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Benham PM, Cicero C, Escalona M, Beraut E, Fairbairn C, Marimuthu MPA, Nguyen O, Sahasrabudhe R, King BL, Thomas WK, Kovach AI, Nachman MW, Bowie RCK. Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery. Genome Biol Evol 2024; 16:evae067. [PMID: 38566597 PMCID: PMC11088854 DOI: 10.1093/gbe/evae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/01/2024] [Accepted: 03/23/2024] [Indexed: 04/04/2024] Open
Abstract
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.
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Affiliation(s)
- Phred M Benham
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Carla Cicero
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Merly Escalona
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Eric Beraut
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Colin Fairbairn
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Mohan P A Marimuthu
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Oanh Nguyen
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Ruta Sahasrabudhe
- DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Benjamin L King
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, ME 04469, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH 03824, USA
| | - Michael W Nachman
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology, University of California Berkeley, Berkeley, CA 94720, USA
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA 94720, USA
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Ruskin KJ, Herring G, Eagles-Smith CA, Eiklor AB, Elphick CS, Etterson MA, Field CR, Longenecker RA, Kovach AI, Gregory Shriver W, Walsh J, Olsen BJ. Mercury exposure of tidal marsh songbirds in the northeastern United States and its association with nest survival. ECOTOXICOLOGY (LONDON, ENGLAND) 2022; 31:208-220. [PMID: 34783931 DOI: 10.1007/s10646-021-02488-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
The biogeochemistry of tidal marsh sediments facilitates the transformation of mercury (Hg) into the biologically available form methylmercury (MeHg), resulting in elevated Hg exposures to tidal marsh wildlife. Saltmarsh and Acadian Nelson's sparrows (Ammospiza caudacutua and A. nelsoni subvirgatus, respectively) exclusively inhabit tidal marshes, potentially experiencing elevated risk to Hg exposure, and have experienced range-wide population declines. To characterize spatial and temporal variation of Hg exposure in these species, we sampled total mercury (THg) in blood collected from 9 populations spanning 560 km of coastline, including individuals resampled within and among years. Using concurrent nesting studies, we tested whether THg was correlated with nest survival probabilities, an index of fecundity. Blood THg ranged from 0.074-3.373 µg/g ww across 170 samples from 127 individuals. We detected high spatial variability in Hg exposure, observing differences of more than 45-fold across all individuals and 8-fold in mean blood THg among all study plots, including 4-fold between study plots within 4 km. Intraindividual changes in blood Hg exposure did not vary systematically in time but were considerable, varying by up to 2-fold within and among years. Controlling for both species differences and maximum water level, the dominant driver of fecundity in this system, nest survival probability decreased by 10% across the full range of female blood THg concentrations observed. We conclude that Hg has the potential to impair songbird reproduction, potentially exacerbating known climate-change driven population declines from sea-level rise in saltmarsh and Acadian Nelson's sparrows.
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Affiliation(s)
- Katharine J Ruskin
- Ecology and Environmental Sciences, 123 Bryand Global Sciences Center, University of Maine, Orono, ME, 04469, USA.
| | - Garth Herring
- United States Geological Survey, Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA
| | - Collin A Eagles-Smith
- United States Geological Survey, Forest and Rangeland Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA
| | - Alyssa B Eiklor
- Vermont Department of Environmental Conservation, 1 National Life Dr Montpelier, Davis 1, VT, 05620-3520, USA
| | - Chris S Elphick
- Department of Ecology & Evolutionary Biology and Center of Biological Risk, University of Connecticut, 75 North Eagleville Road, U-43, Storrs, CT, 06269, USA
| | - Matthew A Etterson
- United States Environmental Protection Agency, Center for Computational Toxicology and Exposure, Great Lakes Toxicology and Ecology Division, 6201 Congdon Boulevard, Duluth, MN, 55804, USA
| | - Christopher R Field
- Department of Natural Resources Science, University of Rhode Island 45 Upper College Rd, Kingston, RI, 02881, USA
| | - Rebecca A Longenecker
- U.S. Fish and Wildlife Service, Northeast Regional Office, 300 Westgate Center Drive, Hadley, MA, 01035, USA
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, 46 College Road, Durham, NH, 03824, USA
| | - W Gregory Shriver
- Department of Entomology and Wildlife Ecology, University of Delaware, 257 Townsend Hall, Newark, DE, 19716, USA
| | - Jennifer Walsh
- Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY, 14850, USA
| | - Brian J Olsen
- Ecology and Environmental Sciences, 123 Bryand Global Sciences Center, University of Maine, Orono, ME, 04469, USA
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Hart ME, Perez-Umphrey A, Stouffer PC, Burns CB, Bonisoli-Alquati A, Taylor SS, Woltmann S. Nest survival of Seaside Sparrows (Ammospiza maritima) in the wake of the Deepwater Horizon oil spill. PLoS One 2021; 16:e0259022. [PMID: 34699553 PMCID: PMC8547620 DOI: 10.1371/journal.pone.0259022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 10/11/2021] [Indexed: 11/18/2022] Open
Abstract
In 2010, the Deepwater Horizon oil spill released an estimated 4.9 million barrels of oil into the Gulf of Mexico, damaging coastal ecosystems. Seaside Sparrows (Ammospiza maritima)-a year-round resident of Gulf Coast salt marshes-were exposed to oil, as shown by published isotopic and molecular analyses, but fitness consequences have not been clarified. We monitored nests around two bays in Plaquemines Parish, Louisiana, USA from 2012-2017 to assess possible impacts on the nesting biology of Seaside Sparrows. A majority of nests failed (76% of known-fate nests, N = 252 nests, 3521 exposure-days) during our study, and predation was the main cause of nest failure (~91% of failed nests). Logistic exposure analysis revealed that daily nest survival rate: (1) was greater at nests with denser vegetation at nest height, (2) was higher in the more sheltered bay we studied, (3) decreased over the course of the breeding season in each year, and (4) was not correlated with either sediment polycyclic aromatic hydrocarbon concentrations or estimated predator abundance during the years for which we had those data. Although the Deepwater Horizon spill impacted other aspects of Seaside Sparrow ecology, we found no definitive effect of initial oiling or oiled sediment on nest survival during 2012-2017. Because predation was the overwhelming cause of nest failure in our study, additional work on these communities is needed to fully understand demographic and ecological impacts of storms, oil spills, other pollutants, and sea-level rise on Seaside Sparrows and their predators.
