Genetic diversity and population structure

This must be the place: deep learning local adaptation

EcoLocator, a deep learning model, predicts geographic and climate origins from genotypes, outperforming traditional methods and showing practical applicability in conservation.

The ambiguity of "hybrid swarm": inconsistent definitions and applications in existing research

This paper reviews the inconsistent use of the term 'hybrid swarm' in hybridization studies and advocates for clearer terminology.

Comparing the Influence of Habitat Configuration on Population Connectivity and Genetic Structure Using Congeneric Species Across Multiple Taxa

This study compares genetic structure and population connectivity across congeneric species in river habitats, finding higher genetic diversity upstream and lower differentiation in hygropetric microhabitats.

Contrasting effects of forest fragmentation on the genetics and microbiomes of an endangered arboreal primate

This study examines how forest fragmentation affects the genetics and microbiomes of black howler monkeys, finding contrasting patterns where genetic diversity increases in fragmented areas while microbiome diversity decreases.

A selective sweep likely linked to xenobiotic detoxification identified along altitudinal gradients in the pine processionary moth

The study identifies a selective sweep linked to xenobiotic detoxification in the pine processionary moth along altitudinal gradients, suggesting local selective pressures from xenobiotic exposure.

Development of microsatellite markers with the SSRseq method on Glossina palpalis gambiensis, and G. p. palpalis, and analysis of corresponding field samples from three sleeping sickness foci: Boffa, Dubreka (Guinea), and Bonon (Cote d'Ivoire).

The paper develops microsatellite markers using SSRseq in tsetse flies and analyzes field samples to study population structure and evolutionary responses to vector control.

MMM: A deterministic Mendelian mismatch matrix framework for germplasm collection quality assessment, demonstrated in apple and sweet cherry

MMM assesses germplasm collection quality by quantifying Mendelian mismatches, identifying duplicates, and revealing structural patterns in apple and sweet cherry datasets.

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

The paper develops a GT-seq panel to identify species in the Coregonus artedi complex and demonstrates its cross-amplification in related taxa.

Selfing-aware demographic inference highlights local population structure and bottlenecks in Hawaiian Caenorhabditis elegans

The paper applies a selfing-aware demographic inference method to Hawaiian C. elegans populations, revealing population structure, bottlenecks, and the impact of self-fertilization on demographic estimates.

Navigating between global robustness and fine-scale resolution: the potential of demographic inference based on identical-by-descent segments.

This study evaluates two IBD-based methods for estimating effective density and dispersal variance, finding that IBD-Analysis performs better under spatially homogeneous conditions while MAPS captures spatial patterns but introduces noise in uniform landscapes.

Convergent molecular changes in populations of two pipefish species in the Baltic Sea

This study identifies molecular convergence in Baltic Sea pipefish populations despite differing genomic structures and species relationships.

Deep ancestral structure, admixture and peripheral persistence shape diversity in the Papilio bianor species complex

This study analyzes whole-genome variation in butterflies to show how ancestral polymorphism, admixture, and incomplete lineage sorting shape lineage diversity in the Papilio bianor complex.

Tropical rainforest versus savannah: Biome-specific landscape structure mediates adaptive strategies and resilience to environmental change

This study examines how biome-specific landscape structure influences adaptive strategies and resilience in tropical rainbowfish across rainforest and savannah ecosystems.

One species, two lives: cryptic population structure and life-history divergence in a vineyard spittlebug (Aphrophora sp.), a candidate vector for Pierce's disease

The paper analyzes genome data from spittlebugs in vineyards and quasi-natural populations, revealing cryptic population structure, life-history divergence, and insecticide resistance.

Multiple introductions shaped genomic diversity and demographic history of invasive box tree moth (Cydalima perspectalis) populations in North America

The paper investigates the invasion history of box tree moth in North America using genomic and morphological data, finding multiple introductions and genetic structuring.

The Value of Multi-Year Sampling for Detecting Fine-Scale Population Genetic Structure in Marine Fishes: A Case Study of Juvenile Southern Flounder

The paper uses ddRADSeq to analyze genetic structure in southern flounder over multiple years, finding significant differentiation between regions and temporal variability within estuaries.

Evidence of selection in sympatry between two closely related species of rockfish

This study identifies genetic differentiation and directional selection in sympatric rockfish species, suggesting reinforcement maintains species boundaries.

Ancient DNA perspectives on North American cervids identify fluctuations in genetic diversity

This study uses ancient DNA from North American cervids to trace genetic diversity changes over time, revealing historical population dynamics and impacts of external pressures.

A chromosome-level reference genome assembly reveals extreme loss of Y-chromosomal diversity in the Saimaa ringed seal (Pusa saimensis)

The paper uses a chromosome-level reference genome to analyze Y-chromosomal diversity in Saimaa ringed seals, finding extreme loss of diversity compared to other ringed seal populations.

Cryptic diversity in Astyanax (Characiformes: Acestrorhamphidae) from the Magdalena basin, Colombia: Insights from molecular and morphometric evidence

The paper identifies cryptic diversity in Astyanax species from the Magdalena basin using molecular and morphometric analyses, revealing two distinct genetic groups and morphospecies.

Genetic connectivity in US Caribbean queen conch (Aliger gigas):Implications for management and forensic assignment

This study uses whole-genome sequencing to analyze genetic connectivity among queen conch populations in US Caribbean waters, finding a connected system with substantial gene flow and geographic differentiation.

One species or several? Genomic evidence for deep divergence within the widely distributed anemonefish Amphiprion clarkii species complex

This study uses whole genome re-sequencing to reveal deep divergence within the Amphiprion clarkii species complex, identifying five lineages and challenging the taxonomic status of A. tricinctus.

How small is too small? Genetic signatures from naturally small populations of a large island vertebrate, the Turks and Caicos Rock Iguana

This study examines genetic diversity and population structure in small island populations of the Turks and Caicos rock iguana, finding low genetic diversity but limited inbreeding and suggesting a low threshold for population persistence.

Gene tree patterns help answer: vicariance or dispersal?

The paper shows gene tree patterns differ predictably between vicariance and founder event speciation, suggesting new methods to distinguish these drivers.

Dispersal, gene flow and adaptive differentiation in hierarchically structured populations

This study quantifies the balance between local adaptation and gene flow in hierarchically structured Atlantic salmon populations using SNP data and spatial genetic analysis.

Extensive nuclear introgression accompanied ancient mitochondrial capture in the common ancestor of two sister hare species

The paper quantifies and localizes nuclear introgression in two hare species by combining demographic, phylogenomic, and polarisation-based methods, revealing extensive gene flow from mountain hare.

Species-specific loss of genetic diversity and inbreeding following agricultural intensification

The paper examines genetic diversity loss and inbreeding in butterflies due to agricultural intensification, finding reduced diversity and increased isolation in a grassland specialist species.

Unmasking genetic load: Genomic inbreeding drives growth depression in captive critically endangered Chinese Bahaba (Bahaba taipingensis)

The paper investigates genomic inbreeding effects on growth depression in captive Chinese bahaba, identifying genetic factors linked to skeletal and immune pathways.

Accounting for pseudo-replication of Linkage Disequilibrium for contemporary Ne estimation

The paper introduces a method to correct confidence intervals for pseudo-replication in linkage disequilibrium data to improve Ne estimation in Anopheles gambiae.

Reproductive isolation and structural variation among sympatric lineages of an international mosquito pest

The paper identifies three cryptic lineages of Aedes notoscriptus mosquitoes using population genomics, revealing reproductive isolation and structural variants between lineages.