Genetic diversity and population structure

Estimation of effective population size and effective number of breeders in an abundant and heavily exploited marine teleost

The paper estimates effective population size (Ne) and effective number of breeders (Nb) for snapper using SNP data and bias correction methods, showing that single-cohort samples yield more reliable results.

Pitfalls and windfalls of detecting demographic declines using population genetics in long-lived species

The paper shows that comparing genomes of young and old individuals can help detect recent demographic declines in long-lived species, especially when declines are severe.

Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate

This study uses population genomics of northern shrimp to identify drivers of population structure and predict climate vulnerability across its wide distribution.

Hierarchical population genetic structure and signatures of adaptation in Lates calcarifer

This study identifies hierarchical genetic structure and adaptive divergence in Lates calcarifer across different regions and time periods.

Continent-wide genomic analysis of the African buffalo (Syncerus caffer).

This study presents a continent-wide genomic analysis of African buffalo, revealing three main lineages and signatures of selection related to immune response.

Population divergence manifested by genomic rearrangements in a keystone Arctic species with high gene flow

The paper identifies genomic rearrangements in polar cod, showing their role in population divergence and potential local adaptation despite high gene flow.

Using runs of homozygosity and machine learning to disentangle sources of inbreeding and infer self-fertilization rates

The paper uses ROHs and machine learning to distinguish inbreeding sources and estimate self-fertilization rates, showing success even with complex demography.

Hybridization load introduced by Alpine ibex hybrid swarms

The paper estimates hybridization load in Alpine ibex due to hybridization with domestic goats, finding increased loss-of-function mutations in hybrids compared to non-hybrids.

Genetic Structuring and Conservation of Asian Sockeye Salmon: Identification of Regional Stock Complexes

The paper analyzes SNP variability in Asian sockeye salmon to identify regional stock complexes and their genetic divergence patterns.

Limited parallelism in genetic adaptation to brackish water bodies in European sprat and Atlantic herring

The paper analyzes genetic adaptation in European sprat and Atlantic herring to brackish waters, finding limited parallelism in genetic changes despite similar environmental pressures.

An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

The paper develops an amplicon panel for genotyping Pacific oysters to support breeding programs and identifies null alleles affecting parentage analysis.

MAXTEMP: A method to maximize precision of the temporal method for estimating Ne in genetic monitoring programs

MAXTEMP improves precision of Ne estimation by leveraging multigenerational temporal data in genetic monitoring programs.

Practical considerations regarding estimating Ne when generations overlap

The paper examines how overlapping generations affect estimates of effective population size (Ne) and provides conditions under which unbiased estimates can be achieved.

Information theoretic inference of magnitude and direction of gene flow in metapopulation networks using nyemtaay, with potential for applications in metastasizing cancer clonal cell origin analysis

Covering the bases: population genomic structure of Lemna minor and the cryptic species L. japonica in Switzerland

This study uses whole-genome sequencing to analyze population genomic structure in Lemna minor and the cryptic species L. japonica in Switzerland, revealing distinct genetic clusters and population patterns.

Island demographics and trait associations in white-tailed deer

The paper analyzes genetic diversity and trait associations in island white-tailed deer populations to identify genes linked to leucism, malocclusions, and body size.

Previously unmeasured genetic diversity explains part of Lewontin's paradox in a k-mer-based meta-analysis of 112 plant species

The paper investigates Lewontin's paradox by comparing k-mer-based and SNP-based genetic diversity metrics across 112 plant species, finding that k-mer diversity scales more strongly with population size.

Inference of continuous gene flow between species under misspecified models

This study investigates biases in inferring gene flow between species under misspecified models and finds that pulse introgression models are more robust to model misspecification than continuous migration models.

Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring

This study identifies copy number variation and high genetic diversity at immune-related loci in herring, showing these regions are blind spots in short-read genome scans.

Distinct genome architecture underlies fine-scale population differentiation in two common European bumblebees (Bombus pascuorum and Bombus lapidarius)

The paper analyzes whole-genome data from two European bumblebee species to reveal fine-scale population structure and species-specific genomic divergence patterns, including a chromosomal inversion in B. pascuorum.

Unraveling Genome- and Immunome-wide Genetic Diversity in Jaguars (Panthera onca): Implications for Targeted Conservation

This study analyzes genetic diversity in jaguars across three geographic regions, identifying population structure and immune gene variability to guide conservation strategies.

Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

The paper analyzes genome-wide polymorphic data from the Balearic lizard Podarcis lilfordi to explore its population genetics and phylogeographic history, finding well-differentiated populations and evidence of origin in Mallorca.

Population genomic analysis reveals cryptic population structure in the commercially important Lake Malawi cichlid Copadichromis mloto

The paper analyzes whole-genome sequencing data of Lake Malawi cichlids to reveal cryptic population structure and potential undescribed species diversity in Copadichromis mloto.

Steep logarithmic increase of genetic variation in natural Arabidopsis thaliana accessions across geographic scales

The paper compares genetic variation across different geographic scales in Arabidopsis thaliana, finding that local populations contain a significant proportion of continental variation and a logarithmic relationship between genetic and geographic distance.

Recent adaptation in an imperiled salmonid revealed by museum genomics

The paper uses museum genomics to compare historical and contemporary steelhead populations, finding minimal introgression and a decline in migration-associated haplotypes over time.

genomalicious: serving up a smorgasbord of R functions for performing and teaching population genomic analyses

GENOMALICIOUS provides an R package with functions for population genomic analyses, simplifying data manipulation and visualization across different tools and environments.

Decoupled genetic and epigenetic variation in the montane endemic Erodium cazorlanum (Geraniaceae) and a widespread congener

The paper investigates genetic and epigenetic variation in two Erodium species, finding no genetic structure but significant epigenetic variation, particularly in DNA methylation patterns.

Computationally efficient demographic history inference from allele frequencies with supervised machine learning

This paper introduces donni, a machine learning-based method for demographic history inference that is faster and more efficient than dadi while maintaining similar accuracy.

Adaptation across a precipitation gradient from niche center to niche edge

The paper examines adaptive genetic variation in Lactuca serriola along a precipitation gradient, identifying candidate genes under selection and predicting adaptive shifts in response to climate change.

Universal baleen whale microsatellite panel for individual identification and power to detect parentage

The paper develops a universal set of microsatellite loci for baleen whale individual identification and parentage analysis, showing its utility across four species.