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Genetic Architecture Reconciles Linkage and Association Studies of Complex Traits

This (zipped) folder contains 3 sub-folders: #********************************************************************************************************** The "bin" folder contains fuctions and gentic maps needed for analyes bin \     predLink.R - function to predict linkage      sibREML_v0.1.1.R  - function to run SibREML     sim-sib-array.R   - script to simulate sib-pairs from parental haplotypes     Summarised_genetic_map_bcf.txt - genetic map per 0.5-cM long segments, based on map from bcftools          (BCFtools: https://samtools.github.io/bcftools/bcftools.html)     Summarised_genetic_map_OMNI.txt - genetic map per 0.5-cM long segments, based on OMNI map          (https://github.com/joepickrell/1000-genomes-genetic-maps/tree/master/interpolated_OMNI) #**********************************************************************************************************   #********************************************************************************************************** The "SIM" folder contains the simulation pipeline (scripts 01-15)  as well as IBD sharing and simulated phenotypes for Simulated sib-pairs. SIM \     01_sim-sib-array.sh          *pre-run*     02_bed_recode_bcf_map.sh     *pre-run*     03_make_merlin.R             *pre-run*     04_error_merlin.sh           *pre-run*     05_merlin_IBD.sh             *pre-run*     06_sample_causal_snps.R      *pre-run*     07_simulate_pheno.sh         *pre-run*     08_bhat_gwas.R               *can be run using provided data*      09_Linkage_VH.R              *can be run using provided data*       10_predLink.R                *can be run using provided data*     11_phi_hat.R                 *can be run using provided data*     12_IBD_Mb.R                  *can be run using provided data*     13_IBD_cM_recombrate_stratified.R       *can be run using provided data*     14_SibREML.R                 *can be run using provided data*     15_SibREML_stratified_Q4.R   *can be run using provided data*     causal_snps \                *provided causal SNPs*     IBD_results \                *provided IBD-probabilities for 1000 simulated sib-pairs*     Linkage_VH_results \      pheno \                      *provided simulated phenotypes (h2=1) for 8 genetic architectures*     Phi_hat_results.txt     predicted \     README     SibREML_results.txt     SibREML_stratified_Q4.txt The data can be used to run Linkage analysis, predict linkage, estimate phi_hat,  as well as estimate non-stratified and recombination rate stratified sib-heritability (h2_FS and c). The README is provided within the folder.  #**********************************************************************************************************   #********************************************************************************************************** The "HT_BMI" folder contains data and scripts to predict linkage and estimate phi_hat for height and BMI. HT_BMI \     01_predLink_HT_BMI.R     02_phi_hat_HT_BMI.R     gws_sumstats \              *provided summary GWAS summary statistics to predict linkage for height and BMI*     Linkage_results \           *provided linkage meta-analysis results for height and BMI from this study*     Phi_hat_results_HT_BMI.txt     PREDLINK_bmi.txt     PREDLINK_height.txt     README The README is provided within the folder. #**********************************************************************************************************

opencc-zeroDec 2023View details →

Data from: harnessing the power of regional baselines for broad-scale genetic stock identification: a multistage, integrated, and cost-effective approach

In mixed-stock fishery analyses, genetic stock identification (GSI) estimates the contribution of each population to a mixture and is typically conducted at a regional scale using genetic baselines specific to the stocks expected in that region. Often these regional baselines cannot be combined to produce broader geographical baselines due to non-overlapping populations and genetic markers. In cases where the mixture contains stocks spanning across a wide area, a broad-scale baseline is created, but often at the cost of resolution. Here, we introduce a new GSI method to harness the resolution capabilities of baselines developed for regional applications in the analysis of mixtures containing individuals from a broad geographic range. This method employs a multistage framework that allows disparate baselines to be used in a single integrated process that produces estimates along with the propagated errors from each stage. All individuals in the mixture sample are required to be genotyped for all genetic markers in the baselines used by this model, but the baselines do not require overlap in genetic markers or populations representing the broad-scale or regional baselines. We demonstrate our integrated multistage GSI model using a synthesized data set made up of Chinook salmon, Oncorhynchus tshawytscha, from the North Bering Sea of Alaska. The data set is designed to be run using R package, Ms.GSI, and it does not represent the composition of the real fishery. The results show an improved accuracy for estimates using an integrated multistage framework, compared to the conventional framework of using separate hierarchical steps. The integrated multistage framework allows GSI of a wide geographic area without first developing a large scale, high-resolution genetic baseline or dividing a mixture sample into smaller regions beforehand. This approach is more cost-effective than updating range-wide baselines with all regionally important markers.

