New genome assemblies have been arriving at a rapidly increasing pace, thanks to decreases in sequencing costs and improvements in third-generation sequencing technologies^1–3. For example, the number of vertebrate genome assemblies currently in the NCBI (National Center for Biotechnology Information) database⁴increased by more than 50% to 1,485 assemblies in the year from July 2018 to July 2019. In addition to this influx of assemblies from different species, new human de novo assemblies⁵are being produced, which enable the analysis of not only small polymorphisms, but also complex, large-scale structural differences between human individuals and haplotypes. This coming era and its unprecedented amount of data offer the opportunity to uncover many insights into genome evolution but also present challenges in how to adapt current analysis methods to meet the increased scale. Cactus⁶, a reference-free multiple genome alignment program, has been shown to be highly accurate, but the existing implementation scales poorly with increasing numbers of genomes, and struggles in regions of highly duplicated sequences. Here we describe progressive extensions to Cactus to create Progressive Cactus, which enables the reference-free alignment of tens to thousands of large vertebrate genomes while maintaining high alignment quality. We describe results from an alignment of more than 600 amniote genomes, which is to our knowledge the largest multiple vertebrate genome alignment created so far.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity^1,2,3,4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference⁵, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions^1–3. Here we address these issues by analysing the genomes of 363 bird species⁴ (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous–Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Terebelliformia—“spaghetti worms” and their allies—are speciose and ubiquitous marine annelids but our understanding of how their morphological and ecological diversity evolved is hampered by an uncertain delineation of lineages and their phylogenetic relationships. Here, we analyzed transcriptomes of 20 terebelliforms and an outgroup to build a robust phylogeny of the main lineages grounded on 12,674 orthologous genes. We then supplemented this backbone phylogeny with a denser sampling of 121 species using five genes and 90 morphological characters to elucidate fine-scale relationships. The monophyly of six major taxa was supported: Pectinariidae, Ampharetinae, Alvinellidae, Trichobranchidae, Terebellidae and Melinninae. The latter, traditionally a subfamily of Ampharetidae, was unexpectedly the sister to Terebellidae, and hence becomes Melinnidae, and Ampharetinae becomes Ampharetidae. We found no support for the recently proposed separation of Telothelepodidae, Polycirridae and Thelepodidae from Terebellidae. Telothelepodidae was nested within Thelepodinae and is accordingly made its junior synonym. Terebellidae contained the subfamily-ranked taxa Terebellinae and Thelepodinae. The placement of the simplified Polycirridae within Terebellinae differed from previous hypotheses, warranting the division of Terebellinae into Lanicini, Procleini, Terebellini and Polycirrini. Ampharetidae (excluding Melinnidae) were well-supported as the sister group to Alvinellidae and we recognize three clades: Ampharetinae, Amaginae and Amphicteinae. Our analysis found several paraphyletic genera and undescribed species. Morphological transformations on the phylogeny supported the hypothesis of an ancestor that possessed both branchiae and chaetae, which is at odds with proposals of a “naked” ancestor. Our study demonstrates how a robust backbone phylogeny can be combined with dense taxon coverage and morphological traits to give insights into the evolutionary history and transformation of traits.

Amphisamytha has five currently recognized species. One of these, A. galapagensis has been reported from numerous hydrothermal vents and methane seeps across the Pacific Ocean. Here, a collection of Amphisamytha from a range of Pacific habitats, as well as Amathys lutzi from Atlantic hydrothermal vents, were studied using morphology and DNA sequences from mitochondrial (COI and 16S rRNA) and nuclear (18S rRNA) genes. Phylogenetic analyses revealed a deep-sea clade comprised of the previously recognized Amphisamytha species, and three lineages that are treated as new species. The morphologically distinct Amathys lutzi was nested within Amphisamytha and the monotypic Amathys is treated as a junior synonym of Amphisamytha, with a resulting name change to Amphisamytha lutzi comb. nov. A revision of the other Amphisamytha species, the description of three new species, and a key are provided. The geographic range of the ‘cosmopolitan’ A. galapagensis is restricted to hydrothermal vents of the East Pacific Rise and the Galápagos Ridge. Amphisamytha fauchaldi, previously only known from sedimented hydrothermal vents of the Guaymas Basin (Gulf of California, Mexico), is recorded from cold seeps off the coasts of Costa Rica and Oregon. Amphisamytha carldarei sp. nov. is described from hydrothermal vents of the northeast Pacific (Juan de Fuca), while A. jacksoni sp. nov. spans much of the East Pacific Rise and is sympatric with A. galapagensis for part of its range. Amphisamytha julianeae sp. nov. is found at western Pacific vent systems in sympatry with A. vanuatuensis. Relaxed molecular clock analyses were calibrated using the vicariant event involving the Farallon-Pacific Ridge in the northern Pacific Ocean. This provides mean dates for the origin of the deep-sea Amphisamytha clade at 44 or 55 million years ago, and the separation of the Pacific–Atlantic sister-species pair at 13 or 21 million years ago, depending on the tree used. http://www.zoobank.org/urn:lsid:zoobank.org:pub:502BC05E-FFB9-4FFB-B367-95F628AD6456