic stasis despite genetic divergence and differentiation in Caenorhabditis elegans.

# Data for the manuscript : Phenotypic stasis despite genetic divergence and differentiation in Caenorhabditis elegans.https://doi.org/10.1101/2022.05.28.493856 The data directory contains:- the raw transition rates in  Final_merged_data_NGM.txt- population male frequencies estimates : population_rep_male_freqs.txt- fertility data from the Cemee: fertility.rda (from Noble et al. 2017)- Mean state frequencies in the movies : State_freq_NGM.txt The Rcode directory contains all code to reproduce the analysis is available on github:https://github.com/ExpEvolWormLab/Mallard_Stasis

Data from: Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants

Premise: Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self-pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. Methods: To evaluate whether relatedness decreases with local density, we analysed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. Results: There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation-by-distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1–3%. EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. Conclusions: The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates, or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.

Behavioral estimates of mating success corroborate genetic evidence for pre-copulatory selection

In promiscuous species, fitness estimates obtained from genetic parentage may often reflect both pre- and post-copulatory components of sexual selection. Directly observing copulations can help isolate the role of pre-copulatory selection, but such behavioral data are difficult to obtain in the wild and may also overlook post-copulatory factors that alter the relationship between mating success and reproductive success. To overcome these limitations, we combined genetic parentage analysis with behavioral estimates of size-specific mating in a wild population of brown anole lizards (Anolis sagrei). Males of this species are twice as large as females and multiple mating among females is common, suggesting the scope for both pre- and post-copulatory processes to shape sexual selection on male body size. Our genetic estimates of reproductive success revealed strong positive directional selection for male size, which was also strongly associated with the number of mates inferred from parentage. In contrast, a male's size was not associated with the fecundity of his mates or his competitive fertilization success. By simultaneously tracking copulations in the wild via the transfer of colored powder to females by males from different size quartiles, we independently confirmed that large males were more likely than small males to mate. We conclude that body size is primarily under pre-copulatory sexual selection in brown anoles, and that post-copulatory processes do not substantially alter this pre-copulatory selection. Our study also illustrates the utility of combining both behavioral and genetic methods to estimate mating success to disentangle pre- and post-copulatory processes in promiscuous species.

Data from: Genetic signatures of lineage fusion closely resemble population decline

Accurate interpretation of the genetic signatures of past demographic events is crucial for reconstructing evolutionary history. Lineage fusion (complete merging, resulting in a single panmictic population) is a special case of secondary contact that is seldom considered. Here, the circumstances under which lineage fusion can be distinguished from population size constancy, growth, bottleneck, and decline were investigated. Multi-locus haplotype data were simulated under models of lineage fusion with different divergence versus sampling lag times (D:L ratios). These pseudo-observed datasets also differed in their allocation of a fixed amount of sequencing resources (number of sampled alleles, haplotype length, number of loci). Distinguishability of lineage fusion versus each of 10 untrue non-fusion scenarios was quantified based on six summary statistics (neutrality tests). Some datasets were also analyzed using extended Bayesian skyline plots. Results showed that signatures of lineage fusion very closely resemble those of decline—high distinguishability was generally limited to the most favorable scenario (D:L = 9), using the most sensitive summary statistics (FS and ZnS), coupled with the optimal sequencing resource allocation (maximizing number of loci). Also, extended Bayesian skyline plots often erroneously inferred population decline. Awareness of the potential for lineage fusion to carry the hallmarks of population decline is critical.

Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

Genetic structure and distribution patterns of modern floras are strongly affected by climatic change and geographical isolation. In the present study, we applied restriction-site-associated DNA sequencing (RAD-seq) to analyze the genetic structure and to simulate the demographic history of two extant Cryptomeria species in Japan (C. japonica) and Southeastern China (C. japonica var. sinensis). Thirteen natural populations representing the entire species distributed in East Asia were collected from Japan and China. At the species level, the genetic diversity of Cryptomeria was moderate (Ho = 0.217, He = 0.203) with a significant genetic differentiation among populations (85.30%, P < 0.001), especially between Japan and China lineages (FST = 0.147). Except for the Lushan (LS) population in China, all populations were clustered into two lineages (Japanese and Chinese), which was consistent with their geographical distribution. Approximate Bayesian computations (ABC) model indicated that the current two geographical lineages diverged from a common ancestral lineage and that their divergence time was about 0.417 ~ 0.139 million years ago (Mya). Geographical isolation, climate change in the Quaternary, and human disturbance played important roles in genetic variation and distribution patterns of Cryptomeria in East Asia. Our results shed light on the speciation processes of Cryptomeria and provide a reference for the conservation of this species.