Genetic diversity and population structure

The paper uses ddRAD-seq to analyze genetic divergence and population structure in two Apodemus species in northern Poland, finding clear species differentiation and limited population structure within A. flavicollis.

This study identifies a chromosome inversion and sex-determining region in chum salmon by analyzing linkage disequilibrium patterns, showing the importance of considering LD in genetic analyses.

The paper investigates genetic diversity and demographic history of the Raso lark using RAD-seq data and a reference genome, revealing ancient population expansions and neo-sex chromosomes.

FGTpartitioner rapidly and accurately partitions large genome alignments into ancestry blocks without requiring haplotype phasing, enabling efficient phylogenomic analysis of non-model organisms.

The paper uses genetic data to reveal population structure and recent decline in leopards across the Indian subcontinent, showing a 75-90% population decline over the past 120-200 years.

This study uses RAD sequencing to distinguish sympatric coregonine fish forms in Lake Superior, revealing high genetic differentiation and limited hybrid success.

The paper presents draft genome assemblies of Brassica cretica and finds no genetic support for subspecies classification.

The paper compares pedigree, genetic, and genomic methods for estimating relatedness in two endangered birds to improve pairing decisions in conservation breeding programs.

The paper develops and validates ten microsatellite markers for the endangered cactus species Coleocephalocereus purpureus using whole genome shotgun sequencing.

This study compares genetic diversity between wild and laboratory zebrafish strains using RAD-seq, finding higher diversity in wild populations and distinct patterns in different regions.

The paper introduces a network-based method for analyzing population structure in genomic data, demonstrating its application in Arabidopsis thaliana and human populations.

The paper reports the discovery of Drosophila melanogaster in African wilderness areas and provides genomic insights into its geographic expansion history.

The paper develops a simulation framework to study the dynamics of genomic islands of divergence under various population genetic scenarios and identifies key factors influencing their formation.

The paper presents unbiased estimators for linkage disequilibrium statistics from unphased data, improving accuracy across populations and LD scales.

The paper uses whole genome sequencing of ten Phaeodactylum tricornutum accessions to reveal genetic polymorphism, structure, and functional diversity across geographic and temporal scales.

The paper introduces a low-cost, highly multiplexed RADseq library preparation method called 2RAD/3RAD, which improves efficiency and compatibility with sequencing platforms.

The paper examines how urbanization affects gene flow and genetic diversity in pumas across rural and urban landscapes in Colorado, finding reduced gene flow in urban areas but no change in genetic diversity.

The paper identifies 492 SNPs associated with climate variables in loblolly pine, showing adaptation is driven by allele frequency shifts with moderate to small effects.

The paper develops 24 polymorphic microsatellites for the hoverfly Eupeodes corollae and finds weak genetic differentiation across four populations in China, indicating high gene flow.

Stacks 2 improves RADseq-based population genomics by using paired-end sequencing to assemble and genotype de novo datasets with high accuracy.

This paper extends Hardy-Weinberg equilibrium tests to account for population structure, introducing a new test called structural HWE (sHWE) that automatically selects tuning parameters and identifies structural models.

The paper uses whole genome sequencing of a Dryas monkey to show its evolutionary relationship with vervets and suggests the Congo River's dynamic history and the species' genetic resilience.

This paper introduces a Bayesian method called BESTT for inferring population size changes using Tajima’s coalescent, showing it is computationally efficient and accurate for both simulated and human data.

The paper standardizes and validates a cross-species microsatellite panel for individual identification of dholes, revealing genetic subpopulations and population decline.

This study uses comparative genomics to analyze genetic diversity and introgression in dwarf lemurs, finding low diversity and signs of ancient admixture linked to hibernation-related genes.

The paper uses genomic data to show that Amazonian manatees have colonized the Guianas coastline and hybridized with West Indian manatees, supporting the need for a special conservation area.

This study uses genetic analyses to assess strain reliability in Cannabis sativa, finding genetic inconsistencies within strains and no clear genetic distinction between Sativa, Indica, or Hybrid types.

The paper identifies a supergene linked to migration in Atlantic cod, showing reduced genetic diversity and population collapse due to overfishing.

The paper analyzes the mitochondrial DNA of Sicilian wolf specimens to determine their genetic identity and relationship to other wolf populations.

The paper uses coalescent theory to analyze migration network motifs and their impact on genetic diversity and differentiation in small population networks.