Models trained with noisy genomes extend bacterial phenotype prediction into deep time

Predicting phenotype from genotype in extant organisms is increasingly tractable through the accumulation of genome sequences and the development of machine-learning algorithms. Here we show that mach...

biorxiv.org

Gene swapping helped build the planet's decomposers

A new study reveals that horizontal gene transfer contributed to the repeated evolution of fungi-like, absorption-feeding life across eukaryotes.

oist.jp

Phylogenomic mixture models outperform homogeneous and partitioned models

Abstract. Significant advances have been made in resolving the tree of life, but many nodes remain debated. The last two decades saw the emergence of mixtu

academic.oup.com

Conflict in ant phylogeny results from complex interaction between multiple evolutionary signals and tree reconstruction artifacts

Abstract. Ants, Formicidae, are a group of small social insects that inhabit nearly all terrestrial environments. Three competing hypotheses of ant relatio

academic.oup.com

100 million years ago, an ‘evolutionary fuse’ was lit in the deep ocean, sparking squid diversification

New evolutionary mapping suggests deep sea origins and mass extinction triggered diversification of modern squid and cuttlefish.

oist.jp

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature

Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgardarchaeota, in conditions that may have given rise to early eukaryotes.

go.nature.com

a man walking in a field with an umbrella

ALT: a man walking in a field with an umbrella

media.tenor.com

Postdoctoral researcher Phylogenomics and metagenomics

Are you just as excited as we are about the fascinating world of microorganisms? Do you want to contribute to exploring and genomically characterize novel prokaryotic lineages? Do you have a PhD degre...

wur.nl

'Jumping genes’ help scientists resolve tree of life

Termite study provides researchers with template to solve ancient evolutionary mysteries.

oist.jp

The evolutionary mysteries of a rare parasitic plant

New study maps the strange genomes of Asia-Pacific Balanophora species, giving new insights into the evolution of parasitic plants and an unconventional role of plastids.

oist.jp

GTRpmix: A Linked General Time-Reversible Model for Profile Mixture Models

Abstract. Profile mixture models capture distinct biochemical constraints on the amino acid substitution process at different sites in proteins. These mode

academic.oup.com

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature

Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.

nature.com

Complex life developed earlier than previously thought

New evidence-based evolutionary model provides access to the beginning of complex life with unprecedented accuracy.

oist.jp

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature

Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...

nature.com

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature

Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex ar...

nature.com

Phylogenetic reconciliation supports a methanogenic ancestor of the Archaea and a derived origin for host-associated lineages

The phylogeny of the Archaea continues to be revisited and revised as new groups are discovered and phylogenetic methods improve, but key questions about their early evolution remain. It has been sugg...

biorxiv.org

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution

Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

nature.com

Fungi set the stage for life on land hundreds of millions of years earlier than thought

From fossils and rare genetic ‘gene-swap’ clues, researchers reconstruct fungi’s deep timeline and reveal how they helped shape early Earth ecosystems.

oist.jp

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution

Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

doi.org

Island ant communities show signs of ‘insect apocalypse’

79% of endemic species show signs of decline, highlighting the vulnerability of island biodiversity to ecosystem changes.

oist.jp

Molecular mechanism of ultrafast transport by plasma membrane Ca2+-ATPases - Nature

Structural insights into ultrafast Ca2+ transport by plasma membrane Ca2+-ATPases are provided, highlighting an essential role for PtdIns(4,5)P2 dynamics.

dx.doi.org

Genomic signatures indicate biodiversity loss in an endemic island ant fauna

Insect populations have declined worldwide, but the extent and drivers of these declines are debated. Most studies rely on field surveys performed in the past century, leaving gaps in our understandin...

science.org