Mark Blaxter

Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate ¹ . However, the evolutionary history of bats and the understanding of these adaptations remain unresolved. We analysed chromosome-level, long-read genome assemblies from 103 bat species, including 42 new assemblies, representing all 21 bat families. This dataset, expanded in scope and assembly quality, yielded a new bat phylogeny. We placed Myzopodidae as the earliest branch within Vespertilionoidea, and resolved yangochiropteran relationships, identifying Emballonuroidea and Vespertilionoidea as sister groups. Our analysis revealed a mosaic evolutionary history across bats and explained why previous phylogenetic studies were misled. Chromosomal ancestral-state reconstructions supported 26 ancestral bat chromosomes. We integrated a morphological dataset of 699 characters for 65 species, including 44 pre-Quaternary fossils and representatives of most living bat families, with neutrally evolving genomic sites. Fossilized birth–death and dispersal–extinction cladogenesis analyses showed that bats, and thus powered flight, probably originated in Europe in the late Palaeocene, refuting African and North American origins. Placement of the fossil † Vielasia in the oldest ‘Eochiroptera’ clade indicates that laryngeal echolocation predates crown-bat diversification. Total evidence dating, including the fossil taxa, significantly reduced unrepresented basal branch lengths compared with molecular-only divergence estimates. By integrating comprehensive genomic and morphological datasets, analysed using innovative methods, we resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats.

Sex determination (SD) in amphibians is poorly understood due to their large genomes, homomorphic sex chromosomes, and unresolved mechanisms. Examining new reference genomes of Eurasian fire-bellied toads (Bombina), we inferred err1Y as a Y-chromosomal sex determining gene. We mapped male-specific markers to a single-copy region on chromosome 2. This region contained err1Y, a duplicate of err1, an autosomal estrogen-related receptor. Err1Y is male- diagnostic in 24-chromosome Bombina, supporting a conserved XY-SD-system. Functional and structural analyses show that err1Y is enriched in juvenile testes and antagonizes estrogen signaling through a ligand-binding domain that lacks co-activator and DNA-binding function, promoting male differentiation. This is the first genetic SD-mode directly targeting the estrogen response, revealing a new route to poikilothermic vertebrate SD through neofunctionalization of duplicated nuclear receptor err1.

Identifying nematode species is challenging due to morphological plasticity and few diagnostic characters, especially in Panagrolaimus, which has many genetically distinct but morphologically similar cryptic species adapted to extreme environments. Morphology-based methods often fail to distinguish divergent Panagrolaimus, limiting discovery. Genome assemblies address these challenges by providing a detailed genetic blueprint for identification. We combined genome sequencing, phylogenetic analyses using 18S rRNA and ultra-conserved elements, and morphology to describe three novel species: Panagrolaimus einhardi sp. nov. (formerly Panagrolaimus sp. ES5, Rhineland, Germany), Panagrolaimus shuimeiren sp. nov. (Namib Desert, Namibia), and Panagrolaimus nebliphilus sp. nov. (Atacama Desert, Chile). Panagrolaimus einhardi is named after Prof. Einhard Schierenberg, a renowned expert and valued member of the nematode community, who isolated the species himself. The identifications are supported by high-quality assemblies from PacBio HiFi or Oxford Nanopore long reads. The P. einhardi assembly was scaffolded using Hi-C, yielding a 116 Mb collapsed assembly with 44 scaffolds (N50: 28 Mb). Panagrolaimus shuimeiren has an assembly size of 69 Mb (49 scaffolds, N50: 13 Mb), and P. nebliphilus an assembly size of 70 Mb (24 scaffolds, N50: 13 Mb). Integrating morphology and genomics clarifies biological diversity in cryptic-rich lineages like Panagrolaimidae, resolving relationships where morphology alone is ambiguous.

Summary: In animals, the germline is usually set aside early in development and its genome is protected to ensure faithful transmission of genetic information to future generations. Genetic alterations in somatic cells are not inherited by progeny, and the somatic genome does not have to be protected from change in the same way. In some species, programmed DNA elimination (PDE) results in the directed loss of genetic material from somatic cells. Here, we report extreme PDE in Auanema rhodense , a free-living nematode with a remarkable, trioecious life history and unusual patterns of sex chromosome inheritance. We find that nearly two thirds of the A. rhodense germline genome is eliminated from somatic cells, with DNA lost from chromosome ends as well as within chromosomes, resulting in fragmentation of the seven germline chromosomes into fourteen somatic chromosomes. Most eliminated DNA comprises multi-megabase tandem repeat blocks. Eliminated DNA on the X chromosome harbours germline-restricted repeats that are distinct from those on the autosomes. The eliminated DNA includes many highly-repeated non-coding RNA loci but few protein-coding genes. Elimination sites are strongly associated with a palindromic sequence motif that likely directs DNA breakage and new telomere repeat array addition. Cytologically, PDE begins at the 12-cell stage of embryogenesis, is synchronous across all chromosomes, and is characterised by the formation of transient micronucleus-like bodies. Together, these findings reveal unusually extensive PDE in a free-living nematode and raise the possibility that germline-restricted repeat architecture may contribute to the atypical sex chromosome inheritance observed in Auanema .

