Genetic diversity and population structure

Temporal persistence of admixed phenotypes in a damselfly hybrid zone

The paper examines a hybrid zone between two damselfly species, finding persistent hybrid phenotypes and genetic admixture across sympatric localities.

Fiat lux: A hotspot of Luciola fireflies on Western Mediterranean islands

The paper investigates firefly diversity in the Tuscan Archipelago and Italian Peninsula, finding high genetic differentiation and six distinct mitochondrial lineages, suggesting multiple species and highlighting the area as a conservation priority.

Rapid speciation in Harlequin Toads (Anura: Bufonidae) endemic to the Sierra Nevada de Santa Marta

This study uses genomic data to investigate rapid speciation in four endemic Atelopus species in the Sierra Nevada de Santa Marta, finding recent divergence without gene flow and suggesting topography and ecological factors drove speciation.

Life-history traits may buffer genetic erosion under isolation in mountain sky-island systems

The paper investigates genetic resilience in Xatartia scabra under isolation, finding moderate diversity and low inbreeding despite small population sizes and strong isolation.

Resolving the Taxonomic Status of the Marbled Toad (Bufonidae: Incilius marmoreus): 2RAD-based Phylogeography Including an Isolated Population in Veracruz, Mexico

This paper reevaluates the phylogeography and taxonomy of the Marbled Toad using genomic and morphological data, finding support for the current classification and a historical north-south split followed by an east-west split.

Ancient DNA from shells reveals delayed genomic erosion and rapid immune adaptation in the critically endangered black abalone

The paper uses ancient DNA from shells to analyze genetic stability and immune adaptation in black abalone post-bottleneck, finding delayed genomic erosion and rapid immune-related selection.

Evolutionary transitions to self-fertilization influence the inference of introgression history

This study shows that transitions to self-fertilization can mislead introgression inferences, and coalescent statistics help correct these biases in demographic models.

Transcriptome-based genome-wide analysis reveals hybridization dynamics and genetic structure of Japanese giant salamanders

This study uses transcriptome data to analyze hybridization dynamics and genetic structure in Japanese and Chinese giant salamanders, identifying hybrid groups and genetic contributions.

Range-wide phylogeography, population genomics, and demography of three widespread Ara macaws (Psittacidae)

This study uses genomic data to analyze the evolutionary history and demographic processes of three Ara macaw species, identifying genetic structure and adaptation signals across different biomes.

Genomic history and ecology of local adaptation in sky-island Arabidopsis thaliana

This study examines local adaptation in Arabidopsis thaliana across East African sky-islands, finding limited parallel adaptation and evidence of divergent selection based on climate.

Genomic Architecture, Differentiation, and Adaptation in Three Large Falcons

This study analyzes genomic divergence in three large falcon species, linking chromosomal rearrangements to patterns of recombination, diversity, and differentiation.

Census and genetic analysis of the United States marmoset population

The paper analyzes the genetic diversity and population structure of US marmosets, revealing pre-colony population structure and generating a pedigree-based recombination map.

An exact formula for the contribution of sampling error to r2, a common measure of linkage disequilibrium

The paper derives an exact formula for the contribution of sampling error to r2, showing it equals 1/(S - 1) when sampling error is the only factor affecting LD.

Genomic footprints of selfing, introduction history, and long-distance dispersal in an invasive alien plant

This study uses genome-wide data to investigate the colonization history and genetic structure of the invasive plant Cotula coronopifolia, revealing multiple lineages, high selfing rates, and the role of dispersal in its spread.

kinference: Pairwise kinship detection for Close-Kin Mark-Recapture

The paper introduces the kinference R package for detecting close-kin pairs in genetic data to support demographic analysis in wildlife management.

Genomic forecasts of maladptation in Lycaeides butterflies

This study estimates genomic offsets in Lycaeides butterflies to predict maladaptation under past, present, and future climates, finding that genetic diversity and gene flow influence adaptation potential.

Loss of Adaptive Capacity Drives Climate Vulnerability Across Taxonomic Scales in an Alpine Specialist Species Complex

The paper assesses adaptive capacity in an alpine species complex using genomics and ecology to identify climate vulnerability across taxonomic scales.

lcUMAPtSNE: Use of non-linear dimensionality reduction techniques with genotype likelihoods

The paper develops a workflow using UMAP and t-SNE on genotype likelihoods from low-coverage sequencing to analyze population structure in scimitar-horned oryx.

Woodland age, ancient trees, and population size as proxies of genetic diversity

The paper examines how woodland age, ancient trees, and population size affect genetic diversity in tree populations using seed collection data and functional trait analysis.

Historically Small Population Size Limits Purging of Deleterious Mutations in a Conservation-Reliant Species, the Kirtlands Warbler

The paper uses historical DNA to show that a small population's genetic load was not purged after a bottleneck, despite demographic recovery.

A classification of structured coalescent processes with migration, conditional on the population pedigree

The paper extends coalescent models to account for pedigree effects in populations with subdivision and migration, finding pedigree effects in three out of four scenarios.

Evolutionary history and genomic vulnerability of the extinct giant deer Megaloceros giganteus

This study reconstructs the genomic history of the extinct giant deer, revealing genetic vulnerabilities linked to its extinction.

Sustained multigenerational fitness benefits of natural immigration

The study quantifies multigenerational fitness effects of immigrant lineages in Florida scrub-jays, finding additive benefits and heterosis persisting across generations.

Ecotypes, Wolbachia, and urbanization shape Culex pipiens population structure in a West Nile virus hotspot

The paper analyzes population structure in Culex pipiens using genomic data from a WNV hotspot, finding that ecotypes, Wolbachia infection, and habitat type drive genetic variation.

Extremely low effective population size in a captive-bred population: partial mitigation through management practices

The paper estimates effective population size in a captive-bred Saimaa salmon population and finds that management practices slightly increase Ne, but survival variability remains a major factor.

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome

The paper uses population genomics to identify three yellow-eyed penguin subspecies and links candidate genes to respiratory distress syndrome.

Wolves in black: multiple introgressions and natural selection may explain melanism in Italian wolves

The paper investigates the genomic basis of melanism in Italian wolves, finding evidence of multiple introgression events and balancing selection involving the KB allele from domestic dogs.

Genetic polymorphisms in a mate choice locus are maintained by balancing selection in a wild medaka population

The paper identifies a genomic region in Oryzias sakaizumii showing signs of balancing selection, potentially linked to sexual selection and female mating behavior.

Haplotype tagging sheds light on speciation between two divergent cryptic species of the brown algae Ectocarpus

The paper uses linked-read whole-genome data to study reproductive isolation and hybridization patterns between two cryptic brown algal species, revealing polygenic genome-wide barriers to gene flow.

Diversification and divergence in Myioborus warblers: insights into evolutionary relationships and plumage genetics

The paper uses whole-genome sequencing of Myioborus warblers to study evolutionary relationships and plumage genetics, finding patterns of colonization, hybridization, and genomic differentiation.