Life Sciences Commons^™

Genomic Analysis Reveals New Species And Subspecies Of Butterflies, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Large-scale genomic sequencing of butterfly taxa reveals new findings that are presented here. While we focus on detecting species by comparative genomics and define subspecies as groups of populations genetically differentiated from each other but not as strongly as species (that is, subspecies as species in the making), we report other adjustments to butterfly classification. As a result, 4 subgenera, 11 species, and 6 subspecies are proposed as new. New subgenera are: Rapis Grishin, subgen. n. (type species Papilio rapae Linnaeus, 1758, genus Pieris Schrank, 1801) in Pieridae Swainson, 1820 and Callitera Grishin, subgen. n. (type species Eurygona? pulcherrima …

Reassessment Of Amblyscirtes Hegon (Hesperiidae) As A Complex Of Four Distinct Species Revealed By Genomic Analysis, Harry Pavulaan, Ricky Patterson, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

After the discovery of a unique phenotype in the southern United States with a different ventral ground color than nominotypical Amblyscirtes hegon (Scudder, 1863), which occurs in the northeastern United States, genomic analysis revealed that A. hegon is a species complex. Phenotypic, genitalic, and genomic differences of the complex are presented here. Four species are identified: A. hegon; A. nemoris (W. H. Edwards, 1864), stat. rest.; A. matheri Patterson, Pavulaan & Grishin, sp. n. (TL: USA, Mississippi, Warren County); and A. gelidus Grishin, Patterson & Pavulaan, sp. n. (TL: USA, Michigan, Van Buren County).

Accelerated Evolution Of Sars-Cov-2 In Free-Ranging White-Tailed Deer, Dillon S. Mcbride, Sofya K. Garushyants, John Franks, Andrew F. Magee, Steven H. Overend, Devra Huey, Amanda M. Williams, Seth A. Faith, Ahmed Kandeil, Sanja Trifkovic, Lance Miller, Trushar Jeevan, Anami Patel, Jacqueline M. Nolting, Michael J. Tonkovich, J. Tyler Genders, Andrew J. Montoney, Kevin Kasnyik, Timothy J. Linder, Sarah N. Bevins, Julianna B. Lenoch, Jeffrey C. Chandler, Thomas J. Deliberto, Eugene V. Koonin, Marc A. Suchard, Philippe Lemey, Richard J. Webby, Martha I. Nelson, Andrew S. Bowman

USDA Wildlife Services: Staff Publications

The zoonotic origin of the COVID-19 pandemic virus highlights the need to fill the vast gaps in our knowledge of SARS-CoV-2 ecology and evolution in non-human hosts. Here, we detected that SARS-CoV-2 was introduced from humans into white-tailed deer more than 30 times in Ohio, USA during November 2021-March 2022. Subsequently, deer-to-deer transmission persisted for 2–8 months, disseminating across hundreds of kilometers. Newly developed Bayesian phylogenetic methods quantified how SARS-CoV-2 evolution is not only three-times faster in white-tailed deer compared to the rate observed in humans but also driven by different mutational biases and selection pressures. The long-term effect of …

Rapid Evolution Of A(H5n1) Influenza Viruses After Intercontinental Spread To North America, Ahmed Kandeil, Christopher Patton, Jeremy C. Jones, Trushar Jeevan, Walter N. Harrington, Sanja Trifkovic, Jon P. Seiler, Thomas Fabrizio, Karlie Woodard, Jasmine C. Turner, Jeri Carol Crumpton, Lance Miller, Adam Rubrum, Jennifer Debeauchamp, Charles J. Russell, Elena A. Govorkova, Peter Vogel, Mia Kim-Torchetti, Yohannes Berhane, David Stallknecht, Rebecca Poulson, Lisa Kercher, Richard J. Webby

USDA Wildlife Services: Staff Publications

Highly pathogenic avian influenza A(H5N1) viruses of clade 2.3.4.4b underwent an explosive geographic expansion in 2021 among wild birds and domestic poultry across Asia, Europe, and Africa. By the end of 2021, 2.3.4.4b viruses were detected in North America, signifying further intercontinental spread. Here we show that the western movement of clade 2.3.4.4b was quickly followed by reassortment with viruses circulating in wild birds in North America, resulting in the acquisition of different combinations of ribonucleoprotein genes. These reassortant A(H5N1) viruses are genotypically and phenotypically diverse, with many causing severe disease with dramatic neurologic involvement in mammals. The proclivity of …

