Genetic diversity and population structure

slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes

The paper introduces slendr, an R package for simulating spatio-temporal population genomic data, and demonstrates its features through example workflows.

Applying genomic approaches to identify historic population declines in European forest bats

This study uses genomic data to identify historic population declines in European forest bats, finding significant declines linked to habitat loss and human activity.

Chloroplast genome-based genetic resources for Japan's threatened subalpine forests via genome skimming

The paper develops chloroplast genome-based genetic resources for 12 subalpine tree and shrub species using genome skimming, identifying SNPs and SSRs for phylogeographic and conservation studies.

Reversing the decline of threatened koala (Phascolarctos cinereus) populations in New South Wales: Using genomics to define meaningful conservation goals

The paper uses genomics to assess genetic diversity in koalas and highlights the need for conservation strategies based on threat severity rather than genetic value.

Harnessing the power of regional baselines for broad-scale genetic stock identification: A multistage, integrated, and cost-effective approach

This paper introduces a multistage GSI method that integrates regional baselines to improve broad-scale stock identification without requiring overlapping markers or populations.

Inferring multi-locus selection in admixed populations

The paper develops a method to identify and quantify the effects of multiple linked selected sites in admixed populations, finding that linkage impacts selection estimates.

Including the Invisible Fraction in Whole Population Studies: a Guide to the Genetic Sampling of Unhatched Bird Eggs

This paper describes methods to collect and extract DNA from unhatched bird eggs to study early embryo mortality and its genetic factors.

A genome-wide segmentation approach for the detection of selection footprints

The paper introduces a genome-wide segmentation method to detect selection footprints using FST, demonstrating its efficiency and accuracy in animal and human population genetics.

Environmental drivers behind the genetic differentiation in mountain chickadees (Poecile gambeli)

This study identifies environmental drivers of genetic differentiation in mountain chickadees using ddRAD data and environmental variables.

GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples

GGoutlieR identifies and visualizes geo-genetic outliers in biological samples to improve landscape genomics analyses.

Development of genomic resources for cattails (Typha), a globally important macrophyte genus

The paper develops genomic resources for Typha, a wetland plant genus, by sequencing 140 samples and identifying SNPs and plastome sequences to study genetic diversity and hybridization.

Genomic diversity of wild and cultured Yesso scallop Mizuhopecten yessoensis from Japan and Canada

This study compares genetic diversity between wild Japanese and cultured Canadian Yesso scallops using ddRAD-sequencing, finding reduced polymorphism and genetic differentiation in cultured populations.

Conservation implications of diverse demographic histories: the case study of green peafowl (Pavo muticus, Linnaeus 1766)

The paper analyzes the genetic structure and demographic history of green peafowls using whole-genome sequencing data to identify distinct populations and inform conservation strategies.

disperseNN2: a neural network for estimating dispersal distance from georeferenced polymorphism data

disperseNN2 estimates dispersal distance from georeferenced polymorphism data, outperforming existing methods by 33-48% in error reduction.

Population genomic analysis reveals genetic structure and thermal-tolerant genotypes in remnant Tasmanian giant kelp populations

The paper analyzes population genomic data from Tasmanian giant kelp to identify genetic structure and loci associated with thermal tolerance.

Hidden in the sand: phylogenomics unravel an unexpected evolutionary history on the desert-adapted vipers of the genus Cerastes

This study uses genome-wide data to reveal an unexpected evolutionary history of Cerastes vipers, showing introgression and challenging previous mitochondrial and morphological classifications.

A simple method to genetically differentiate invasive F1 Typha hybrids (T. x glauca) and advanced-generation/backcrossed hybrids from parent species (T. latifolia and T. angustifolia) in eastern Canada and northeastern USA

The paper presents five genetic markers to distinguish invasive Typha hybrids from parent species and advanced-generation hybrids in eastern Canada and northeastern USA.

The ghost of selection past: evolution and conservation relevance of the kakapo color polymorphism

The paper uses genomic and phenotypic data to study the evolution of kakapo color polymorphism, finding genetic variants and evidence of balancing selection.

Optimising ddRAD sequencing for population genomic studies with ddgRADer

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

Genetic diversity of the Atacama Desert shrub Huidobria chilensis in the context of geography and climate

The paper analyzes genetic diversity of Huidobria chilensis in the Atacama Desert using GBS data, revealing geographic genetic clusters and the influence of topography and hydrology on population structure.

High standing diversity masks extreme genetic erosion in a declining snake.

The paper shows that high average heterozygosity in adders may mask severe genetic erosion due to recent bottlenecks, suggesting whole-genome sequencing is better for assessing genetic risk.

Mitochondrial genome analyses uncover intriguing population structure across the invasive trajectory of an iconic invader

The paper analyzes mitochondrial genomes of cane toads across their invasion trajectory, revealing genetic bottlenecks and previously underestimated diversity in introduced populations.

ONeSAMP 3.0: Effective Population Size via SNP Data for One Population Sample

ONeSAMP 3.0 estimates genetic effective population size (Ne) from SNP data of a single population using Approximate Bayesian Computation and local linear regression, showing robustness and accuracy in simulated and empirical data.

Genomic differentiation among European perch in the western Baltic Sea reflects colonization history and local adaptation

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.

Whole genome analyses reveal weak signatures of population structure and environmentally associated local adaptation in an important North American pollinator, the bumble bee Bombus vosnesenskii

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.

Inconsistent estimates of hybridization frequency in newts revealed by SNPs and microsatellites

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

Species-wide genomics of kakapo provides transformational tools to accelerate recovery

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.

Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer

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

Bayesian Tests for Random Mating in Polyploids

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

Inbreeding or outbreeding depression? How to manage an endangered and locally adapted population of red grouse Lagopus scotica

This study shows that Irish red grouse have higher inbreeding and genetic divergence from British populations, suggesting local adaptation and potential risks from translocations.