Genetic diversity and population structure

The paper uses genomic data from Mojave desert tortoises to infer demographic parameters in a spatially explicit ecological model, showing a simple statistical method can estimate population density and migration distance within 10% accuracy.

The paper examines how Pleistocene glaciations shaped genomic and karyotypic diversity in Atlantic salmon through trans-Atlantic divergence, admixture, and adaptive evolution.

The paper uses whole-genome sequences of spotted owls to show long-term population declines and isolation-by-distance patterns in California, with no genetic differentiation between northern subspecies.

The paper uses microsatellite markers to analyze genetic diversity and structure in two Corso-Sardinian plant species, finding high genetic variation and differentiation, supporting their classification as separate species.

POPSICLE improves genotype-phenotype predictions by integrating population genetics and GWAS methods using whole genome sequencing data.

The paper assesses genetic diversity in common carp stocks using RAPD markers and finds significant polymorphism and genetic differentiation among populations.

The paper uses genome-wide sequencing to show that Canada lynx populations exhibit neutral genetic differentiation and cryptic epigenetic plasticity, particularly in Newfoundland, which may explain island dwarfism.

The paper introduces Quetzal, a C++ library for implementing coalescence-based environmental demogenetic models using Approximate Bayesian Computation.

The paper derives three new properties of coalescent gene trees to characterize the present-day impacts of historical events.

The paper introduces a graphical model method for inferring population relationships from DNA sequences and validates it on simulated data.

BITE, an R package, wraps SNP quality control, Kolmogorov-Smirnov-checked representative subsampling, color-consistent ancestry plots, and bootstrap-supported TreeMix gene-flow trees for biodiversity genomics.

The paper analyzes coat color alleles and mtDNA haplotypes in Russian cats to study population genetics and phylogeography, finding genetic homogeneity and unique mitotypes.

The paper analyzes genome-wide diversity of Hymenoscyphus fraxineus in Asia and Europe, finding a bottleneck in Europe and suggesting Russia as the likely origin of the introduced population.

The paper develops methods to infer generalized coalescent models and quantify uncertainty in their parameters using site-frequency spectra from Atlantic cod mitochondrial data.

HaploDistScan detects genomic regions of deep divergence using haplotype distances without prior population information, identifying balancing selection in ruff and Darwin's finch data.