Genetic diversity and population structure

Bhutan sequences complete the range-widemitochondrial phylogeography for red pandas, Ailurus fulgens

This study adds Bhutanese red panda mitochondrial sequences to a global dataset, showing they form a single species with a genetic cline across their range, not distinct subspecies.

Population Genomics of P. miniata along the Pacific Coastline Reveal Subtly Diverging Genomics Along an Extensive Range Gap

This study uses whole-genome sequencing to show genetic disjunction and divergence in the bat star Patiria miniata despite its long-lived planktonic larvae, suggesting recent ecological or oceanographic barriers.

When migration leaves a clean trace: Decoupling migration from coalescence in the Structured Serial Coalescent

The paper develops a framework to infer time-varying migration rates by decoupling them from coalescence rates using structured serial coalescent theory.

Ancient introgression explains mitochondrial genome capture and mitonuclear discordance among South American collared Tropidurus lizards

The paper investigates mitonuclear discordance in Tropidurus lizards, finding that ancient mitochondrial introgression and demographic processes explain the observed genetic mismatches.

Performance of Sequential Markovian Coalescence Methods when Populations are Structured

This study evaluates SMC methods' performance in structured populations, finding systematic biases in IICR estimation during transition phases.

Evaluating genomic offset predictions in a forest tree with high population genetic structure

This study evaluates genomic offset predictions in maritime pine using multiple methods and data sources, finding strong associations with mortality but not height.

Genomic differentiation of the black-chinned tilapia (Sarotherodon melanotheron) along a fresh-to-hypersaline water gradient

This study identifies adaptive genetic variation in black-chinned tilapia along a salinity gradient, highlighting osmoregulation and immune-related pathways.

Population genetics of the nidicolous soft tick Ornithodoros phacochoerus in the context of African swine fever sylvatic cycle

This study analyzes the population genetics of Ornithodoros phacochoerus ticks in Mozambique, finding isolation between two reserves and suggesting tick movement driven by warthog activity, which may contribute to African swine fever virus transmission.

Comparing the genetic diversity of two threatened Rhyticeros hornbill species with contrasting geographic range sizes

The paper compares genetic diversity between two hornbill species, finding the island-endemic Narcondam Hornbill has significantly lower genetic diversity than the Wreathed Hornbill.

The genomic imprint of chromosomal inversions and demographic history in island populations of deer mice

This study examines chromosomal inversions and demographic history in deer mice populations across islands and mainland, finding shared balancing selection and ancient divergence.

Large haplotypes linked to climate and life history variation in divergent lineages of Atlantic salmon (Salmo salar)

The paper identifies a large haplotype block in Atlantic salmon linked to climate and life history traits, showing continent-specific haplotypes and introgression patterns.

Navigating sampling bias in discrete phylogeographic analysis: assessing the performance of an adjusted Bayes factor

This paper evaluates an adjusted Bayes factor method to reduce sampling bias in discrete phylogeographic analysis using CTMC models.

Parallel polygenic urban adaptation despite high gene flow in a coastal marine invertebrate

The paper investigates genomic signals of urban adaptation in Pacific purple sea urchins across three coastal cities, finding parallel polygenic adaptation despite high gene flow.

How social and economic policies have affected the genome of mezcal agaves: the contrasting stories of Bacanora and Espadin

This study uses genomic data to show how social and political policies in Mexico influenced genetic diversity in two agave species, Espadin and Bacanora.

Behind the shadow play: Shedding light on the population genetics of partially clonal organisms through clone age distributions

This study simulates partially clonal populations to explore how clonality rates affect clone age distributions and genetic diversity over time.

Harnessing landscape genomics to evaluate genomic vulnerability and future climate resilience in an East Asia perennial

The paper uses landscape genomics to assess genomic vulnerability and climate resilience in Rheum palmatum, identifying genetic clusters and seed zones for conservation strategies.

Climate Shaped the Global Population Structure of Leopards and their Extinction in Europe

This study uses climate and genetic data to show that climate change shaped leopard population dynamics, leading to extinction in Europe and structuring populations in Asia and Africa.

Estimating the effective population size across space and time in the Critically Endangered western chimpanzee in Guinea-Bissau: challenges and implications for conservation management

The paper estimates effective population size (Ne) of western chimpanzees in Guinea-Bissau using genetic data to inform conservation strategies.

Genomic signatures of climate-driven (mal)adaptation in an iconic conifer, the English yew (Taxus baccata L.)

This study assesses climate maladaptation risk in English yew populations using genomic offset methods, identifying climate-associated loci and predicting vulnerability in Mediterranean and high-elevation populations.

Recent divergence and microgeographic genetic structure in an endangered Australian songbird: the southern black-throated finch

This study examines genetic differentiation and demographic history of the endangered southern black-throated finch using sequencing, finding genetic distinctness between subspecies and microgeographic structure due to habitat modification.

Full Mitochondrial Phylogeny of Cutthroat Trout with Comments on Species Delimitation and Taxonomy

The paper analyzes mitochondrial genomes of Cutthroat Trout to assess lineage relationships and taxonomy, finding 11 ancient lineages but no strong distinction among major subspecies.

Phylogeography and genetic structure of the steppe marmot (Marmota bobak Muller, 1776)

This study investigates the genetic structure of the steppe marmot using mitochondrial markers and identifies two phylogroups that challenge the existing subspecies classification.

Behavioral and phenotypic constraint belie deep genomic divergence and seasonal adaptation in a widespread desert lizard

The paper integrates genomic, morphological, climatic, and behavioral data to show that behavioral flexibility constrains phenotypic divergence despite deep genomic differentiation in desert lizards.

Transcriptome differentiation in Cryptomeria japonica trees with different origins growing in the north and south of Japan

The paper identifies gene modules associated with local adaptation in Cryptomeria japonica trees from different geographic origins in Japan.

Uncovering the Genetic Blueprint of the UAE's National Tree: Genomic Evidence to Guide Prosopis cineraria (L.) Druce Conservation

This study presents the first population genomics analysis of Prosopis cineraria in the UAE, identifying genetic clusters and diversity patterns to inform conservation strategies.

Genome-wide signatures of reproductive isolation shape the varied genomic landscape of the roundtail horned lizard (Phrynosoma modestum)

This study analyzes whole genome sequences of roundtail horned lizards to understand how demographic history and evolutionary pressures shape genetic diversity and reproductive isolation.

Genomic and Dietary Insights from Non-Invasive Sampling of Western Capercaillie in Tyresta National Park (Sweden)

This study uses genomic and dietary data from non-invasive samples to assess the genetic health and diet of a Western Capercaillie population in Sweden, finding low inbreeding but risks from small size and isolation.

A method for identifying spatially divergent selection in structured populations.

The paper introduces a method to detect spatially divergent selection by incorporating population structure into genetic variance comparisons, showing improved performance over traditional methods.

Genetic diversity and variation in heterozygosity in Macadamia

This study analyzes genetic diversity and heterozygosity in Macadamia species using whole-genome sequencing, finding reduced diversity in domesticated varieties and a correlation between heterozygosity and yield efficiency.

Reference genome choice compromises population genetic analyses

This study shows that using a conspecific reference genome improves variant detection and genetic diversity estimates compared to heterospecific references in gray foxes.