Genetic diversity and population structure

GENOMALICIOUS provides an R package with functions for population genomic analyses, simplifying data manipulation and visualization across different tools and environments.

The paper investigates genetic and epigenetic variation in two Erodium species, finding no genetic structure but significant epigenetic variation, particularly in DNA methylation patterns.

This paper introduces donni, a machine learning-based method for demographic history inference that is faster and more efficient than dadi while maintaining similar accuracy.

The paper examines adaptive genetic variation in Lactuca serriola along a precipitation gradient, identifying candidate genes under selection and predicting adaptive shifts in response to climate change.

The paper develops a universal set of microsatellite loci for baleen whale individual identification and parentage analysis, showing its utility across four species.

The paper estimates effective (Ne) and census (Nc) population sizes and densities for invasive riverine meta-populations of Silurus glanis using genetic and demographic data combined with simulation and statistical methods.

The paper uses a new long-read genome assembly to improve population history and recombination landscape analysis in Chironomus riparius, revealing divergence timing and TE impacts.

The paper uses genome-wide data to show that mega-landslides on Tenerife caused cyclical range fragmentation and secondary contact in weevils, mediated by Quaternary climate oscillations.

The paper assesses how genetic mountain pine beetle populations from outbreaks alter the genetic structure of established populations over time.

This study tracks the phylogeographic dynamics and genetic diversity of invasive golden apple snails in Taiwan to inform management strategies.

This study uses ddRADseq and climate modeling to analyze the evolutionary patterns of Rubus ser. Glandulosi, revealing geographic parthenogenesis driven by secondary contact and complex reticulate evolution involving six ancestral species.

The paper assesses genetic diversity and connectivity of three goatfish species in the Mediterranean Sea using mitochondrial DNA markers.

autoStreamTree fits genomic variation to geospatial networks, demonstrating its use in analyzing genetic variation in Speckled Dace.

The paper uses ancient mitogenomes to show that Southern Hemisphere mergansers may share a common ancestor with Northern Hemisphere mergansers, suggesting a single dispersal event.

The paper analyzes SNP data from Thuja plicata in UK woodlands to assess genetic diversity and effective population size under CCF management.

The paper develops a method to infer dispersal parameters and effective population density in spatially heterogeneous populations using shared haplotype segments.

The paper examines genetic structure in Cannabis sativa across nine collections, finding inconsistent clustering and greater diversity in modern cultivars compared to landraces.

The paper examines the genomic structure of a clownfish hybrid zone, identifying first-generation hybrids and early backcrosses, and suggests adaptive introgression from one parent species.

This study reveals genetic admixture, population decline, and wide sourcing of white-bellied pangolins in West Africa, highlighting conservation concerns and the need for multi-locus trade tracking.

The paper identifies structural variants, SNPs, and indels in Atlantic salmon populations to explore their role in local adaptation.

The paper uses genotyping-by-sequencing to analyze genetic diversity and population structure in harbour seals across the eastern Pacific and western Atlantic, finding elevated diversity in the Pacific and subspecies differentiation.

The paper identifies Helicoverpa armigera-H. zea hybrids using genome admixture analysis and highlights the importance of reference datasets for accurate predictions.

The paper uses genomic analyses to study demographic changes in deer populations due to climate and human pressures, finding evidence of population decline and recovery.

The paper describes relatedness coefficients for gene triplets and quartets, focusing on statistical methods and challenges in estimation using genetic marker data.

This study uses SNP analysis to show that white clover populations in Brazil have high within-population genetic diversity, with some populations showing admixture with cultivars and others having distinct genetic backgrounds, confirming its naturalization.

The paper investigates introgressive hybridization in nine-spined sticklebacks, finding that selection on introgressed variation varies across genomic regions and that adaptive introgression occurs in response to environmental conditions.

This study evaluates genomic offset methods for predicting maladaptation to future environments across simulated datasets, finding performance depends on local adaptation and environmental complexity.

This paper develops a method to accurately compute genetic statistics from low-depth sequencing data, improving the reliability of population tree inference.

The paper investigates gene flow between mainland and island vampire bat populations in Trinidad, finding genetic distinctness and male-biased gene flow, with implications for rabies virus spread.

This study analyzes genetic diversity and population dynamics of feral horses in the Western US using microsatellite markers, finding variation influenced by management practices and geographic proximity.