Federico Lopez

The genetic foundations of convergent traits Nature Reviews Genetics, Published online: 02 February 2026; doi:10.1038/s41576-026-00933-7Convergent phenotypic evolution, the independent acquisition of similar or nearly identical traits in multiple species, is widespread. Allard and Kumar explore the spectrum of molecular convergence in multicellular organisms, evaluate computational and artificial intelligence-based methods for detecting adaptive genetic convergence, and highlight how comparative genomics of convergent phenotypes informs complex trait evolution and human health.

New online! The genetic foundations of convergent traits

Emergence and evolution of protein-coding de novo genes Nature Reviews Genetics, Published online: 28 January 2026; doi:10.1038/s41576-025-00929-9De novo gene evolution entails the birth of new genes from previously non-coding DNA. In this Review, Bornberg-Bauer and Eicholt overview how protein-coding de novo genes are identified, the mechanistic and evolutionary processes underlying their emergence and evolution, and the patterns in their encoded protein structures.

ICYMI: New online! Emergence and evolution of protein-coding de novo genes

What were the first animals? The fierce sponge–jelly battle that just won’t end For almost two decades, scientists have debated whether sponges or comb jellies are the first animal lineage. Now some are calling for a more harmonious approach.

For almost two decades, scientists have debated whether sponges or comb jellies are the first animal lineage. A feature in Nature describes how some researchers are calling for a more harmonious approach. #evosky 🧪

Disgusting.

I wrote today about AlphaGenome, Google DeepMind's AI for DNA. It's powerful, experts told me, but it won't solve the mysteries of the genome overnight. Gift link: nyti.ms/4k5NFIl

This is figure 1, which shows AlphaGenome model architecture, training regimes and comprehensive evaluation performance.

A paper in Nature presents AlphaGenome, a deep learning model that can predict the function of long DNA sequences, up to one million base pairs. The tool can predict how DNA sequence variations affect different biological processes. go.nature.com/4t5JQa7 🧬 🧪

Structural genomics sheds light on protein functions and remote homologs across the insect tree of life - Cell Research Cell Research - Structural genomics sheds light on protein functions and remote homologs across the insect tree of life

A phylogeny of 4'854 #insects --- with structural #genomics shedding light on protein functions & remote homologs www.nature.com/articles/s41... #biodiversity

We've got ISSUES. Literally.

We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?

arxiv.org/abs/2601.07563

A 🧵 1/n

This is Kupiansk today. Once a thriving town of 25,000 in Kharkiv region, now nothing but ruins and ash.

Russia obliterated it. Murdered or drove out its people, and bombed it into dust.

A Beginner's Guide to Structural Variants in Eco‐Evolutionary Population Genomics Whole-genome sequencing (WGS) has greatly expanded researchers' ability to study structural variants (SVs), that is, the variation in the presence, number, orientation or position of a DNA sequence. ....

📄 A beginner's guide to structural variants in eco-evolutionary population genomics 🧬

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onlinelibrary.wiley.com/doi/10.1111/...

A photo of a pink grasshopper perched on two crossed blades of grass.

Ever seen a pink grasshopper? A genetic mutation called erythrism (overproduction of red pigment) leaves some individuals looking pretty in pink! Though these rare insects are beautiful, their vivid coloring makes hiding from predators more difficult.
Photo: Back from the Brink, CC BY-NC 2.0, flickr

russia is preparing another massive combined attack to freeze us, Ukrainians to death.

This is a large-scale crime against humanity, unfolding right now, live.

The species problem evolving in the Anthropocene Nature Reviews Biodiversity, Published online: 16 January 2026; doi:10.1038/s44358-025-00125-xThe question of how to define a species has a long history and continued relevance for ongoing biological and conservation research. This Review describes the history of the species problem, and explores how novel evolutionary pressures and constraints of the Anthropocene might be complicating species definitions even further.