Lichens are symbiotic associations between filamentous fungi and photosynthetic micro-organisms, such as green algae and/or cyanobacteria, that result in a single anatomically complex structure that can thrive in environments inhospitable to most organisms, including arctic tundra, high mountains, and deserts. Recent evidence suggests that lichens may be even more complex than previously appreciated, containing multiple microbial constituents, but how genomes of the principal fungal symbiont (which provides the majority of biomass in lichen tissue) have been shaped during evolution is largely unexplored. Recently, giant transposable elements called Starships have been found in many genomes of filamentous fungi, but to which extent they occur in lichen-forming fungi is not known. In this report, we describe a Starship element from the lichen fungus Xanthoria parietina . This element, named Tangerine , contains several genes that have signatures of horizontal gene transfer from nonlichen-forming fungi, most likely from black yeasts of the Chaetothyriales, that are often lichen-associated. Repetitive sequences carried by Tangerine , and found in other sites in Xanthoria genomes, are affected by repeat-induced point mutation, a mechanism of genome defense against transposable elements, consistent with fungal sexual reproduction which always precedes new lichen formation by X. parietina . Tangerine ’s “captain” belongs to a newly defined family of tyrosine recombinases specific to lichen-forming Lecanoromycetes. Several other captain clades have signatures of horizontal gene transfer between distantly related lichen-forming fungi and nonmycobiont lichen-associated fungi. We speculate that Starships may play a significant, yet hitherto unrecognized role, in lichen genome evolution and provide a roadmap for further investigation.

We present a genome assembly of Thelazia callipaeda (nematode; Nematoda; Chromadorea; Rhabditida; Thelaziidae). The genome sequence has a total length of 117.59 megabases. Most of the assembly (75.82%) is scaffolded into 4 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has been assembled, with a length of 13.66 kilobases.

In recent years, many high-quality reference genome sequences for arthropod species have been generated. Although most genome papers describe their protocols and metrics, no consensus exists on the data that should be included in genome reports. Here, we review current standards across seven key stages of an arthropod genome project (budgeting, sourcing and vouchering, sample preparation and sequencing, genome assembly, analysis reproducibility, databasing, and genome annotation) and identify persistent gaps in standards as well as their implementation. To assess current standards reporting in the community, we surveyed 100 arthropod genome papers published in 2024. The use of long reads to assemble highly contiguous arthropod genomes is now standard practice when adequate input DNA is available, and basic assembly contiguity and conserved gene content statistics are consistently reported. However, there is less standardization in pre- and post-assembly procedures and metrics. When comparing Darwin Tree of Life (DToL) genome notes to other journals, publications from the latter group were less likely to describe compliance with ethical collection practices, sample vouchering, post-assembly curation steps, and assembly quality metrics beyond basic contiguity and completeness values. Genome annotation practices are highly variable: some genome note formats do not explicitly require annotation, and while the reporting rate of protein-coding gene annotations is higher in non-DToL publications, the submission rate of annotations to centralized sequence databases is much lower. Our findings highlight critical opportunities to harmonize reporting standards and promote their dissemination, ensuring that future arthropod genomes are both comparable and maximally reusable for large-scale comparative and applied research.

How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction—for example, parthenogens with rare sex or species where the paternal genome is set aside—have been found to carry either no sex chromosomes or sex chromosomes but no male-specific sex chromosome (i.e. no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome evolved once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare (∼10%) males that are needed for fertilization but that do not contribute to the female genome. Analyzing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: (i) they accumulated male-beneficial genes, and (ii) they display a strong fertilization drive, in that mainly Y-bearing sperm fertilize female oocytes. Both features are likely evolutionarily favorable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly “genetically useless,” males.

The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all vertebrate orders, families, genera, and eventually all species. Here we present the completion of VGP Phase I, delivering reference genomes for ∼97% of vertebrate orders, along with additional lineages within those orders, totaling 815 species and 1.6 trillion base pairs of main haplotype sequence. These genomes were assembled and annotated over an 8-year period (2018-2026) of rapid advances in genome sequencing, assembly, and annotation methods, alongside the growth of associated consortium initiatives and international collaborations. They represent some of the highest-quality vertebrate genomes currently available, and most have become the primary reference for their respective species in public databases. Comparative analyses across a subset of 579 species when we reached a threshold of 85% of orders allowed us to reconstruct the genome of the last common ancestor of all vertebrates 500 million years ago, identify diverse modes of sex chromosome evolution, reveal clade-specific three-dimensional genome architecture, discover methylated epigenetic landscapes across vertebrates, and provide a framework for studying gene and pseudogene evolution, immune loci, cancer-associated genes, and other trait-associated loci. Approximately a quarter of this subset are listed as Vulnerable to Critically Endangered by the IUCN Red List of Threatened Species, and have enabled more advanced genomic investigations of extinction risk. VGP Phase I delivers the reference backbone for vertebrate genomics, enabling discoveries that would otherwise remain out of reach across evolution, conservation, and medicine.

Tropical rainforests, and Amazonia in particular, contain more tree species than anywhere else, most of which arose through rapid evolutionary radiations ^1–3 . Rapid radiations are often catalysed by ecological opportunity ^4–6 , which in rainforest trees is presented by intense insect herbivore pressure, spurring the evolution of novel plant defence chemistry to escape it ⁷ . However, we do not understand how long-lived trees can adapt quickly enough to keep pace with rapidly-evolving insect herbivores. Here we show that hybridisation in rainforest trees, which was considered rare, allows exchange of gene clusters used in chemical defence against herbivore attack, facilitating rapid adaptation and diversification. Using genome sequencing for 461 individuals from the genus Inga , a characteristic Amazonian tree radiation, we find that regional tree communities form syngameons - networks of closely related, co-occurring species connected by gene flow. Integrating these genomes with herbivore abundance data from the same communities across the tropical Americas, we show that herbivore compositional turnover coincides with local, recurrent interspecific transfer of defence gene clusters that are retained by balancing selection, consistent with fluctuating selective pressure imposed by shifting herbivore communities. Together, our results demonstrate that hybridisation allows long-lived tropical trees to rapidly evolve chemical defences, fuelling adaptation to the relentless insect herbivory that structures the world’s most species-rich forests.