A lack of genetic diversity and minimal adaptive evolutionary divergence in introduced Mysis shrimp after 50 years

The successes of introduced populations in novel habitats often provide powerful examples of evolution and adaptation. In the 1950's, opossum shrimp (Mysis diluviana) individuals from Clearwater Lake in Minnesota, USA were transported and introduced to Twin Lakes in Colorado, USA by fisheries managers to supplement food sources for trout. Shrimp were subsequently introduced from Twin Lakes into numerous lakes throughout Colorado. Because managers kept detailed records of the timing of the introductions, we had the opportunity to test for evolutionary divergence within a known time interval. Here, we used reduced representation genomic data to investigate patterns of genetic diversity and test for genetic divergence between populations and for evidence of adaptive evolution within the introduced populations in Colorado. We found overall very low levels of genetic diversity across all populations, with evidence for some genetic divergence between the Minnesota source population and the introduced populations in Colorado. There was also little differentiation among the Colorado populations, consistent with the known provenance of a single founding population, with the exception of the population from Gross Reservoir, Colorado. Demographic modeling suggests that the population in Gross Reservoir is of hybrid origin, with an earlier founding population from an unknown source being later supplemented from another population. Despite the overall low genetic diversity we observed, FST outlier and environmental association analyses identified multiple loci exhibiting signatures of selection and adaptive variation related to elevation and lake depth. The success of introduced species is thought to be limited by genetic variation, but our results imply that populations with limited genetic variation can become established in a wide range of novel environments.

opencc-by-4.0Dec 2021View details →

Figure 3 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 3. – Projection of Procrustes coordinates and scores of canonical variate on Aphanius fasciatus shape analysis (A) and comparative transformation grids (B). LM: Mellah lagoon, M: Mellah marsh, BZ: Lagoon of Bizerte, LA: Ayata Lake.

opencc-by-4.0Dec 2021View details →

Figure 2 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 2. – Landmarks distribution on fish body of Aphanius fasciatus. 1: Eye position, 2: Dorsal opercular limit, 3: Beginning of dorsal fin, 4: End of dorsal fin, 5: Dorsal limit of caudal peduncle, 6: Median limit of caudal peduncle, 7: Ventral limit of caudal peduncle, 8: End of anal fin, 9: Beginning of anal fin, 10: Pelvic fin insertion, 11: Ventral opercula limit, 12: Dorsal limit of pectoral fin, 13: Ventral limit of pectoral fin, 14: Mouth.

opencc-by-4.0Dec 2021View details →

Figure 1 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats

Figure 1. – Map of the west Mediterranean basin with North African sample sites. 1: Mellah lagoon (LM), 2: Mellah marsh (M), 3: Lagoon of Bizerte (BZ), 4: Ayata Lake (LA).

opencc-by-4.0Dec 2020View details →

Figure 2 in Extant because important or important because extant? On the scientific importance and conservation of a genetically pure Sicilian population of the threatened Salmo cettii Rafinesque, 1810

Figure 2. – Individual Salmo cettii from Tellesimo Stream (for the morphological and phenotypical characteristics of Sicilian trout see: Duchi, 1988; Fruciano et al., 2014; Duchi, 2018).

Naked mole rats have distinctive cardiometabolic and genetic adaptations to their underground low-oxygen lifestyles (non-genetic data)

The naked mole-rat Heterocephalus glaber is a eusocial mammal exhibiting extreme longevity (37-year lifespan), extraordinary resistance to hypoxia and absence of cardiovascular disease. To identify the mechanisms behind these exceptional traits, metabolomics and RNAseq of cardiac tissue from naked mole-rats were compared to other African mole-rat genera. We identified metabolic and genetic adaptations unique to naked mole-rats including elevated glycogen, thus enabling glycolytic ATP generation during cardiac ischemia. Elevated normoxic expression of HIF-1α was observed while downstream hypoxia-responsive genes were down-regulated, suggesting adaptation to low-oxygen environments. Naked mole-rat hearts showed reduced succinate build-up during ischemia and negligible tissue damage following ischemia-reperfusion injury. These adaptive evolutionary traits reflect a unique hypoxic and eusocial lifestyle that collectively may contribute to their longevity and health span.