Species Richness Of Moths In Parks Surrounded By Varying Levels Of ​Urbanization Around Nashville, Tennessee, Maxwell Stone, Allie Bennett

Science University Research Symposium (SURS)

Moths can act as indicators of environmental wellness due to their pollution sensitivity and the complexity of biodiversity required to support their life cycles. Urbanization can impact the occurrence of moths in protected green spaces. Higher moth species richness was hypothesized to occur in parks surrounded by more rural areas. Three metropolitan parks were chosen in the Nashville area: downtown, within a suburban neighborhood, and in a rural area. Tree canopy cover and degree of impervious surfaces were assessed for each park and surrounding area using iTreeCanopy. Moths were attracted to a white sheet using a mercury vapor bulb, UV …

Pathogenicity In Chickens And Turkeys Of A 2021 United States H5n1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b Wild Bird Virus Compared To Two Previous H5n8 Clade 2.3.4.4 Viruses, Mary J. Pantin-Jackwood, Erica Spackman, Christina Leyson, Sungsu Youk, Scott A. Lee, Linda M. Moon, Mia K. Torchetti, Mary L. Killian, Julianna B. Lenoch, Darrell R. Kapczynski, David E. Swayne, David L. Suarez

USDA Wildlife Services: Staff Publications

Highly pathogenic avian influenza viruses (HPAIVs) of subtype H5 of the Gs/GD/96 lineage remain a major threat to poultry due to endemicity in wild birds. H5N1 HPAIVs from this lineage were detected in 2021 in the United States (US) and since then have infected many wild and domestic birds. We evaluated the pathobiology of an early US H5N1 HPAIV (clade 2.3.4.4b, 2021) and two H5N8 HPAIVs from previous outbreaks in the US (clade 2.3.4.4c, 2014) and Europe (clade 2.3.4.4b, 2016) in chickens and turkeys. Differences in clinical signs, mean death times (MDTs), and virus transmissibility were found between chickens and …

Raccoon Spatial Ecology In The Rural Southeastern United States, Jacob E. Hill, Madison L. Miller, James L. Helton, Richard B. Chipman, Amy Gilbert, University Of Georgia, Guha Dharmarajan, Olin E. Rhodes Jr.

USDA Wildlife Services: Staff Publications

The movement ecology of raccoons varies widely across habitats with important implications for the management of zoonotic diseases such as rabies. However, the spatial ecology of raccoons remains poorly understood in many regions of the United States, particularly in the southeast. To better understand the spatial ecology of raccoons in the southeastern United States, we investigated the role of sex, season, and habitat on monthly raccoon home range and core area sizes in three common rural habitats (bottomland hardwood, upland pine, and riparian forest) in South Carolina, USA. From 2018–2022, we obtained 264 monthly home ranges from 46 raccoons. Mean …

Skin Lipids Alone Enable Conspecific Tracking In An Invasive Reptile, The Argentine Black And White Tegu Lizard (Salvator Merianae), M. Rockwell Parker, Eric A. Tillman, Lauren A. Nazarian, Megan L. Barlowe, Julianna M. Lincoln, Bryan M. Kluever

USDA Wildlife Services: Staff Publications

Locating potential mates in non-native habitats is one of the most important challenges faced by invasive vertebrate species. The Argentine black and white tegu lizard (Salvator merianae) is a major invasive reptile species in the contiguous United States and is rapidly expanding its range across Florida and the Southeast, in part due to inadequate management strategies and tools. Because a wide array of reptiles, especially squamates (snakes and lizards), have been well-studied for their reliance on chemical cues to locate conspecifics, our project aimed to isolate chemical cues from tegus and assess the ability of adult males and …

Examination Of The Status Of Phyciodes Tharos Distincta Bauer, 1975, Confirming It As A Valid Subspecies, Harry Pavulaan

The Taxonomic Report of the International Lepidoptera Survey

The subspecific status of Phyciodes tharos distincta is reexamined. A specimen series from southern Arizona reveals that distincta shows a distinct, unique phenotype dissimilar from eastern North American nominotypical P. t. tharos. Subspecies distincta occupies a very limited range in extreme southeastern California, southern Arizona, and northwestern Mexico. A lectotype is designated.

