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The Yellow Warbler (Setophaga petechia) is a small songbird in the wood-warbler family (Parulidae) that exhibits phenotypic and ecological differences across a widespread distribution and is important to California's riparian habitat conservation. Here, we present a high-quality de novo genome assembly of a vouchered female Yellow Warbler from southern California. Using HiFi long-read and Omni-C proximity sequencing technologies, we generated a 1.22 Gb assembly including 687 scaffolds with a contig N50 of 6.80 Mb, scaffold N50 of 21.18 Mb, and a BUSCO completeness score of 96.0%. This highly contiguous genome assembly provides an essential resource for understanding the history of gene flow, divergence, and local adaptation in Yellow Warblers and can inform conservation management of this charismatic bird species.

Understanding the source of non-native introduced populations is crucial for forecasting geographic invasion potential and understanding the ecological consequences of potential establishment. Here we use genomics to identify the source populations and invasion dynamics of two non-native introduced populations from the iconic avian lineage of ‘great speciators’ known as white-eyes (genus Zosterops). We established confidently for the first time that introduced Zosterops populations in Hawaii and southern California are completely unrelated and derived from independent introductions of the species Z. japonicus and Z. simplex, respectively. We used descriptive population genetic statistics to identify a reduction in genetic diversity and increase in private alleles in the southern California population supporting a recent, potentially ongoing, genetic bottleneck in this population. In contrast, the introduced population in Hawaii showed no such characteristics, likely due to a larger founding population size and repeated introductions in this intentionally introduced population. Ecological niche modeling indicated that there is little environmentally suitable habitat for Z. simplex across the continent of North America, suggesting limited invasion potential, assuming niche conservatism. Yet, portions of the introduced Z. simplex population have already surpassed areas projected as suitable, likely because the urbanized environment of southern California offers biotic resources and microhabitats not captured by our model. Because Z. simplex appears to have overcome both the ‘invasion paradox’ of low founding genetic diversity and relatively unfamiliar environmental conditions in southern California, we suggest that this population may continue expanding beyond our environmental niche model projections in other temperate, urban regions.

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.

Aim: Introduced species offer insight on whether and how organisms can shift their ecological niches during translocation. The genus Amazona offers a clear test case, where sister species Red‐crowned (A. viridigenalis) and Lilac‐crowned Parrots (A. finschi) have established breeding populations in southern California following introduction via the pet trade from Mexico where they do not coexist. After establishment in the 1980s, introduced population sizes have increased, with mixed species flocks found throughout urban Los Angeles. Here, we investigate the differences between the environmental conditions of the native and introduced ranges of these now co‐occurring species. Location: Southern California and Mexico. Methods: Using environmental data on climate and habitat from their native and introduced ranges, we tested whether Red‐crowned and Lilac‐crowned Parrots have divergent realized niches between their native ranges, and whether each species has significantly shifted its realized niche to inhabit urban southern California. We also analysed data from Texas and Florida introductions of Red‐crowned Parrots for comparative analysis. Results: There are significant differences in the native‐range niches of both parrot species, but a convergence into a novel, shared environmental niche into urban southern California, characterized by colder temperatures, less tree cover and lower rainfall. Texas and Florida Red‐crowned Parrots also show evidence for niche shifts with varying levels of niche conservatism through the establishment of somewhat different realized niches. Main Conclusions: Despite significant niche shifts, introduced parrots are thriving, suggesting a broad fundamental niche and an ability to exploit urban resources. Unique niche shifts in different U.S. introductions indicate that Amazona parrots can adapt to diverse environmental conditions, with cities offering a resource niche and the timing of introduction playing a crucial role. Cities can potentially serve as refugia for threatened parrot species, but the risk of hybridization between species emphasizes the need for ongoing monitoring and genetic investigations. [ABSTRACT FROM AUTHOR]

Hybrid zones can be studied by modeling clines of trait variation (e.g. morphology, genetics) over a linear transect. Yet, hybrid zones can also be spatially complex, can shift over time, and can even lead to the formation of hybrid lineages with the right combination of dispersal and vicariance. We reassessed Sibley's (1950) gradient between Collared Towhee (Pipilo ocai) and Spotted Towhee (Pipilo maculatus) in Central Mexico to test whether it conformed to a typical tension-zone cline model. By comparing historical and modern data, we found that cline centers for genetic and phenotypic traits have not shifted over the course of 70 years. This equilibrium suggests that secondary contact between these species, which originally diverged over 2 million years ago, likely dates to the Pleistocene. Given the amount of mtDNA divergence, parental ends of the cline have very low autosomal nuclear differentiation (F ST = 0.12). Dramatic and coincident cline shifts in mtDNA and throat color suggest the possibility of sexual selection as a factor in differential introgression, while a contrasting cline shift in green back color hints at a role for natural selection. Supporting the idea of a continuum between clinal variation and hybrid lineage formation, the towhee gradient can be analyzed as one population under isolation-by-distance, as a two-population cline, and as three lineages experiencing divergence with gene flow. In the middle of the gradient, a hybrid lineage has become partly isolated, likely due to forested habitat shrinking and fragmenting as it moved upslope after the last glacial maximum and a stark environmental transition. This towhee system offers a window into the potential outcomes of hybridization across a dynamic landscape including the creation of novel genomic and phenotypic combinations and incipient hybrid lineages. [ABSTRACT FROM AUTHOR]

Genomic data continue to advance our understanding of species limits and biogeographic patterns. However, there is still no consensus regarding appropriate methods of phylogenomic analysis that make the best use of these heterogeneous data sets. In this study, we used thousands of ultraconserved element (UCE) loci from alligator lizards in the genus Gerrhonotus to compare and contrast species trees inferred using multiple contemporary methods and provide a time frame for biological diversification across the Mexican Transition Zone (MTZ). Concatenated maximum likelihood (ML) and Bayesian analyses provided highly congruent results, with differences limited to poorly supported nodes. Similar topologies were inferred from coalescent analyses in Bayesian Phylogenetics and Phylogeography and SVDquartets, albeit with lower support for some nodes. All divergence times fell within the Miocene, linking speciation to local Neogene vicariance and/or global cooling trends following the mid-Miocene Climatic Optimum. We detected a high level of genomic divergence for a morphologically distinct species restricted to the arid mountains of north-eastern Mexico, and erected a new genus to better reflect evolutionary history. In summary, our results further advocate leveraging the strengths and weaknesses of concatenation and coalescent methods, provide evidence for old divergences for alligator lizards, and indicate that the MTZ continues to harbour substantial unrecognized diversity. [ABSTRACT FROM AUTHOR]

The impact of preserved museum specimens is transforming and increasing by three-dimensional (3D) imaging that creates high-fidelity online digital specimens. Through examples from the openVertebrate (oVert) Thematic Collections Network, we describe how we created a digitization community dedicated to the shared vision of making 3D data of specimens available and the impact of these data on a broad audience of scientists, students, teachers, artists, and more. High-fidelity digital 3D models allow people from multiple communities to simultaneously access and use scientific specimens. Based on our multiyear, multi-institution project, we identify significant technological and social hurdles that remain for fully realizing the potential impact of digital 3D specimens., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Institute of Biological Sciences.)