Genetic diversity and population structure

This study examines how sample size affects demographic parameter estimates in bird populations using SNP data, finding that effective population size is underestimated at low sample sizes.

This study examines how spatial, environmental, and ploidy factors influence genomic diversity and resilience in the grass species Themeda triandra.

The paper uses genetic data to define conservation units in speckled dace, identifying four putative ESUs and highlighting hybridization and relic populations in the Death Valley ecosystem.

The paper develops a 3K SNP array for Araucaria angustifolia using RNA-seq and RAD-seq data, revealing genetic diversity and structure across 15 populations and improving upon microsatellite-based assessments.

This study evaluates eight DNA extraction protocols for Hypostomus commersoni, finding that ocular tissue with extended lysis buffer incubation and high Proteinase K concentration yields the best results.

This study identifies diverse recolonization pathways and northern glacial refugia shaping genetic diversity in Arctic marine forests using genetic data from 109 seaweed species.

The paper uses genetic analyses to determine the natal origins of non-native Chinook salmon caught at-sea and in estuaries in South America.

This study shows that copy number variants (CNVs) better reveal genotype-temperature associations than SNPs in American lobster populations.

ADMIXPIPE processes large non-model organism datasets to infer population structure and optimal K-values for ADMIXTURE analysis.

This study compares the population genomics of two invasive mosquitoes in the Indo-Pacific to understand their invasion pathways and dispersal ecology.

The paper develops a GT-seq panel for walleye and outlines a workflow for creating efficient amplicon panels in non-model organisms.

The paper introduces kNN-based genome-scan methods for detecting selection and introgression, showing strong performance across various parameters.

This study uses population genomics to identify the Indochinese peninsula as the main source of brown planthopper migration into temperate China, challenging the previous role of the Philippines.

This study identifies coding loci and a large inversion associated with local adaptation in Pinus sylvestris using landscape genomics and targeted sequencing.

The paper uses RNA sequencing to analyze genetic variation in walleye from Lake Winnipeg, finding low population divergence and latitudinal transcript variation, suggesting a connected metapopulation for conservation management.

The paper evaluates how geographic and environmental data can improve ex situ conservation by capturing more genetic diversity and differentiation, particularly for adaptive loci.

The paper introduces a deep learning method called Locator to predict geographic locations from genetic variation, achieving high accuracy and speed across different species.

The paper uses genome-wide sequencing to show how environmental heterogeneity drives genetic structure and local adaptation in the alpine herb Circaeaster agrestis.

The paper uses genomic data and coalescent-based methods to study demographic responses of Rapa Nui endemic reef fish species to Pleistocene climatic fluctuations, finding common population expansions linked to sea level changes.

This paper develops genus-specific HRM primers for Cyclopia Vent., tests HRM's haplotype discrimination against Sanger sequencing, and detects novel haplotypes in wild C. subternata with high accuracy.

This study examines genomic differentiation and population structure between two mosquito subspecies, finding monophyletic clusters and signs of admixture in one subspecies.

The paper presents a streamlined SSRseq workflow for microsatellite genotyping across diverse species, showing that de novo primer design improves reliability and multiplexing compared to using existing assays.

The paper presents a chromosomal-level genome assembly for the scimitar-horned oryx and analyzes genetic diversity and demographic history in captive populations.

This paper introduces GTmix, a coalescent-based maximum likelihood method for inferring admixture networks from local gene genealogies, showing improved accuracy with smaller datasets.

The paper introduces mixnmatch and ancestryinfer, tools for simulating admixture scenarios and inferring local ancestry, highlighting factors affecting inference accuracy.

RADinitio simulates RADseq experiments to optimize protocol selection and identifies library preparation and sequencing as major sources of missing data.

This paper shows that epiRADseq can generate SNPs comparable to ddRADseq for population genomic analyses, reducing costs and enabling combined genetic and epigenetic studies.

The paper analyzes the genomic diversity and global distribution of Saccharomyces eubayanus, identifying population structure and climatically suitable regions.

The paper examines genetic variation in Pacific oyster populations across the Northern Hemisphere, identifying genetic differentiation and selection signatures linked to translocation history and aquaculture practices.

This study investigates how continuous spatial structure affects population genetic analysis, finding biases in summary statistics, demographic inference, and GWAS when using discrete models.