ICYMI: New online! The species problem evolving in the Anthropocene

How can natural history museums help nature recover? It is widely accepted that we face a biodiversity crisis due to human activities, and we need active conservation interventions to address it. Natural history museums have recently made public commitments to play a more active role in helping to address the biodiversity crisis. What role might they play in helping nature recover? To answer this question, we recognise a hierarchy of conservation interventions (species, community and whole systems) and illustrate the role that museums can play in these. We also discuss how museums enable people to engage with conservation science. While barriers remain, there are significant opportunities for the conservation community to better integrate collections into their research. We need museums to help enable this to happen.

Online now: How can natural history museums help nature recover?

January issue: Review from Alexander Pyron examining the challenges and questions for the species problem in the Anthropocene. 🧪🌎
Web link: go.nature.com/4pK9s9C
Readcube: rdcu.be/eZInO

Harvard slipped on a global college ranking list as Chinese universities raced ahead, recent evidence of a troubling trend for U.S. academia as the Trump administration slashes research funding. Educators and experts say the shift is a problem for the U.S. as a whole. nyti.ms/4qSP0UO

New work from @miyapan.bsky.social and our team, bringing ant, bee, and wasp labs together. @chuanxinyu.bsky.social shows that the ANTSR locus we discovered in ants has determined sex for 150+ My across bees and stinging wasps 🐜🐝, despite virtually no sequence conservation 😮 doi.org/10.1073/pnas...

That is what a Denial of Peer-Review Attack looks like (DOPRA: credit to @lpachter.bsky.social for the term) x.com/lpachter/sta...

Pesticides and habitat loss additively reduce wild bees in crop fields - Nature Ecology & Evolution The authors synthesize bee assemblage data from 681 crop fields across three continents, finding that local pesticide hazards and decreasing adjacent semi-natural habitats both negatively affected wil...

Our new paper, co-authored by Riho and Péter, titled "Pesticides and habitat loss additively reduce wild bees in crop fields", is published in Nature Ecology & Evolution. The study emphasizes the need to reduce pesticide impacts and restore habitats for promoting wild bees. doi.org/10.1038/s415...

This is figure 1, which gives an overview of the approach to generate and integrate genomic data on the 4D nucleome.

A paper in Nature presents a detailed map of human chromosomes within the nucleus. This resource provides a foundation for an improved understanding of how the physical layout of human DNA is associated with biological expression. go.nature.com/4pI8knB 🧬 🧪

This is figure 1, which shows a summary of the systematic review dataset.

Genetic diversity has declined within two-thirds of more than 600 species over the past three decades, according to research published in Nature in January. The findings highlight the need for conservation efforts to prevent genetic diversity loss. go.nature.com/42EpVo5 🧪

MBE | SLiM 5: Eco-evolutionary Simulations Across Multiple Chromosomes and Full Genomes

Haller, Ralph & Messer present SLiM 5, a major extension of the SLiM simulation framework for simulating multiple chromosomes, enabling a heightened level of realism for full-genome simulations.

🔗 doi.org/10.1093/molbev/msaf313

#evobio #molbio #compbio

#Kyiv

This is terror.
This is what Russia does.

Christmas attack on civilians in Kyiv. Sure, the Russians want peace

Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism - Nature Ecology & Evolution Population genetics analysis in a phylogenetic framework shows convergent evolution in the genomes of five brood-parasitic species, including selection on genes involved in spermatogenesis, sperm func...

📄 Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism 🧬🐦

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www.nature.com/articles/s41...

Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual - Nature Communications Insect genomics is entering a telomere-to-telomere (T2T) era. This study presents a 596-Mb T2T genome of an individual male Bactrocera dorsalis—a species with atypical telomeres, centromeres, and sex-...

📄 Telomere-to-telomere genome assembly of the Dipteran Bactrocera dorsalis from a single individual 🧬🪰

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www.nature.com/articles/s41...

Promises kept...

The past and future of known biodiversity: Rates, patterns, and projections of new species over time The number of known species on Earth is increasing rapidly, suggesting unexpectedly large numbers of many groups.

Fascinated to learn that we are still discovering new species at the highest rate ever. Mapping Earth's biodiversity is far from over, and while we learn more and more about it, let's protect what we do know as well as we can!
www.science.org/doi/10.1126/...

Ukraine gave up nuclear warheads for security promises that collapsed when Russia attacked.

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