Butterfly Classification And Species Discovery Using Genomics, Jing Zhang, Qian Cong, Jinhui Shen, Leina Song, Nick V. Grishin

The Taxonomic Report of the International Lepidoptera Survey

Genomic sequencing of worldwide butterfly fauna followed by phylogenetic analysis of protein-coding genes informs butterfly classification throughout the taxonomic hierarchy, from families to species. As a rule, we attribute the same taxonomic rank to more prominent clades of comparable divergence (that is, at the same level in the tree). For species delimitation, we use criteria based on relative genetic differentiation and the extent of gene exchange between populations. We analyze the current taxonomic classification of butterflies in the light of genomic phylogenies and encounter clades that correspond to yet unnamed taxa. As a result, 11 tribes, 33 subtribes, 2 genera, …

H5n1 Highly Pathogenic Avian Influenza Clade 2.3.4.4b In Wild And Domestic Birds: Introductions Into The United States And Reassortments, December 2021–April 2022, Sungsu Youk, Mia Kim Torchetti, Kristina Lantz, Julianna B. Lenoch, Mary Lea Killian, Christina Leyson, Sarah N. Bevins, Krista Dilione, Hon S. Ip, David E. Stallknecht, Rebecca L. Poulson, David L. Suarez, David E. Swayne, Mary J. Pantin-Jackwood

USDA Wildlife Services: Staff Publications

Highly pathogenic avian influenza viruses (HPAIVs) of the A/goose/Guangdong/1/1996 lineage H5 clade 2.3.4.4b continue to have a devastating effect on domestic and wild birds. Full genome sequence analyses using 1369 H5N1 HPAIVs detected in the United States (U.S.) in wild birds, commercial poultry, and backyard flocks from December 2021 to April 2022, showed three phylogenetically distinct H5N1 virus introductions in the U.S. by wild birds. Unreassorted Eurasian genotypes A1 and A2 entered the Northeast Atlantic states, whereas a genetically distinct A3 genotype was detected in Alaska. The A1 genotype spread westward via wild bird migration and reassorted with North American …

Limited Accumulation And Persistence Of An Influenza A Virus In Tadpole Snails (Physa Spp.), Paul T. Oesterle, J. Jeffrey Root, Darcy S.O. Mora, Heather Schneider, Alan B. Franklin, Kathryn P. Huyvaert

USDA Wildlife Services: Staff Publications

Waterfowl infected with avian influenza A viruses (IAVs) shed infectious virus into aquatic environments, providing a mechanism for transmission among waterfowl, while also exposing the entire aquatic ecosystem to the virus. Aquatic invertebrates such as freshwater snails are likely exposed to IAVs in the water column and sediment. Freshwater snails comprise a significant portion of some waterfowl species’ diets, so this trophic interaction may serve as a novel route of IAV transmission. In these experiments, tadpole snails (Physa spp.) were exposed to a low-pathogenicity IAV (H3N8) to determine whether snails can accumulate the virus and, if so, how long virus …

South Coast Offshore Crustacean Resource Of Western Australia Harvest Strategy, Department Of Primary Industries And Regional Development, Western Australia

Fisheries management papers

Harvest strategies for aquatic resources in Western Australia (WA) that are managed by the Department of Primary Industries and Regional Development (DPIRD, the Department) are formal documents that ensures decision-making processes are consistent with the principles of Ecologically Sustainable Development (ESD; Fletcher 2002) and Ecosystem Based Fisheries Management (EBFM; Fletcher et al. 2012). The objectives of ESD are reflected in the objects of the Fish Resources Management Act 1994 (FRMA) and the Aquatic Resources Management Act 2016 (ARMA), which is anticipated replace the FRMA once enacted. At this point, the Fish Resources Management Regulations 1995 (FRMR) is also anticipated to …

The Nebraska Bird Review (September 2023) 91(3), Whole Issue

Nebraska Bird Review

Summer Field Report, June–July 2023, by W. Ross Silcock

2023 Limpkin at Crystal Cove Park, Dakota County, NE, by Bill Huser

2022 (34th) Report of the NOU Records Committee, by Mark A. Brogie

Subscription and Organization Information

2022 (34th) Report Of The Nou Records Committee, Mark A. Brogie

Nebraska Bird Review

The functions and methods of the Nebraska Ornithologists’ Union Records Committee (NOURC) are described in its bylaws (NOURC 2010). The committee’s purpose is to provide a procedure for documenting unusual bird sightings and to establish a list of all documented birds for Nebraska. Species for which the NOURC seeks documentation (NOURC Review List) can be found at the NOU website www.NOUbirds.org. Starting in 2020, the NOURC decided to deal mainly with those species deemed as Accidental on the “Official List of the Birds of Nebraska.” Casual species and out-of-range species are now summarized in the “Seasonal Reports” of the …

