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Conceptualising the Last Eukaryotic Common Ancestor (LECA) is essential for unravelling early evolution, yet there is disagreement over what form LECA took. Here the authors examine four potential forms of LECA: an abstract phylogenetic state, a single cell, a population, and a consortium of organisms.

The root of the eukaryote Tree of Life is estimated from a new, larger dataset of mitochondrial proteins including all known eukaryotic supergroups, showing it lies between two multi-supergroup assemblages.

The Archaea was recognized as a third domain of life 40 years ago. In this Review, Emeet al. outline a brief history of the changing shape of the tree of life and examine how the recent discovery of diverse archaeal lineages has changed our understanding of the evolutionary relationships between the three domains of life and the origin of the eukaryotic cell.

This Review summarizes key events in the emergence of cellular complexity via eukaryogenesis in the light of developments in environmental and comparative genomics during the past decade.

Sexual reproduction in eukaryotes involves gamete fusion, mediated by fusogenic proteins. Here, the authors identify fusogenic protein homologs encoded within mobile genetic elements in archaeal genomes, solve the crystal structure of one of the proteins, and show that its ectopic expression can fuse mammalian cells, suggesting potential roles in cell-cell fusion and gene exchange.

An investigation of plant receptor-like kinases identifies regions of these proteins that control whether immune or symbiotic signalling pathways are activated, with minimal changes to specific residues in one of these regions being sufficient to alter signalling specificity.

Eukaryotic Argonaute proteins participate in RNA-guided RNA silencing pathways and are divided into AGO and PIWI clades, with functional and mechanistic differences. Here, the authors show that a deep-branching PIWI protein from Asgard archaea (the closest prokaryotic relatives of eukaryotes) displays hybrid features and may reflect an ancestral molecular architecture that preceded the divergence of eukaryotic AGOs and PIWIs.

It is unclear whether naturally evolved de novo proteins have stable, folded structures. Here, systematic identification and structural modeling of de novo genes, this study reveals that a small subset of these proteins may have well-folded structures, and were likely born with these structures.

A large phylogenomics study reveals that the symbiotic event that led to the emergence of organelles known as mitochondria may have occurred later in the evolution of complex cells than was thought. See Letter p.101

The pathogenic bacterium Pseudomonas aeruginosa can be found in vacuoles and cytoplasm within infected cells. Here, Schator et al. show that extracellular bacteria use a type-III secretion system to induce Ca²⁺ influx into host cells and promote vacuole escape of intracellular bacteria and in vivo dissemination.

The Aurora kinases orchestrate chromosome segregation and cell division. Zeeshan et al. studied divergent Plasmodium ARK2 and EB1 using live cell imaging, proteomics and functional genetics. These are critical components for atypical spindle dynamics during transmission stages.

RNA-binding motifs in eukaryotic proteins are presented in a comprehensive resource.

The mechanisms for replicating and segregating DNA are highly conserved across eukaryotes. A comparative genomic analysis of a free-living protist finds a surprising lack of protein complexes involved in these processes, suggesting that the organism uses alternative mechanisms to process DNA.

The ESCRT pathway is crucial for membrane remodelling in eukaryotes. Here, Hatano et al. explore the phylogeny, structure, and biochemistry of homologues of the ESCRT machinery and the associated ubiquitylation system in Asgard archaea, the closest living relatives of eukaryotes.

Pl@ntBERT is a language-based AI model that learned the ‘syntax’ of plant assemblages, predicting likely species and inferring habitats by modelling biotic relationships.

Single-cell sequencing of flagellated heterotrophic unicellular eukaryotes provides insights into the dynamics of mitochondrial genome evolution.

The role of wild and domesticated animals on alpine ecosystems is unclear. Here, the authors use sedaDNA from 14 European alpine lakes to demonstrate a positive association between wild and domesticated animal and plant diversity through the past 14 thousand years.

A species-level phylogenetic analysis of the high-elevation flora of the European Alps reveals that the flora is young and colonist rich. Its assembly was primarily driven by the Pleistocene climatic cycles, rather than ancient orogenic events.

An environmentally safe means of mosquito control is the application of Bacillus thuringiensis israelensis, which produces a cocktail of four naturally crystalline proteins exclusively toxic to mosquito. Here the authors report the atomic-resolution structures of Bti Cry11Aa and related Btj Cry11Ba solved de novo through Serial Femtosecond Crystallography on naturally-occurring nanocrystals.

The high-resolution global model of soil temperature and snow cover change in mountain ecosystems developed here shows that areas nearby glaciers are warming faster than other mountain regions, and these effects are particularly rapid in tropical mountains.

At a time when protecting the environment is urgent, dealing with inherent uncertainties in the responses of biodiversity to disturbances is essential. This study promotes a promising tool to assess the vulnerability of species assemblages to guide protection efforts even if species response and disturbance regimes are poorly documented.

Here, the authors use full-plastome phylogenomics and multiclade comparative models to reconstruct the tempo and drivers of six European Alpine angiosperm lineages before and during the Pleistocene. They find that geographic divergence and bedrock shifts drive speciation events, while diversification rates remained steady.

Using 32 ecological networks (host–parasite, plant–pollinator, plant–herbivore and other food webs), the authors show that several network properties scale with the size of the sampling area, suggesting a new type of biodiversity–area relationship.

A large-scale metagenomic analysis of plant and mammal environmental DNA reveals complex ecological changes across the circumpolar region over the past 50,000 years, as biota responded to changing climates, culminating in the postglacial extinction of large mammals and emergence of modern ecosystems.

Here, the authors use sedimentary DNA, pollen, fungal spores, chironomids, and microcharcoal from an alpine lake core to reconstruct vegetation across 12,000 years. They find that vegetation responded to climate in the early Holocene, followed by a shift to human activity from 6000 years onward corresponding with an increase in deforestation and agropastoralism.

Rewetting of plant litter accumulated in dry riverbeds releases pulses of CO₂, reveals a global analysis of intermittent rivers and ephemeral streams.

Bacillus thuringiensis israelensis (Bti) produces the naturally-crystalline proteinaceous toxin Cyt1Aa that is toxic to mosquito larvae. Here the authors grow recombinant nanocrystals of the Cyt1Aa protoxin in vivo and use serial femtosecond crystallography to determine its structure at different redox and pH conditions and by combining their structural data with further biochemical, toxicological and biophysical analyses provide mechanistic insights into the Cyt1Aa bioactivation cascade.

Analysis of two-million-year-old ancient environmental DNA from the Kap København Formation in North Greenland shows there was an open boreal forest with diverse plant and animal species, of which several taxa have not previously been detected at the site, representing an ecosystem that has no present-day analogue.

Climate warming has driven increased rockfall from an unstable mountain slope in the Swiss Alps, according to a record of rockfall activity spanning the past century based on tree damage.

Agricultural expansion to grow food, fibre and biofuel will further threaten biodiversity. This study finds that almost 90% of terrestrial vertebrate species will lose habitat to such expansion, but proactive food policies could reduce these threats.

By analysing plant and nematode DNA from sites all around the Arctic, it is shown that vegetation before about 10,000 years ago contained more forbs (non-graminoid herbaceous vascular plants) than previously believed, which changes our understanding about the functioning of the diverse northern ecosystem that existed at this time.