High-density genetic linkage mapping in Sitka spruce advances the integration of genomic resources in conifers

In species with large and complex genomes such as conifers, dense linkage maps are a useful for supporting genome assembly and laying the genomic groundwork at the structural, populational and functional levels. However, most of the 600+ extant conifer species still lack extensive genotyping resources, which hampers the development of high-density linkage maps. In this study, we developed a linkage map relying on 21,570 SNP makers in Sitka spruce (Picea sitchensis [Bong.] Carr.), a long-lived conifer from western North America that is widely planted for productive forestry in the British Isles. We used a single-step mapping approach to efficiently combine RAD-Seq and genotyping array SNP data for 528 individuals from two full-sib families. As expected for spruce taxa, the saturated map contained 12 linkages groups with a total length of 2,142 cM. The positioning of 5,414 unique gene coding sequences allowed us to compare our map with that of other Pinaceae species, which provided evidence for high levels of synteny and gene order conservation in this family. We then developed an integrated map for P. sitchensis and P. glauca based on 27,052 makers and 11,609 gene sequences. Altogether, these two linkage maps, the accompanying catalog of 286,159 SNPs and the genotyping chip developed herein opens new perspectives for a variety of fundamental and more applied research objectives, such as for the improvement of spruce genome assemblies, or for marker-assisted sustainable management of genetic resources in Sitka spruce and related species.

Main model fits and substitution rate predictions for: A quantitative genetic model of background selection in humans

Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This can be thought of as a "linked selection signal" that reflects the impact of selection varying according to the placement of functional regions and recombination rates along the genome. Previous work has shown that negative selection against the steady influx of new deleterious mutations into conserved regions is the predominant mode of selection in humans. However, the theoretic model that underpins these results, classic Background Selection theory, is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of the linked selection, which models the effects of weak draft created according to how polygenic additive fitness variance is distributed along the genome. We use a recent model that jointly predicts the equilibrium fitness variance and substitution rates due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three human populations. While our model can accommodate weaker selection, we initially find evidence across three human populations of very strong selection against deleterious mutations consistent with previous work. However, the corollary predicted substitution rates for conserved regions are unreasonably low, and in disagreement with observed rates. We hypothesize this could be due to selected sites experiencing a further diminished population size due to selective interference. When we account for this in our method, we find evidence of weakly deleterious mutations in conserved regions which brings the predicted substitution rate into agreement with observations. However, these models lead to implausibly large mutation rate estimates. Overall, while our model of the genomic linked selection signal brings us a step towards uniting population and quantitative genetic selection models with the substitution process, our work suggests considerable uncertainty remains about the processes generating fitness variance in humans.

opencc-zeroFeb 2024View details →

Rare, long-distance dispersal underpins genetic connectivity in the pink sea fan, Eunicella verrucosa

Characterising patterns of genetic connectivity in marine species is of critical importance given the anthropogenic pressures placed on the marine environment. For sessile species, population connectivity can be shaped by many processes, such as pelagic larval duration, oceanographic boundaries, and currents. This study combines restriction-site associated DNA sequencing (RADseq) and passive particle dispersal modelling to delineate patterns of population connectivity in the pink sea fan, Eunicella verrucosa, a temperate octocoral. Individuals were sampled from 20 sites covering most of the species' northeast Atlantic range, and a site in the northwest Mediterranean Sea to inform on connectivity across the Atlantic-Mediterranean transition. Using 7,510 neutral SNPs, a geographic cline of genetic clusters was detected, partitioning into: Ireland, Britain, France, Spain (Atlantic), and Portugal and Spain (Mediterranean). Evidence of significant inbreeding was detected at all sites, a finding not detected in a previous study of this species based on microsatellite loci. Genetic connectivity was characterised by an isolation by distance pattern (IBD) (r2 = 0.78, p<0.001), which persisted across the Mediterranean-Atlantic boundary. In contrast, exploration of ancestral population assignment using the program ADMIXTURE indicated genetic partitioning across the Bay of Biscay, which we suggest represents a natural break in the species' range, possibly linked to a lack of suitable habitat. As the pelagic larval duration (PLD) is unknown, passive particle dispersal simulations were run for 14 and 21 days. For both modelled PLDs, inter-annual variations in particle trajectories suggested that in a long-lived, sessile species, range-wide IBD is driven by rare, longer dispersal events which act to maintain gene flow. These results suggest that oceanographic patterns may facilitate range-wide stepping-stone genetic connectivity in E. verrucosa, and highlight that both oceanography and natural breaks in a species' range should be considered in the designation of ecologically coherent MPA networks.

