Genetic diversity and population structure

Small-scale within-drainage spawning behavior causes population differentiation in Atlantic salmon

This study finds population differentiation in Atlantic salmon within a small river system due to spawning behavior, despite overall genetic connectivity.

Forging together: Parallel adaptation to minewater pollution in brown trout (Salmo trutta L.).

This study identifies parallel and unique genetic adaptations in brown trout to metal-polluted environments using genome resequencing.

Contrasting Mitochondrial Diversity of Endemic Corbicula Clams in Sulawesis Ancient Lakes: Phylogeography and Implications for Conservation

This study examines mitochondrial diversity in two endemic Corbicula clams from Sulawesi lakes, revealing deep divergence and distinct phylogeographic patterns with conservation implications.

Anthropogenic effects, not climatic, shaped Holocene population expansion of an insular bee fauna

The paper investigates the impact of human activity versus climate change on bee population expansion in Fiji, finding that human occupation, not climate, drove population growth in lowland species.

Towards genetic indicators in ectomycorrhizal fungi: estimating the effective population size

The paper estimates effective population size (Ne) in ectomycorrhizal fungi using genetic data and finds biases in Ne estimation due to clonality and population structure.

Quaternary ice ages shaped protists phylogeography: the case of Arcellinida in the Iberian Peninsula

The study examines how Quaternary ice ages influenced the phylogeography of Arcellinida protists in the Iberian Peninsula, finding genetic diversity hotspots aligned with glacial refugia and supporting the GLQ paradigm for microbial eukaryotes.

Southern Iberia as a hotspot of wild grapevine genetic diversity

This study identifies three ancestral populations and four genetic refugia in southern Iberia, showing gene flow from North Africa to Iberian wild grapevines during the late Pleistocene and early Holocene.

The effects of post-divergence gene flow on simultaneous divergence time (SDT) testing

This study evaluates how post-divergence gene flow affects the accuracy of simultaneous divergence time estimates using simulations and Bayesian methods.

Ancient inversion polymorphisms are locally adaptive in a widespread butterfly species

This study identifies ancient chromosomal inversions in the zebra longwing butterfly that are associated with local adaptation to environmental stressors.

From migrants to residents: Genomic insights into adaptive strategies in European robins (Erithacus rubecula)

This study uses whole genome re-sequencing data from European robins to explore how migration behavior influences population structure, demography, and selection pressures across different geographic regions.

Genome-wide SNP diversity in natural and cultivated populations informs restoration ecology with three Calamagrostis species from the Northwest Territories of Canada

The paper uses ddRAD and GT-seq to analyze genetic diversity in three Calamagrostis species, informing seed sourcing strategies for restoration in northern Canada.

How robust are genomic offset predictions to methodological choices? Insights from perennial ryegrass

This study compares two methods for detecting outliers in genomic offset predictions and finds that non-linear methods are less sensitive to sampling biases.

Genvectors: exploring patterns and unveiling processes driving the geographic distribution of genetic lineages

This paper introduces genvector analysis to infer biogeographic drivers of genetic turnover by decomposing genetic dissimilarities into eigenvectors and testing null models.

Inferring fine-scale rates of mutation and recombination in the coppery titi monkey (Plecturocebus cupreus)

The paper infers fine-scale mutation and recombination rates in the coppery titi monkey using divergence and polymorphism data and a high-quality genome, aligning with rates in other primates.

High-resolution insights into the geographic differentiation and hybridisation of Odontobutis gobies through integrated eDNA and SNP analyses

This study uses integrated eDNA and SNP analyses to reveal geographic differentiation and hybridization in Odontobutis gobies, showing hybrid origin of O. hikimius.

Comparing genomic inbreeding of an isolated rhesus macaque study population to wild populations

The paper compares genomic inbreeding levels between an isolated rhesus macaque population on Cayo Santiago and wild populations using runs of homozygosity.

CoalMiner: a coalescent model generator for fastsimcoal2

CoalMiner generates coalescent models for fastsimcoal2 to improve demographic inference by exploring model space efficiently.

Latitude, not geography, globally structures Oscheius tipulae into three deeply divergent lineages

The paper analyzes genome-wide variation in Oscheius tipulae and finds three deeply divergent lineages structured by latitude rather than geography.

Increased rates of hybridization in swordtails are associated with water pollution

The paper investigates how water pollution affects hybridization between two swordtail fish species by analyzing genomic and environmental data.

The contribution of recent and historical demographic histories to genomic diversity and conservation status in plant species

This study assesses conservation status in 101 plant species by analyzing demographic parameters and genomic diversity, finding that census size is the best predictor of extinction risk.

Color polymorphism in the saddleback clownfish, Amphiprion polymnus: species or complex?

The paper investigates whether color polymorphism in the saddleback clownfish represents intraspecific variation or multiple species using genomic and image data.

Nucleotide diversity is a poor predictor of short-term adaptive potential

This paper shows that molecular genetic diversity poorly predicts adaptive potential, using evolvability as a measure of heritable variation across species.

Genomic predictions of climate change vulnerability in the emblematic mountain butterfly Parnassius apollo

This study uses genomic data to predict climate change vulnerability in the Apollo butterfly, identifying populations at varying risk based on genetic diversity and adaptation potential.

Conservation rescued the Mauritius kestrel from extinction but not from genomic erosion

The paper uses genomic data and simulations to show that conservation efforts saved the Mauritius kestrel from extinction but did not prevent genomic erosion and reduced reproductive success.

A cryptic local genetic cluster in Northern France amid the European mosaic of flat oyster lineages revealed by integrating SNP array and whole-genome sequencing

Integrating genomic and tagging data reveals spatio-temporal population structure in Northeast Atlantic European sea bass

The paper integrates genomic and tagging data to show how seasonal movements shape genetic structure in European sea bass while maintaining demographic subdivision.

Global population structures and demographic history of Suillus luteus, a pine co-introduced ectomycorrhizal fungus associated with exotic forestry and invasion.

This study analyzes the population genetics of Suillus luteus, showing all introductions originated from Europe and showing genetic differentiation in introduced regions linked to forestry practices.

Genomic offset is not predictive of recent demographic trends in Lycaeides butterflies

This study evaluates genomic offset (GO) as a predictor of population trends in Lycaeides butterflies and finds it is not a reliable predictor despite methodological variations.

Modelling and Inferring Large-scale Demographic Fluctuations in Structured Populations Through Simulations and PSMC-based Methods.

This study simulates structured populations to assess PSMC's ability to infer demographic history, finding it fails to recover older fluctuations but works better for recent periods.

Ancient admixture catalyzes homoploid hybrid speciation and intense genomic erosion in an Asian langur genus

The paper investigates how ancient admixture drives homoploid hybrid speciation and genomic erosion in Asian langurs, identifying key genetic mechanisms and consequences.