Andrea Manica

The paper analyzes diversity in Ediacaran Avalon assemblage communities, finding that alpha diversity is more influenced by local assembly than broader environmental factors.

geoGraph models organism movement and connectivity across geographic space using hexagonal grids, improving accuracy over rectangular grids by avoiding distortion.

The paper evaluates active vs passive riparian restoration in oil palm plantations, finding active restoration provides better thermal stability and microhabitat diversity under current and future climates.

The paper identifies recent positive selection of MEFV mutations in Armenians linked to the first Yersinia pestis plague pandemic, suggesting resistance to plague as the selective agent.

The paper examines parallel visual adaptations in two coral reef fish species pairs under different light environments, finding convergent shifts in cone sensitivities achieved through distinct opsin gene sets.

This paper investigates how reproductive mode influenced community dynamics and diversity patterns in Ediacaran animal communities, finding that stolon reproduction limited diversification until the onset of sexual reproduction.

This study identifies fine-scale population structure within Madagascar using genome-wide data, revealing distinct subpopulations and historical migration patterns.

The paper shows that cultural norms and mobility patterns in hunter-gatherer societies influence genetic diversity and reduce homozygosity, preserving fitness.

tidypopgen provides an R package for streamlined population genetic analysis of SNP data, demonstrating a complete workflow in under 25 lines of code.

This study reconstructs the evolutionary history of sperm across 32 species, identifying a conserved core of gene families and linking ancient sperm components to human infertility.

This study compares genomic adaptations in two distantly related reef fish families to environmental changes post-Isthmus of Panama formation, finding limited molecular parallelism despite shared selective pressures.

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.

This study investigates how biological legacies influenced recolonisation dynamics in Avalon palaeocommunities by analyzing spatial patterns of Fractofusus fragments and survivor fronds.

This study combines palaeoproteomic and genetic analyses to show that dairy consumption in Armenia dates back to the late fourth millennium BCE, but lactase persistence variants remained rare, suggesting cultural adaptations to fermented dairy.

The paper investigates community ecology dynamics on Fiji reefs, finding depth and soft coral density influence benthic community structure and diversity.

tidygenclust provides an R package for population genetics clustering, integrating ADMIXTURE, fastmixture, and Clumppling with improved workflow and visualisation.

This paper retrieves ancient enamel protein sequences from a 21-24 Ma rhinocerotid, providing new phylogenetic insights into Rhinocerotidae diversification during the middle Eocene-Oligocene.

The paper estimates malaria transmission risk in sub-Saharan Africa over 74 kya and shows humans avoided malaria hotspots, shaping demography and population structure.

The paper models Homo sapiens evolution as a Pan-African metapopulation, showing how climate and connectivity shaped genetic and morphological diversity over 200,000 years.

The paper links changes in stone tool attributes during the Middle-to-Late Stone Age transition in eastern Africa to climatic seasonality, showing a correlation between tool size and shape with environmental variability.

Low-ABC improves demographic inference from low-coverage whole-genome data by using genotype likelihoods instead of called genotypes, enabling reliable analysis of population history.

This study links Acheulean handaxe production in Europe to specific climate and ecological conditions, showing associations with winter temperatures and precipitation patterns.

The paper curates a dataset of 34 high-coverage shotgun human genomes, including ancient and modern samples, along with the genetic pipeline used for processing.

This paper models the impact of climate and terrain on human ancestral genetic lineages, showing that these factors explain lineage divergence and migration patterns.

The paper introduces mtDNAcombine, a tool for combining mtDNA sequences from multiple studies to facilitate demographic analysis.

The paper shows Ancient Beringians have admixture from Amur River Basin populations and are not the deepest American lineage.

This study shows that aligning ancient DNA data to variation graphs reduces reference bias and improves indel detection compared to traditional linear reference methods.

The paper analyzes the whale shark genome to identify genetic features correlated with body size, metabolic rate, and lifespan, finding unique genomic traits in this species.

This study analyzes genomic data to show Armenians remained unadmixed until the Bronze Age, then experienced a Sardinian-like genetic input, suggesting large-scale population movements in the Middle East.

This study compares the cost-effectiveness and quality of chromosome-scale genome assemblies using PromethION and PacBio sequencing for the Korean reference genome KOREF, finding PromethION to be more cost-effective with comparable or better quality.