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.

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale.

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No evidence for an association between Clock gene allelic variation and migration timing in a long-distance migratory shorebird (Limosa lapponica baueri). Oecologia, 191(4), 843-859.

While avian migration timing is clearly influenced by both breeding and non-breeding geography, it is challenging to identify the relative and interdependent roles of endogenous programs, early-life experience, and carry-over effects in the development of adult annual schedules. Bar-tailed godwits Limosa lapponica baueri migrate northward from New Zealand toward Asian stopover sites during the boreal spring, with differences in timing between individuals known to relate to their eventual breedingground geography in Alaska. Here, we studied the timing of northward migration of individual godwits at three sites spanning 1,100 km of New Zealand's 1,400-km length. A lack of morphological or genetic structure among sites indicates that the Alaskan breeding population mixes freely across all sites, and larger birds (southern breeders) tended to migrate earlier than smaller birds (northern breeders) at all sites. However, we unexpectedly found that migration timing varied between the sites, with birds from southern New Zealand departing on average 9.4-11 days earlier than birds from more northerly sites, a difference consistent across 4 years of monitoring. There is no obvious adaptive reason for migration timing differences of this magnitude, and it is likely that geographic variation in timing within New Zealand represents a direct response to latitudinal variation in photoperiod. Using resightings of marked birds, we show that immature godwits explore widely around New Zealand before embarking on their first northward migration at age 2-4 years. Thus, the process by which individual migration dates are established appears to involve: (1) settlement by sub-adult godwits at non-breeding sites, to which they are highly faithful as adults; (2) a consequent response to environmental cues (i.e., photoperiod) that sets the local population's migration window; and (3) endogenous mechanisms, driven by breeding geography, that establish and maintain the well-documented consistent differences between individuals. This implies that behavioral decisions by young godwits have long-lasting impacts on adult annual-cycle schedules, but the factors guiding non-breeding settlement are currently unknown.