Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. 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.

The extent to which prehistoric migrations of farmers influenced the genetic pool of western North Africans remains unclear. Archaeological evidence suggests that the Neolithization process may have happened through the adoption of innovations by local Epipaleolithic communities or by demic diffusion from the Eastern Mediterranean shores or Iberia. Here, we present an analysis of individuals' genome sequences from Early and Late Neolithic sites in Morocco and from Early Neolithic individuals from southern Iberia. We show that Early Neolithic Moroccans (∼5,000 BCE) are similar to Later Stone Age individuals from the same region and possess an endemic element retained in present-day Maghrebi populations, confirming a long-term genetic continuity in the region. This scenario is consistent with Early Neolithic traditions in North Africa deriving from Epipaleolithic communities that adopted certain agricultural techniques from neighboring populations. Among Eurasian ancient populations, Early Neolithic Moroccans are distantly related to Levantine Natufian hunter-gatherers (∼9,000 BCE) and Pre-Pottery Neolithic farmers (∼6,500 BCE). Late Neolithic (∼3,000 BCE) Moroccans, in contrast, share an Iberian component, supporting theories of trans-Gibraltar gene flow and indicating that Neolithization of North Africa involved both the movement of ideas and people. Lastly, the southern Iberian Early Neolithic samples share the same genetic composition as the Cardial Mediterranean Neolithic culture that reached Iberia ∼5,500 BCE. The cultural and genetic similarities between Iberian and North African Neolithic traditions further reinforce the model of an Iberian migration into the Maghreb.

One Sentence Summary: 40The passenger pigeon's abundance and recombination landscape led to natural selection 41 dominating genome-wide neutral site evolution. 42 43 44 3 Abstract: 45The extinct passenger pigeon was once the most abundant bird in North America, and 46 possibly the world. While theory predicts that large populations will be more genetically 47 diverse, passenger pigeon genetic diversity was surprisingly low. To investigate this, we 48 analysed 41 mitochondrial and 4 nuclear genomes from passenger pigeons and 2 genomes 49 from band-tailed pigeons, which are passenger pigeons' closest living relatives. Passenger 50pigeons' large population size appears to have allowed for faster adaptive evolution and 51 removal of harmful mutations, driving a huge loss in their neutral genetic diversity. These 52 results demonstrate the impact selection can have on a vertebrate genome, and contradict 53 results that suggested population instability contributed to this species' surprisingly rapid 54 extinction. 55 56 Main text: 57The passenger pigeon (Ectopistes migratorius) numbered between 3 and 5 billion individuals 58 prior to its 19th century decline and eventual extinction (1). Passenger pigeons were highly 59 mobile, bred in large social colonies, and their population lacked clear geographic structure 60 (2). Few vertebrates have populations this large and cohesive and, according to the neutral 61 model of molecular evolution, this should lead to a large effective population size (N e ) and 62 high genetic diversity (3). Preliminary analyses of passenger pigeon genomes have, 63 however, revealed surprisingly low genetic diversity (4). This has been interpreted within the 64 framework of the neutral theory of molecular evolution as the result of a history of dramatic 65 demographic fluctuations (4). However, in large populations, natural selection may be 66 particularly important in shaping genetic diversity: population genetic theory predicts that 67 selection will be more effective in large populations (3), and selection on one locus can 68 cause a loss of diversity at other loci, particularly those that are closely linked (5-8). It has 69 4 been suggested that this could explain why the genetic diversity of a species is poorly 70 predicted by its population size (9-11). 71 72We investigated the impact of natural selection on passenger pigeon genomes through 73 comparative genomic analyses of both passenger pigeons and band-tailed pigeons 74 (Patagioenas fasciata). While ecologically and physiologically similar to passenger pigeons, 75 band-tailed pigeons have a present-day population size three orders of magnitude smaller 76 than their close relative the passenger pigeon (2, 12, 13). 77 78We applied a Bayesian skyline model of ancestral population dynamics to the mitochondrial 79 genomes of 41 passenger pigeons from across their former breeding range ( Fig. 1A and 80 table S1) (14). This returned a most recent effective population size (N e ) of 13 million (95% 81 HPD: 2-58 million) and similar, stable N e...

Understanding when species diverged aids in identifying the drivers of speciation, but the end of gene flow between populations can be difficult to ascertain from genetic data. We explore the use of pairwise sequential Markovian coalescent (PSMC) modelling to infer the timing of divergence between species and populations. PSMC plots generated using artificial hybrid genomes show rapid increases in effective population size at the time when the two parent lineages diverge, and this approach has been used previously to infer divergence between human lineages. We show that, even without high coverage or phased input data, PSMC can detect the end of significant gene flow between populations by comparing the PSMC output from artificial hybrids to the output of simulations with known demographic histories. We then apply PSMC to detect divergence times among lineages within two real datasets: great apes and bears within the genus Ursus. Our results confirm most previously proposed divergence times for these lineages, and suggest that gene flow between recently diverged lineages may have been common among bears and great apes, including up to one million years of continued gene flow between chimpanzees and bonobos after the formation of the Congo River.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.