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Affiliation(s)
- Megan E Hart
- Center of Excellence for Field Biology, and Department of Biology, Austin Peay State University, Clarksville, TN, United States of America
| | - Anna Perez-Umphrey
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA, United States of America
| | - Philip C Stouffer
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA, United States of America
| | - Christine Bergeon Burns
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA, United States of America
| | - Andrea Bonisoli-Alquati
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA, United States of America
| | - Sabrina S Taylor
- School of Renewable Natural Resources, Louisiana State University and AgCenter, Baton Rouge, LA, United States of America
| | - Stefan Woltmann
- Center of Excellence for Field Biology, and Department of Biology, Austin Peay State University, Clarksville, TN, United States of America
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A green wave of saltmarsh productivity predicts the timing of the annual cycle in a long-distance migratory shorebird. Sci Rep 2020; 10:20658. [PMID: 33244082 PMCID: PMC7693269 DOI: 10.1038/s41598-020-77784-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 11/17/2020] [Indexed: 12/03/2022] Open
Abstract
Understanding how migratory animals respond to spatial and temporal variation in habitat phenology is critical for identifying selection pressures and tradeoffs at different life history stages. We examined the influence of breeding habitat phenology on life history timing of the eastern willet (Tringa semipalmata semipalmata) across a latitudinal gradient of breeding sites on the east coast of North America. To describe migration and life history timing, we deployed light-level geolocators on willets at breeding sites in New Jersey, Massachusetts and Maine, USA and evaluated additional data on life history timing and migratory connectivity from previous studies, eBird and band recoveries. Willets from Nova Scotia to Georgia winter exclusively on the Atlantic coast of northern South America and share common stopover sites. The timing of wintering site departure, breeding site arrival, nesting and southbound departure was later for birds breeding at higher latitudes while the duration of all life phases was similar across sites. Regardless of latitude, nesting corresponded with a consistent stage of seasonal salt marsh biomass accumulation and with peak spring temperature acceleration (GDD jerk). Temperature acceleration and salt marsh biomass were closely correlated with each other across the 11° latitudinal gradient we examined and with the timing of nest initiation across the northern 6° of this gradient. For this northern 6° of latitude, these results suggest that the timing of migration and breeding events in the annual cycle of eastern willets is constrained by a phenological “green wave” of spring salt marsh productivity at breeding sites.
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Benvenuti B, Walsh J, O'Brien KM, Kovach AI. Plasticity in nesting adaptations of a tidal marsh endemic bird. Ecol Evol 2018; 8:10780-10793. [PMID: 30519406 PMCID: PMC6262926 DOI: 10.1002/ece3.4528] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 11/15/2022] Open
Abstract
If individuals can perceive and manage risks, they may alter their behaviors based on prior experience. This expectation may apply to nest site selection of breeding birds, for which adaptive behavioral responses may enhance fitness. Birds that nest in tidal marshes have adapted to the challenges posed primarily by periodic, monthly tidal flooding and secondarily by predation. We investigated adaptive responses in nesting behavior of the saltmarsh sparrow (Ammospiza caudacutus), an obligate tidal-marsh-breeding bird, using 536 nests monitored across 5 years. Using linear mixed effects models, we tested whether nest characteristics differed among nests that were successful, depredated, or flooded, and we investigated whether females made changes in nest structure and placement according to outcome of their previous nesting attempt. Nest characteristics differed among females with different nest fates. Fledged and depredated nests were built higher in the vegetation and in higher elevation areas of the marsh than those that flooded. Successful nests had more canopy cover and were comprised of a lower proportion of high marsh vegetation (Spartina patens) than those that were flooded or depredated. Females with nests that failed due to flooding constructed subsequent nests higher in the vegetation and at higher elevation than those that were successful in their prior attempt, consistent with a response to previous experience. Eighty-five percent of females renested within the average home range core area distance (77 m), indicating a high degree of nest placement fidelity. Females for which nests were depredated in their prior nesting attempt renested at a greater distance than females for which the previous nesting attempts were successful. Our findings suggest saltmarsh sparrows exhibit plasticity in nesting behavior, which may be important for balancing selective pressures in a dynamic environment. This plasticity, however, is insufficient to enable them to adapt to the increased flooding predicted with sea-level rise.
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Affiliation(s)
- Bri Benvenuti
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire
| | - Jennifer Walsh
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire
- Present address:
Fuller Evolutionary Biology ProgramCornell Laboratory of OrnithologyIthacaNew York
| | - Kathleen M. O'Brien
- Rachel Carson National Wildlife RefugeUnited States Fish and Wildlife ServiceWellsMaine
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew Hampshire
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