A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them

Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi

academic.oup.com

Unifying Retaria Research: A Common Framework for Studying Foraminifera and Radiolaria

Research on Foraminifera and Radiolaria has predominantly focused on their fossil remains. This synthesis identifies the “Big Five” disciplines of a unified Retaria research: diversity and evolution,...

onlinelibrary.wiley.com

Estimating Organism Abundance Using Within‐Sample Haplotype Frequencies of eDNA Data

Environmental DNA (eDNA) provides powerful insights into species presence and community composition but remains limited in its capacity to infer species abundance or population structure. Here, we sh...

onlinelibrary.wiley.com

Estimating recombination using only the allele frequency spectrum

Abstract. Standard methods for estimating the population recombination parameter, ρ, are dependent on sampling individual genotypes and calculating various

academic.oup.com

Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies

Abstract. Genomes contain the mutational footprint of an organism’s evolutionary history, shaped by diverse forces including ecological factors, selective

doi.org

Genomic insights into the origin of ecotypes

A century after Turesson introduced ecotypes as locally adapted subunits of species, their origins and nature remain debated. Recent advances in molecular ecology have breathed new life into the ecotype concept and significantly expanded our understanding of how ecotypes form. Here, we clarify how ecotypes can be distinguished from other forms of local adaptation, outline criteria for their recognition, and synthesise evidence on the ecological and evolutionary processes that give rise to them. We then evaluate what genomics has uncovered about the origin of ecotypes, revealing pronounced roles of pre-existing variation, large-effect loci, structural variants, gene regulation, and complex demographic histories. Our framework refines Turesson’s concept and highlights outstanding questions about the predictability, persistence, and evolutionary significance of ecotypes.

dlvr.it

Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos

Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...

doi.org

Ancient origin of an urban underground mosquito

Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...

science.org

A global coral phylogeny reveals resilience and vulnerability through deep time - Nature

The most recent common ancestor of the stony coral Scleractinia dates to about 460 million years ago and was probably a solitary, heterotrophic and free-living organism.

nature.com

Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation

The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...

biorxiv.org

GhostParser: A highly scalable phylogenomic approach for the identification of ghost introgression

A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed t...

biorxiv.org

The molecular evolutionary basis of species formation revisited

How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers lead to the origin of new species was proposed nea...

cell.com

Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods - Nature Communications

Accurate estimation of effective population size is critical for understanding population history but is often confounded by structure and data quality. Here, the authors show that GONE2 and currentNe...

nature.com

Coalescence and Translation: A Language Model for Population Genetics

Probabilistic models such as the sequentially Markovian coalescent (SMC) have long provided a powerful framework for population genetic inference, enabling reconstruction of demographic history and an...

biorxiv.org

Sex-biased Migration and Demographic History of the Big European Firefly Lampyris noctiluca

Abstract. Differential dispersion between the sexes can impact the colonization process and demographic history of a species. Here, we explored the demogra

academic.oup.com

Estimates of the Mutation Rate per Year Can Explain Why the Molecular Clock Depends on Generation Time

Abstract. Rates of molecular evolution are known to vary across species, often deviating from the classical expectation of a strict molecular clock. In man

academic.oup.com

A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies

Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic app...

onlinelibrary.wiley.com

Patterns and drivers of diatom diversity and abundance in the global ocean - Nature Communications

Using the Tara Oceans dataset, this study describes global patterns of diatom diversity, abundance and adaptation. The authors identify 25 distinct communities, with the Arctic as a hotspot, and highl...

nature.com