Genetic diversity and population structure

Likelihood of social-ecological genetic model

This paper proposes a probabilistic framework integrating genetic and social-ecological processes to model species distribution and demographic history using coalescent methods and Bayesian inference.

Resolving Taxonomic Conflicts in Trichiurus: Chromosome Genomics Clarifies Species and Informs Conservation of Populations in the Northwest Pacific

This study resolves taxonomic conflicts in Trichiurus species using chromosome genomics, identifies a new species, and informs conservation strategies for Northwest Pacific populations.

Genetic population structure of Japanese freshwater crab, Geothelphusa dehaani species complex (Decapoda: Potamidae) using genome-wide SNP

This study uses genome-wide SNPs and mtDNA markers to analyze genetic structure and population dynamics of the Japanese freshwater crab Geothelphusa dehaani species complex across Japan.

Genomic Analysis Reveals Genetic Diversity, Population Structure and Evolutionary Dynamics in Bluebunch wheatgrass (Pseudoroegneria species)

The paper analyzes genomic variations in seven Bluebunch wheatgrass species to reveal genetic diversity, population structure, and evolutionary dynamics, identifying six genetic clusters and reticulate evolution in Eurasian species.

Postglacial recolonization of the Southern Ocean by elephant seals occurred from multiple glacial refugia

This study uses genetic analysis of ancient seal samples to show that southern elephant seals recolonized the Southern Ocean from multiple glacial refugia during postglacial periods.

Genomic insights into the successful invasion of the avian vampire fly (Philornis downsi) in the Galapagos Islands

This study uses whole-genome sequencing to analyze genetic diversity and selection in Philornis downsi populations from Galapagos and Ecuador, identifying genomic regions linked to invasion success.

Towards Stewardship of Wild Species and Their Domesticated Counterparts: A Case Study in Northern Wild Rice (Zizania palustris L.)

This study genotyped 839 Northern Wild Rice individuals using GBS, identified 5,955 SNPs, and analyzed genetic diversity and population structure, finding geographic clustering in wild populations and genetic distinction between wild and cultivated NWR.

Error rates in Q_ST--F_ST comparisons depend on genetic architecture and estimation procedures

This study shows that error rates in QST-FST comparisons depend on genetic architecture and estimation procedures, with some methods leading to high type I error rates.

President Roosevelt's lions reveal a century of population fragmentation in Africa's largest carnivore

The paper uses whole-genome sequencing of historical and recent lion populations to show population fragmentation and genetic diversity loss in East Africa over the past century.

Genetics in the ocean's twilight zone: Population structure of the Mueller's pearlside across its distribution range

The paper analyzes the population genetic structure of Mueller's pearlside across the North Atlantic and Mediterranean using SNP data, revealing habitat-driven differentiation and temperature-related genetic patterns.

Sample Size Impact (SaSii): an R script for estimating optimal sample sizes in population genetics and population genomics studies

SaSii is an R script that estimates optimal sample sizes for population genetics and genomics studies based on patterns from existing datasets.

Blind genomic tree scans identify loci underlying adaptive peaks in Antirrhinum

The paper identifies genomic loci underlying adaptive peaks in Antirrhinum by analyzing 18 populations and finding two partitions associated with hybrid incompatibility and eco-adaptation.

Population genomics of Marchantia polymorpha subspecies ruderalis reveals evidence of climate adaptation

This study analyzes genetic variation in Marchantia polymorpha subspecies ruderalis to identify climate adaptation signals, finding significant differentiation between European and Japanese populations linked to temperature and precipitation.

Museums and Zoos: Rapid genetic identification of rare species and practical applications for conservation and systematics in a biodiverse country

The paper demonstrates how collaboration between zoos and natural history collections can aid in genetic identification of rare species and support conservation efforts through phylogenetic analysis of olingos.

Distinguishing multiple-merger from Kingman coalescence using two-site frequency spectra

This paper introduces a statistical test to detect deviations from the Kingman coalescent model using the two-site frequency spectrum, showing that Drosophila melanogaster genomic data are inconsistent with the model.

Measuring linkage disequilibrium and improvement of pruning and clumping in structured populations

The paper introduces an adjusted linkage disequilibrium measure that accounts for population structure, improving LD pruning and clumping in structured populations.

Influence of past climate changes and human-mediated introduction on patterns of genetic diversity distribution of the Papuan nutmeg (Myristica argentea) Warb.

This study examines how past climate changes and human activities affect genetic diversity in Papuan nutmeg, finding higher diversity in native populations and fragmentation influenced by geography and climate.

Footprints of human migration in the population structure of wild wine yeast

The paper analyzes S. cerevisiae genomes from trees to show human-assisted migration shaped their distribution and genetic structure.

A simple approach to multiplexed PCR amplicon sequencing of plumage-associated loci in Vermivora warblers

The paper develops an amplicon sequencing method to genotype plumage-associated loci in Vermivora warblers and provides data and scripts for replication.

Avoidable false PSMC population size peaks occur across numerous studies

The paper identifies and resolves false population size peaks in PSMC analyses, showing they result from parameter settings and not true population dynamics.

High microsatellite but no mitochondrial DNA variation in an invasive Japanese mainland population of the parasitoid wasp Melittobia sosui

The paper investigates genetic variation in Melittobia sosui populations, finding no mitochondrial DNA variation in the invasive mainland population but similar microsatellite variation between native and invasive areas.

Seasonality and inter-annual stability in the population genetic structure of Batrachospermum gelatinosum (Rhodophyta)

This study examines the seasonal and inter-annual genetic structure of Batrachospermum gelatinosum, finding stable reproductive patterns despite seasonal shifts in gametophyte genotypes.

Next-generation snow leopard population assessment tool: multiplex-PCR SNP panel for individual identification from feces

The paper develops a SNP panel for identifying snow leopard individuals from fecal samples, validated with zoo and field samples, showing high accuracy and utility for population assessment.

Systematic bias in malaria parasite relatedness estimation

This paper identifies systematic biases in malaria parasite relatedness estimation and proposes practical tools to address them.

Comparative population genomics unveils congruent secondary suture zone in Southwest Pacific Hydrothermal Vents

This study uses comparative population genomics to identify a shared phylogeographic break in seven hydrothermal vent species, revealing patterns of lineage divergence and gene flow in the Southwest Pacific.

Concordant yet unique neutral and adaptive genomic responses to anthropogenically modified landscapes in Rhinella horribilis

This study examines genomic responses of Rhinella horribilis to anthropogenic habitat modification, finding both concordant and unique adaptive patterns in two landscapes.

Whole-genome evaluation of genetic rescue: the case of a curiously isolated and endangered butterfly

The paper evaluates genetic rescue for an endangered butterfly, finding low genetic diversity and potential outbreeding depression, suggesting caution before implementing rescue efforts.

Caudata macrogenetics: Geographic attributes and lineage age predict global patterns of mitochondrial genetic variation in salamanders

This study identifies range size and lineage age as key predictors of mitochondrial genetic variation in salamanders, showing local ecological and geographic factors shape diversity rather than shared ancestry.

Exploring genetic diversity in the species-rich genus Liolaemus: The interplay among isolation by distance, body size, and environmental variability

This study examines how isolation by distance, body size, and environmental variability influence genetic diversity in Liolaemus lizards using mitochondrial gene data.

Hybrid zone analysis using coalescent-based estimates of introgression and migration

The paper uses coalescent analyses to determine the timing and direction of hybrid zone formation in Plateau Fence Lizards, finding divergence around 140 kya and secondary contact around 10 kya.