Genetic diversity and population structure

Unheralded high MHC Class II polymorphism in the abundant Atlantic herring resolved by long-read sequencing

This study identifies highly polymorphic MHC class II genes in Atlantic herring using long-read sequencing, revealing exceptional diversity and coevolution of gene pairs.

Genomic Structural Variation Rescues a Classic Biological Invader from a Population Bottleneck

The paper shows genomic structural variants rescue the brown treesnake population from inbreeding after a severe bottleneck.

An updated assessment of the genomic health of Odocoileus

The paper updates genetic load and runs-of-homozygosity estimates for Odocoileus species, finding elevated inbreeding in Key deer and high loss-of-function mutations in mule deer.

Vicariance and dispersal shape the colonization history of the Galapagos carpenter bee, Xylocopa darwini

This study examines the colonization and diversification of Xylocopa darwini across Galapagos islands, finding long-term isolation, divergence between eastern and western islands, and recent founder events.

Interplay between abiotic conditions and mycorrhizal abundance determines differentiation and potential adaptation in a Mediterranean orchid

This study examines how abiotic conditions and mycorrhizal abundance interact to influence population differentiation and adaptation in the Mediterranean orchid Orchis italica.

Genomic diversity of elm trees for future treescapes

The paper analyzes genomic diversity in elm trees to assess the genetic potential of resistant cultivars for restoration.

Parallel adaptation to geothermally-warmed habitats due to common structural variation and functional developmental pathways

This study identifies parallel genomic mechanisms, including structural variation and functional pathways, in geothermally warmed stickleback populations adapting to increased temperatures.

Mitochondrial DNA haplotypes reveal a fine-scale population structure in sperm whales (Physeter macrocephalus) around Sao Miguel Island (Azores)

This study uses mitochondrial DNA haplotypes from fecal and skin samples to reveal fine-scale population structure in sperm whales around Sao Miguel Island, showing geographic distribution linked to maternal lineages.

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

This study uses non-invasive fecal samples and chromosome 21 target capture sequencing to analyze bonobo population structure, identifying three subpopulations and river barriers influencing genetic differentiation.

HapNet: a new Python package for automated population-aware haplotype network analysis and visualization

HapNet automates haplotype network construction and visualization from FASTA files, incorporating population metadata for population-aware analysis.

High Connectivity, Local Signatures: Genomic and Otolith Evidence from Reef-Associated Snappers.

This study combines genomic and otolith data to assess connectivity in snapper species, finding weak genetic structure but distinct environmental signatures in otoliths, highlighting ecological differentiation within a connected system.

Genomic differentiation of British oaks

This study analyzes genomic differentiation in British oaks, finding hybridization, niche differentiation, and faster growth in triploid trees.

Geographic structuring of genetic variation differs across two contact zones in the Diglossa carbonaria superspecies

The paper examines genetic differentiation and hybridization in three closely related bird taxa at contact zones using RADSeq data, finding weak genetic differentiation and evidence of introgressive hybridization in one zone.

Widespread decoupling between abundance and genetic diversity, and strong local genetic structuring in marine unicellular eukaryotes

The paper examines the relationship between abundance, genetic diversity, and spatial connectivity in marine eukaryotes using environmental DNA data, finding widespread decoupling between abundance and diversity, especially in unicellular organisms.

Inversions support both parallel and location-specific adaptations in snail ecotypes

The paper compares genetic differentiation and inversion patterns in snail ecotypes across two hybrid zones, finding shared and site-specific genomic architectures for adaptation to wave exposure.

Habitat specialization structures population divergence and demographic variation in Amazonian floodplain birds

This study links habitat specialization to genetic structure, divergence, and demographic variation in Amazonian floodplain birds using population genomic data.

Habitat discontinuity and fidelity to migratory routes shape narwhal genetic structure and diversity

This study uses genomic data from narwhals to show that habitat discontinuities and migration fidelity shape population structure, with low genetic diversity and inbreeding in small populations.

Temporal seascape genomics identifies evolutionarily significant units in a highly exploited marine resource, the wedge clam Donax trunculus.

This study uses temporal seascape genomics to identify evolutionarily significant units in the wedge clam Donax trunculus, revealing stable population structure and site-specific genetic diversity changes.

Standing Genomic Variation inferred by popGWAS Predicts Seedling Drought Survival Experiment in Fagus sylvatica

The paper uses popGWAS to identify genomic variation predicting drought survival in Fagus sylvatica seedlings, showing wild-collected material outperforms seed bank sources.

Genomic quantification of inbreeding depression in wild vertebrate populations

This study quantifies genomic inbreeding depression across 20 wild vertebrate populations, finding significant negative fitness effects and no link to conservation status or isolation.

Improved Bayesian inference of hybrids using genome sequences

The paper develops a Bayesian method for inferring hybrids and back-crosses from genome sequences, showing improved handling of population haplotype uncertainty and comparable performance to existing methods.

Population Genetics of Native Red Mulberry at Its Northwestern Boundary Suggests Postglacial Founder Effects

This study examines genetic diversity in native red mulberry populations at its northwestern range boundary, finding higher nuclear microsatellite diversity in southern unglaciated populations compared to northern glaciated ones, supporting postglacial founder effects.

Variation in AMY2B Copy Number and Serum Amylase Activity in Wolves (Canis Lupus), Brown Bears (Ursus arctos), and Red Foxes (Vulpes vulpes) from Bosnia and Herzegovina

The paper examines AMY2B copy number variation and serum amylase activity in wolves, brown bears, and red foxes from Bosnia and Herzegovina, finding species-specific differences in CNV and amylase activity.

Genetic structure of Rattus rattus populations in an endemic plague focus in Madagascar: implications for rodent surveillance and management

This study examines genetic diversity and structure of Rattus rattus in Madagascar, finding higher diversity and connectivity in outdoor subpopulations, suggesting integrated control strategies are needed for plague management.

Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone

Latitudinal Patterns in Immunogenetic and Microbiome Diversity in two anuran species: Bufo bufo and Bufo spinosus

This study compares immunogenetic and microbiome diversity in two toad species across latitudes, finding species-level differences in MHC diversity and microbiome composition that may affect disease susceptibility.

Genetic diversity and conservation insights for the baobab Adansonia suarezensis in northern Madagascar: a whole genome SNP analysis

This study analyzes the genetic structure and diversity of A. suarezensis populations using SNP data, revealing genetic differentiation and inbreeding patterns with conservation implications.

Widespread but cryptic introgression shapes genetic diversity in natural populations

The paper quantifies introgression in 4126 ant colonies, finding 23% of species show introgression, more than double previous estimates, and suggests postzygotic barriers constrain it.

Beyond infinite sites: Generalized ABBA-BABA statistic for deeper phylogenies

The paper introduces D+ and D* statistics to improve detection of gene flow by addressing saturation bias in deeper phylogenies using multiallelic site patterns.

Crowning the King of Fruits: Genomic Evidence of Population Structure and Relatedness in Malaysian Durians

The paper performs whole-genome sequencing of Malaysian durian cultivars to analyze population structure and genetic relatedness, finding clonal cultivars and genetic heterogeneity in Musang King.