Genetic diversity and population structure

Genomic connectivity and adaptation signals of the freshwater sponge Ephydatia muelleri across its distribution

This study examines genetic connectivity and adaptation in Ephydatia muelleri across its range using ddRADseq data, finding low connectivity and polygenic adaptation to environmental factors.

Gene pseudogenization in fertility-associated genes in cheetah (Acinonyx jubatus), a species with long-term low effective population size

The paper identifies pseudogenization events in cheetah fertility-associated genes linked to sterility, using comparative genomic analysis of eight felid genomes.

Comparative Patterns of Variation on the X Chromosome and Autosomes: The Role of the Breeding Sex Ratio

This study uses coalescent simulations to show how breeding sex ratio affects genetic variation patterns on X chromosomes and autosomes, with effects varying by demographic history.

The reasonable effectiveness of domain adaptation for inference of introgression

This paper demonstrates that domain adaptation improves the accuracy of detecting introgression in population genetics, even when unmodelled processes like ghost introgression are present.

Genome Sequencing, Molecular Marker Development and Genetic Diversity Assessment of Economically Important Vulnerable Tree Species Saraca asoca (Roxb.) W.J de Wilde

This study sequences the genome of Saraca asoca and assesses genetic diversity using GBS, identifying SSRs and biosynthesis pathways for flavonoids.

Population genomics reveals strong impacts of genetic drift without purging and guides conservation of bull and giant kelp

The paper uses genome sequencing to show genetic drift impacts bull and giant kelp populations, with no purging of harmful alleles, and suggests conservation strategies.

Inversions Dominate Evolution in the Highly Admixed European Sardine (Sardina pilchardus)

The paper investigates the role of inversions in shaping genetic diversity and population structure in European sardines, finding they drive adaptive allele frequency differences across populations.

Recent rapid radiation of apex predators suggests dramatic biodiversity turnover in an ancient lake

The paper uses genomic and phylogenetic methods to show that Lates fishes colonized Lake Tanganyika ~1-2 Mya, diversified into four species during glacial cycles, and their radiation had significant ecological impacts.

Local genetic adaptation to habitat in wild chimpanzees

This study identifies local genetic adaptation to habitat in wild chimpanzees, particularly to pathogens like malaria, using newly generated exomes.

Characterizing population structure and documenting rapid loss of genetic diversity in Chiricahua Leopard Frogs (Lithobates chiricahuensis) with high throughput microsatellite genotyping

This study uses microsatellite markers to analyze genetic diversity in Chiricahua Leopard Frogs, revealing genetic bottlenecks and rapid diversity loss in managed populations.

Lost in the woods: shifting habitats can lead phylogeography astray

This paper shows that shifting habitats can lead to biased and overconfident phylogeographic inferences due to local density regulation and population dynamics.

Rapid parallel adaptation in distinct invasions of Ambrosia artemisiifolia is driven by large-effect structural variants

The paper identifies large-effect structural variants driving parallel adaptation in multiple invasions of Ambrosia artemisiifolia across different continents.

eDNA metabarcoding and whole genome sequencing detect European-American Eel hybrids in northeastern Canada

Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences

The paper develops a probabilistic model to correct biases in low-pass genome sequencing data, improving population genetic inferences.

A highly divergent mitochondrial genome in extant Cape buffalo from Addo Elephant National Park, South Africa

The paper analyzes mitochondrial genomes of Cape buffalo from Addo Elephant National Park, finding a highly divergent mitogenome likely from introgressive hybridization with an extinct species.

Genomic introgression between critically endangered and stable species of Darwin's tree finches on the Galapagos Islands

The paper examines genomic introgression between a critically endangered and stable Darwin's tree finch species, finding evidence of selection for hybrid alleles associated with immunity and development.

Extensive admixture among karst-obligate salamandersreveals evidence of recent divergence and gene exchangethrough aquifers

This study uses population genomics to analyze karst-obligate salamanders, revealing extensive admixture and recent divergence through aquifers.

Genomic insights into red squirrels in Scotland reveals loss of heterozygosity associated with extreme founder effects

This study analyzes the genomic data of red squirrels in Scotland to reveal loss of heterozygosity linked to extreme founder effects from human impacts.

Parallel genetic adaptation amidst a background of changing effective population sizes in divergent yellow perch (Perca flavescens) populations

The paper uses genome-wide data to analyze demographic histories and genetic adaptation in two yellow perch populations, finding increased effective population sizes and parallel adaptation to reduced visual clarity.

Inferring the demographic history of aye-ayes (Daubentonia madagascariensis) from high-quality, whole-genome, population-level data

This study infers the demographic history of aye-ayes using genomic data, finding two population size reductions linked to human arrival and habitat loss.

Evolution of fast-growing piscivorous herring in the young Baltic Sea

This study shows that piscivorous herring evolved sympatrically in the young Baltic Sea, growing faster and occupying a new niche despite incomplete adaptation to a fish diet.

Mitogenome Diversity and Phylogenetic Insights of Aedes albopictus in Greece

This study analyzes mitochondrial COI gene sequences of Ae. albopictus in Greece to assess genetic diversity and phylogeography, revealing haplotype changes over time and geographic distribution.

Negative selection on baboon admixture is strongest on chromosome X

The paper examines negative selection on baboon admixture, finding stronger selection on the X chromosome in Tanzanian and Ethiopian populations.

Climate drives long-term landscape and rapid short-term promoter evolution in the Western Canaries lizard, Gallotia galloti

The paper examines climate-driven promoter evolution in the Western Canaries lizard, identifying adaptive loci and selection patterns linked to elevation and extreme weather events.

High-Resolution Genome Assembly and Population Genetic Study of the Endangered Maple Acer pentaphyllum (Sapindaceae): Implications for Conservation Strategies

This study presents a high-quality genome of Acer pentaphyllum and analyzes its population genetics to inform conservation strategies.

Characterization of both major histocompatibility complex classes in a wild social mammal: the banded mongoose

This study characterizes MHC class I and II diversity in banded mongooses using high-throughput sequencing, finding higher allelic diversity in MHC-I and evidence of selection acting differently on exons 2 and 3.

Genomic signatures of island colonization in highly diverse primates

The paper compares genomic diversity, inbreeding, and genetic load between insular and mainland populations of three West African primates, finding lower diversity and higher inbreeding in island populations but no evidence of increased deleterious variation.

Genomic-guided conservation actions to restore the most endangered conifer in the Mediterranean Basin

The paper uses genomic data to assess genetic diversity and mating patterns in Sicilian fir, identifying inbreeding and introgression risks and proposing conservation strategies.

Pitfalls and recommendations for large-scale SNP genotyping in a non-model endangered species: the southern damselflies (Coenagrion mercuriale) as a case study.

This study develops and applies SNP genotyping methods for the endangered southern damselfly, identifying challenges and demonstrating improved resolution for genetic structure and conservation analysis.

The Once and Future Fish: 1300 years of Atlantic herring population structure and demography revealed through ancient DNA and mixed-stock analysis

This study uses ancient DNA and mixed-stock analysis to reveal 1300 years of Atlantic herring population structure and demography, showing demographic disruptions from overfishing and climate change.