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Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact of these elements on host genomes. The increased capacity of long-read sequencing technologies to span highly repetitive regions promises to provide new insights into patterns of TE activity across diverse taxa. Here we report the generation of highly contiguous reference genomes using PacBio long-read and Omni-C technologies for three species of Passerellidae sparrow. We compared these assemblies to three chromosome-level sparrow assemblies and nine other sparrow assemblies generated using a variety of short- and long-read technologies. All long-read based assemblies were longer (range: 1.12 to 1.41 Gb) than short-read assemblies (0.91 to 1.08 Gb) and assembly length was strongly correlated with the amount of repeat content. Repeat content for Bell's sparrow (31.2% of genome) was the highest level ever reported within the order Passeriformes, which comprises over half of avian diversity. The highest levels of repeat content (79.2% to 93.7%) were found on the W chromosome relative to other regions of the genome. Finally, we show that proliferation of different TE classes varied even among species with similar levels of repeat content. These patterns support a dynamic model of TE expansion and contraction even in a clade where TEs were once thought to be fairly depauperate and static. Our work highlights how the resolution of difficult-to-assemble regions of the genome with new sequencing technologies promises to transform our understanding of avian genome evolution.

Eco‐phylogeographic approaches to comparative population genetic analyses allow for the inclusion of intrinsic influences as drivers of intraspecific genetic structure. This insight into microevolutionary processes, including changes within a species or lineage, provides better mechanistic understanding of species‐specific interactions and enables predictions of evolutionary responses to environmental change. In this study, we used single nucleotide polymorphisms (SNPs) identified from reduced representation sequencing to compare neutral population structure, isolation by distance (IBD), genetic diversity and effective population size (Ne) across three closely related and co‐distributed saltmarsh sparrow species differing along a specialization gradient—Nelson's (Ammospiza nelsoni subvirgata), saltmarsh (A. caudacuta) and seaside sparrows (A. maritima maritima). Using an eco‐phylogeographic lens within a conservation management context, we tested predictions about species' degree of evolutionary history and ecological specialization to tidal marshes, habitat, current distribution and population status on population genetic metrics. Population structure differed among the species consistent with their current distribution and habitat factors, rather than degree of ecological specialization: seaside sparrows were panmictic, saltmarsh sparrows showed hierarchical structure and Nelson's sparrows were differentiated into multiple, genetically distinct populations. Neutral population genetic theory and demographic/evolutionary history predicted patterns of genetic diversity and Ne rather than degree of ecological specialization. Patterns of population variation and evolutionary distinctiveness (Shapely metric) suggest different conservation measures for long‐term persistence and evolutionary potential in each species. Our findings contribute to a broader understanding of the complex factors influencing genetic variation, beyond specialist‐generalist status and support the role of an eco‐phylogeographic approach in population and conservation genetics. [ABSTRACT FROM AUTHOR]

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Objective: The Striped Bass Morone saxatilis is an anadromous teleost with a native range extending north from the Gulf of Mexico into Canadian waters. Far‐ranging coastal migrations support one of the most popular recreational fisheries in the United States. Identifying the underlying population genetic structure of the spawning populations and the genetic markers capable of differentiating among them advances our understanding of these economically and ecologically important fish and enables more targeted management to occur. Methods: We used a restriction site‐associated DNA sequencing approach to identify neutral and adaptive single‐nucleotide polymorphisms (SNPs), and we determined the population genetic structure of 438 adult Striped Bass sampled from nine spawning locations along the Atlantic coast from the Roanoke River, United States, to the Miramichi River, Canada. Result: The two Canadian populations (Shubenacadie and Miramichi rivers) were genetically distinct from U.S. populations and from each other. Neutral loci differentiated Striped Bass from U.S. waters into four genetically distinct populations: Roanoke River, Hudson–Kennebec River, Upper Chesapeake Bay–Potomac River–Delaware River, and Choptank River (eastern Chesapeake Bay). Outlier loci further differentiated the Delaware River from the Chesapeake Bay tributaries, suggesting that there may be local adaptation in the face of gene flow. We identified 1300 highly informative SNPs (the top 10% [with respect to the genetic differentiation index FST] of the full suite of 13,361 SNPs in our study) capable of assigning fish with at least 90% accuracy to their river of origin; through simulations, we established their applicability for conducting robust mixed‐stock analyses of the coastal migratory Striped Bass fishery. Conclusion: This study demonstrated that neutral and adaptive loci together provide evidence for fine‐scale population structure of migratory Striped Bass, and these loci provide the most informative genetic panel for mixed‐stock analysis of Striped Bass to date, capable of assigning fish to their spawning river of origin. Impact Statement: Migratory Striped Bass that occur along the Atlantic coast of the USA and Canada are structured into genetically distinct populations, corresponding to their spawning river of origin. We identified a suite of genetic markers that will enable fishery managers to determine the stock composition of the mixed coastal Striped Bass fishery. [ABSTRACT FROM AUTHOR]