opencc-zeroMar 2024View details →

Data from: Dominance reversals and the maintenance of genetic variation

Beneficial reversals of dominance reduce the costs of genetic trade-offs and can enable selection to maintain genetic variation for fitness. Beneficial dominance reversals are characterized by the beneficial allele for a given context (e.g. habitat, developmental stage, trait, or sex) being dominant in that context but recessive where deleterious. This context-dependence at least partially mitigates the fitness consequence of heterozygotes carrying one non-beneficial allele for their context and can result in balancing selection that maintains alternative alleles. Dominance reversals are theoretically plausible and are supported by mounting empirical evidence. Here we highlight the importance of beneficial dominance reversals as a mechanism for the mitigation of genetic conflict and review the theory and empirical evidence for them. We identify some areas in need of further research and development and outline three methods (dominance ordination, allele-specific expression, and allele-specific ATAC-Seq) that could facilitate the identification of antagonistic genetic variation. There is ample scope for the development of new empirical methods as well as reanalysis of existing data through the lens of dominance reversals. A greater focus on this topic will expand our understanding of the mechanisms that resolve genetic conflict and whether they maintain genetic variation.

opencc-by-4.0Mar 2024View details →

Genetic architecture of immune cell DNA methylation in the rhesus macaque

Complete model outputs from rhesus macaque (Macaca mulatta) whole blood meQTL and eQTL analyses in article, "Genetic architecture of immune cell DNA methylation in the rhesus macaque".  cis meQTL model output (SNP-CpG associations):  <ol> <li>IMAGE_573_meqtl_model_res_wPVE.txt:  <ul> <li>Model results from IMAGE meQTL mapping including all genome, chromatin state annotations, and PVE estimates</li> </ul> </li> <li>pqlseq_allimagesnps_res_converged_wpve.txt: <ul> <li>Model results from PQLseq meQTL mapping including PVE estimates </li> </ul> </li> </ol> cis eQTL model output (SNP-gene associations):  <ol> <li>eqtl_res_sva5_gemma_172samples_qvalue.txt:  <ul> <li>Model results from GEMMA eQTL mapping </li> </ul> </li> </ol>

opencc-by-4.0Jan 2024View details →

Insights into the genetic diversity of Listeria monocytogenes from bivalves

Fasta files to 30 genomes described in a publication

Fig. 4 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene

Fig. 4. Distribution of pairwise values of genetic distances amongst species with allopatric areas: 1 — for the Western Palearctic genus Sylvaemus; 2 — for the Eastern Palearctic genera Apodemus and Alsomys; 3 — for the Palearctic Muridae as a whole, including species of genera Micromys and Mus.

Fig. 3 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene

Fig. 3. Distribution of pairwise intraspecies genetic distances within: 1 — the Western Palearctic genus Sylvaemus; 2 — the Eastern Palearctic genera Apodemus and Alsomys; 3 — in general for the Palearctic Muridae, including Micromys and Mus.

Fig. 2 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene

Fig. 2. Phenogram of genetic distances (Tamura, Nei, 1993) calculated from cytb sequences amongst representatives of the genera/subgenera Alsomys, Apodemus and genera Micromys, Mus, Rattus, constructed using the UPGMA algorithm. Representatives of the Arvicolidae and Cricetidae as well as S. s. dichrurus, S. flavicollis, S. (K.) mystacinus and S. (K.) epimelas were taken as outgroups.

Fig. 5 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene

Fig. 5. Distribution of pairwise genetic distances amongst taxa: 1 — Western Palearctic genus Sylvaemus, 2 — Eastern Palearctic genera Apodemus, Alsomys, 3 — Western Palearctic genus Sylvaemus and contrarily Eastern Palearctic genera Apodemus, Alsomys.

Fig. 1 in Taxonomic Hierarchy And Evolutionary Scenario Of The Genus Group Apodemus S. L. (Muridae) Of The Palaearctic Based On Genetic Differentiation In The Gene

Fig. 1. Phenogram of genetic distances calculated from cytb sequences amongst representatives of the genera Sylvaemus, Rattus, constructed using the UPGMA algorithm, as mentioned above. Microtus arvalis (Arvicolidae) and Cricetus cricetus (Cricetidae) are used as outgroups.