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...

The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1) plays a key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the functional importance of an amino acid change in humans, we reintroduced the archaic allele into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher surface complexity in cortical organoids with the archaic version of NOVA1. Moreover, levels of synaptic markers and synaptic protein coassociations correlated with altered electrophysiological properties in organoids expressing the archaic variant. Our results suggest that the human-specific substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may have had functional consequences for our species’ evolution.

The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. While theory predicts that large populations will be more genetically diverse and respond more efficiently to selection, passenger pigeon genetic diversity was surprisingly low. To investigate this we analysed 41 mitochondrial and 4 nuclear genomes from passenger pigeons, and 2 genomes from band-tailed pigeons, passenger pigeons’ closest living relatives. We find that passenger pigeons’ large population size allowed for faster adaptive evolution and removal of harmful mutations, but that this drove a huge loss in neutral genetic diversity. These results demonstrate how great an impact selection can have on a vertebrate genome, and invalidate previous results that suggested population instability contributed to this species’ surprisingly rapid extinction.

Many humans carry genes from Neanderthals, a legacy of past admixture. Existing methods detect this archaic hominin ancestry within human genomes using patterns of linkage disequilibrium or direct comparison to Neanderthal genomes. Each of these methods is limited in sensitivity and scalability. We describe a new ancestral recombination graph inference algorithm that scales to large genome-wide datasets and demonstrate its accuracy on real and simulated data. We then generate a genome-wide ancestral recombination graph including human and archaic hominin genomes. From this, we generate a map within human genomes of archaic ancestry and of genomic regions not shared with archaic hominins either by admixture or incomplete lineage sorting. We find that only 1.5 to 7% of the modern human genome is uniquely human. We also find evidence of multiple bursts of adaptive changes specific to modern humans within the past 600,000 years involving genes related to brain development and function.