W. F. Martin

The probability of a unique gene occurrence at the tips of a phylogenetic tree in the absence of horizontal gene transfer (the last-one-out)

The paper calculates the probability of last-one-out gene distributions under a Markovian loss model and shows gene loss can explain observed patterns resembling horizontal gene transfer.

A hydrogen dependent geochemical analogue of primordial carbon and energy metabolism

This paper demonstrates that hydrothermal minerals catalyze CO2 fixation with H2 under alkaline conditions, producing organic compounds similar to the acetyl-CoA pathway.

Bacterial genes outnumber archaeal genes in eukaryotic genomes

This paper analyzes the origin of genes in eukaryotic genomes, finding that bacterial genes outnumber archaeal genes, with photosynthetic lineages showing higher bacterial contributions.

Gene duplications trace mitochondria to the onset of eukaryote complexity

The paper identifies gene duplication events in the last eukaryote common ancestor (LECA) that suggest mitochondrial gene transfer preceded the onset of eukaryotic complexity.

Anomalous phylogenetic behavior of ribosomal proteins in metagenome assembled genomes

The paper shows that Asgard and CPR metagenome assembled genomes (MAGs) fail to meet basic phylogenetic criteria due to their anomalous ribosomal protein evolutionary histories, suggesting they are binning artifacts.

Mitochondria branch within Alphaproteobacteria

The paper investigates the phylogenetic placement of mitochondria within Alphaproteobacteria using alternative methods to address compositional heterogeneity.

Autocatalytic chemical networks preceded proteins and RNA in evolution

The paper identifies autocatalytic networks in ancient microbial metabolism, showing small-molecule catalysis preceded polymers in biochemical evolution.

Adaptation to life on land at 21% O2 via transition from ferredoxin- to NADH-dependent redox balance

The paper shows algae maintain anaerobic metabolism enzymes at 21% O2, while land plants and animals shifted to NADH-based redox balance during terrestrialization.

Nitrogenase inhibition limited oxygenation of the Proterozoic atmosphere

The paper proposes that nitrogenase inhibition by oxygen limited atmospheric oxygenation for over a billion years until terrestrial plants separated O2 production from N2 fixation.

Enlarged and highly repetitive plastome of Lagarostrobos and plastid phylogenomics of Podocarpaceae

This study assembles plastomes from eight Podocarpaceae genera, revealing Lagarostrobos has the largest and most rearranged plastome, and clarifies phylogenetic relationships within the family.

Lipids are the preferred substrate of the protist Naegleria gruberi, relative of a human brain pathogen

This study shows that Naegleria gruberi relies on lipid oxidation for growth and energy metabolism, unlike glucose or amino acids, and suggests similar metabolism in its pathogenic relative N. fowleri.

Count does not recover major events of gene flux in real biological data

The paper tests Count's ability to detect mass gene transfer events and finds it biases towards uniform distribution rather than sporadic acquisition and differential loss.