Genetic diversity and population structure

The paper develops ddgRADer, a webtool to optimize ddRADseq experimental design for population genomics by predicting sequencing efficiency and recommending enzyme pairs.

This study uses genomic data to show that brackish water perch in the Baltic Sea have distinct genetic clusters and that salinity tolerance genes are under selection, reflecting colonization history and local adaptation.

This study uses whole genome resequencing to analyze population structure and environmental adaptation in Bombus vosnesenskii, finding weak signatures of population structure and local adaptation.

The paper reanalyzes hybridization frequency between European smooth and palmate newts using SNPs, finding low hybridization rates and suggesting microsatellites overestimate introgression.

This paper uses whole-genome sequencing of kakapo to analyze genetic diversity and breeding values, showing how conservation management has maintained genetic diversity and providing tools for future recovery efforts.

The paper compares genomic consequences of reintroduction and natural recolonisation in Svalbard reindeer, finding natural recolonisation leads to greater genetic issues than reintroduction.

The paper introduces Bayesian methods to test for random mating in autopolyploids, improving upon frequentist approaches by handling small samples and genotype uncertainty.

This study evaluates the suitability of DNA from shed skin for genotyping-by-sequencing in reptiles, finding it viable with deeper sequencing and accounting for GC content.

This study examines the genetic diversity and demographic history of leopard seals, finding moderate diversity and evidence of population expansion linked to sea ice changes.

The paper analyzes pollen contamination and mating structure in maritime pine seed orchards using SNP markers, finding high variability in contamination rates and self-fertilization.

The paper presents genome assemblies and genomic scans of adaptive variation in two endangered rosewood species, predicting their vulnerability to climate change and proposing species-specific conservation strategies.

poolHelper simulates Pool-Seq data to optimize study design by evaluating parameter combinations for accurate allele frequency estimation with minimal sequencing effort.

The paper investigates the demographic and phylogeographic dynamics of rodent communities in low latitude Asia, finding asynchronous responses to past climate changes.

The paper analyzes the genomes of Sicilian wolves to reveal their complex history of isolation and admixture with ancient dogs, showing admixture with European dog breeds and signs of inbreeding.

This paper introduces apoh, a software tool to estimate admixture pedigrees of recent hybrids using interancestry heterozygosity patterns from SNP data, validated on human and animal datasets.

This study presents whole-genome data from 233 primate species, revealing patterns of genetic diversity, mutation rates, and recurrent missense mutations across primate clades.

The paper examines genomic variation in Atlantic horse mackerel to identify adaptive loci and environmental drivers of local adaptation, finding chromosomal inversions and gene expression differences related to environmental factors.

The paper evaluates SNP and SSR marker panels for detecting European introgression in North American Atlantic salmon and develops a machine learning tool for admixture estimation.

The paper introduces a Bayesian optimization pipeline for demographic inference, showing it outperforms genetic algorithms for larger population counts.

The paper investigates genetic structure and dispersal patterns of invasive earthworms in Minnesota, finding multiple introductions but not from current bait dumping.

This study finds significant genetic population structure in maize weevils from southern Mexico using genome-wide SNP data, suggesting local factors shape genetic differentiation.

The paper presents new mitochondrial genome sequences of sun bears, revealing a deep split between Indochinese and Sundaic lineages and suggesting recent demographic processes reduced mtDNA variation.

GBScleanR improves genotype accuracy by incorporating marker-specific error rates into a hidden Markov model for reduced-representation sequencing data.

The paper expands the stdpopsim species catalog and improves genome simulations by adding non-crossover recombination and species-specific annotations, making simulations more realistic for non-model organisms.

The paper investigates factors shaping runs of homozygosity in red deer, finding population history has the greatest impact, with selection playing a minor role in some regions.

The paper uses genome-wide data to infer isolation-by-distance and population size history in coho salmon, identifying genes associated with latitude and potential osmoregulation roles.

The paper examines how demographic history affects genomic health in three ungulates by analyzing inbreeding, constrained elements, and mutational load.

The paper introduces a fast algorithm for jointly inferring FST parameters and genetic structure trees from allele count data, applied to human populations and individuals.

The paper integrates top-down and bottom-up approaches to study speciation in a monkeyflower hybrid zone, finding that reproductive isolation involves widespread genomic barriers and polygenic traits.