Danny Jackson

Speciation in marine taxa is dynamic and complex, often occurring in the absence of absolute geographic barriers to gene flow. Boobies comprise a clade of seven highly mobile seabird species with high diversity in the eastern Pacific Ocean, where no land barriers separate extant sister species and hybridization is widespread. They exhibit striking diversity in bare-part coloration, an important signal of mate quality, and possess a novel multiple sex chromosome system (Z ₁ Z ₂ Z ₁ Z ₂ / Z ₁ Z ₂ W), likely resulting from a fusion between an ancestral autosomal microchromosome and the W chromosome. To understand speciation processes in the context of gene flow, we sequenced and analyzed 29 short-read booby genomes and assembled a reference northern gannet genome to (1) test for introgression, (2) characterize genomic patterns of divergence across species, and (3) investigate the gene content and evolution of the neo-sex chromosome. We found that divergence among eastern Pacific sister taxa is temporally associated with periods of glacial maxima. Between periods of glacial maxima, two pairs of sister species (blue-footed and Peruvian boobies; masked and Nazca boobies) exhibit strong signatures of episodic introgression, indicating that speciation has occurred over multiple periods of divergence followed by gene flow. However, in the third pair of sister species, genomic signatures showed higher divergence within brown booby populations than between brown and Cocos boobies. We also identified the epidermal differentiation complex – a gene cassette involved in skin, feather, beak, and claw development – on the neo-sex region of the W chromosome, where it spans the boundary between the putatively recombining and non-recombining regions, with interspecific variation in the exact recombination suppression boundary. We inferred that this complex may contribute to diversity in feather and bare part coloration across boobies. Together, these results reveal that diversification and speciation in a clade of highly mobile seabirds emerged from a complex evolutionary history involving historical climate dynamics, introgression, and sex chromosome evolution.

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.

Urbanization has greatly affected wildlife and will continue to do so into the future, but we know little about whether traits of closely related species respond similarly to this environmental change. To address this gap, we tested the association between urbanization and morphological traits of two congeneric songbird species-northern cardinals (Cardinalis cardinalis) and pyrrhuloxia (C. sinuatus)-that largely share a niche in and around the Sonoran Desert city of Tucson, Arizona over 137 years. We measured museum and field-collected specimens and used novel hindcast models of urban areas to score urbanization over time. Both urbanization and time of sampling were associated with larger bills in male pyrrhuloxia and in female northern cardinals, which may affect foraging, song, and heat tolerance. Degree of urbanization was also associated with changes in coloration of male northern cardinal face masks and female northern cardinal breast patches. We demonstrate that the effects of urbanization can differ even in two closely related species, with effects on traits involved in visual signaling, heat tolerance, and foraging.

The mechanisms that restrict gene flow between populations and facilitate population differentiation and speciation vary across the tree of life. In systems where physical barriers to gene flow are dynamic over time and space, such as many marine species, introgression may be a major factor in the speciation process. In sympatric species of seabirds with no land barriers between them, hybridization has been frequently observed but few studies have investigated patterns of introgression. We used whole-genome sequence data to test for interspecific introgression between five pairs of tropical and subtropical seabirds and to test for gene flow within species across major land masses and ocean basins. We found evidence for introgression between blue-footed (Sula nebouxii) and Peruvian boobies (S. variegata); masked (S. dactylatra) and Nazca boobies (S. granti); and blue-footed and Nazca boobies. We found no evidence of introgression between blue-footed and brown boobies (S. leucogaster) and masked and brown boobies despite observed hybridization between these species. We also found evidence for gene flow across several major land masses in three pantropical species: red-footed (S. sula), brown, and masked boobies. Finally, we report evidence for ancient introgression between brown boobies and the ancestor of blue-footed, Peruvian, masked, and Nazca boobies. Our work indicates (1) that interspecific introgression has shaped contemporary booby diversity in the eastern Pacific, and (2) that contemporary physical barriers to gene flow between booby colonies are not impenetrable. Our findings contribute novel insights to the growing body of evidence that suggests introgression is a widespread evolutionary process.

Programmers are told "depend on interfaces, not implementations." But, given a program, is it possible even to assess objectively whether such advice has been followed? Programmers frequently talk in ways like this about dependence, but the very term, like many used in software engineering, has hitherto eluded precise definition. In this work, we resolve a variety of confusions about dependence, and present a formal definition unifying multiple varieties of software dependence, grounded in Halpern and Pearl's theory of actual causation. This definition is parameterized by the formal system characterizing the property of interest, and by constraints on "reasonable changes" to the program. By picking different choices of formal system, one can specialize our definition to characterize several notions of dependence, including build, correctness, and performance dependences. Overall, our work provides a path to making conversations about software dependence fully objective, and might serve as a basis for future work that automatically checks forms of dependence that were previously too abstract or high-level to be candidates for tools.

This chapter covers the physiological process associated with fruit maturation and the factors affecting the rate of maturation and ripening,...

Aspect is a static analysis technique for detecting bugs in code based on three forms of abstraction: declarative specification, data abstraction and partiality (ignoring some behavioural details). Together, they bring efficiency (the checker runs almost as fast as a type checker), modularity (a procedure can be analysed independently of the procedures it calls) and incrementality (allowing the checking of incomplete programs). Aspect can detect errors that are not detectable by other static means, especially errors of omission, which are pervasive but usually hard to detect.