2023 Limpkin At Crystal Cove Park, Dakota County, Ne, Bill Huser

Nebraska Bird Review

On the morning of October 7, 2023, I observed Nebraska’s second Limpkin (Aramus guarauna) at Crystal Cove Park in South Sioux City, and the bird was subsequently seen by several other observers throughout that afternoon. Photo and video records were obtained (https://ebird.org/checklist/S151656716). The summer and fall of 2023 brought fourteen sightings to Iowa, though it is impossible to determine how many birds were involved (eBird, 2023). One of those sightings occurred in the northwestern part of the state at Bacon Creek Park in Sioux City when a single Limpkin was independently reported by two observers on …

Summer Field Report, June–July 2023, W. Ross Silcock

Nebraska Bird Review

There were no new species for Nebraska. This was also a lean season for records of species with few Nebraska records. Probably most significant were continuing Common Ravens in two Sioux Co locations, and possibly the first summer records of Baird’s Sparrow, a recording of the latter currently under NOURC review.

Within-state breeders nesting at new locations. There were several instances of nesting reported away from known breeding areas. These include documented records of first nesting Black-necked Stilts in Cherry Co, Least Terns off river at Offutt Base Lake in Sarpy Co, Mississippi Kite in Adams Co, Yellow-throated Vireo in …

Antiviral Susceptibility Of Clade 2.3.4.4b Highly Pathogenic Avian Influenza A(H5n1) Viruses Isolated From Birds And Mammals In The United States, 2022, Ha T. Nguyen, Anton Chesnokov, Juan De La Cruz, Philippe Noriel Q. Pascua, Vasiliy P. Mishin, Yunho Jang, Joyce Jones, Han Di, Andrei A. Ivashchenko, Mary Lea Killian, Mia K. Torchetti, Kristina Lantz, David E. Wentworth, Charles T. Davis, Alexandre V. Ivachtchenko, Larisa V. Gubareva

USDA Wildlife Services: Staff Publications

Clade 2.3.4.4b highly pathogenic avian influenza (HPAI) A(H5N1) viruses that are responsible for devastating outbreaks in birds and mammals pose a potential threat to public health. Here, we evaluated their susceptibility to influenza antivirals. Of 1,015 sequences of HPAI A(H5N1) viruses collected in the United States during 2022, eight viruses (∼0.8%) had a molecular marker of drug resistance to an FDA-approved antiviral: three adamantane-resistant (M2-V27A), four oseltamivir-resistant (NA-H275Y), and one baloxavir-resistant (PA-I38T). Additionally, 31 viruses contained mutations that may reduce susceptibility to inhibitors of neuraminidase (NA) (n = 20) or cap-dependent endonuclease (CEN) (n = 11). A panel of 22 …

The Devil You Know And The Devil You Don’T: Current Status And Challenges Of Bovine Tuberculosis Eradication In The United States, Daniel J. O'Brien, Tyler C. Thacker, Liliana C.M. Salvador, Anthony G. Duffiney, Suelee Robbe‑Austerman, Mark S. Camacho, Jason E. Lombard, Mitchell V. Palmer

USDA Wildlife Services: Staff Publications

Having entered into its second century, the eradication program for bovine tuberculosis (bTB, caused by Mycobacterium bovis) in the United States of America occupies a position both enviable and daunting. Excepting four counties in Michigan comprising only 6109 km2 (0.06% of US land area) classified as Modified Accredited, as of April 2022 the entire country was considered Accredited Free of bTB by the US Department of Agriculture for cattle and bison. On the surface, the now well-described circumstances of endemic bTB in Michigan, where white-tailed deer (Odocoileus virginianus) serve as a free-ranging wildlife maintenance host, may appear to be …

Leveraging Eco-Evolutionary Models For Gene Drive Risk Assessment, Matthew A. Combs, Andrew J. Golnar, Justin M. Overcash, Alun L. Lloyd, Keith R. Hayes, David A. O'Brochta, Kim M. Pepin

USDA Wildlife Services: Staff Publications

Engineered gene drives create potential for both widespread benefits and irreversible harms to ecosystems. CRISPR-based systems of allelic conversion have rapidly accelerated gene drive research across diverse taxa, putting field trials and their necessary risk assessments on the horizon. Dynamic processbased models provide flexible quantitative platforms to predict gene drive outcomes in the context of system-specific ecological and evolutionary features. Here, we synthesize gene drive dynamic modeling studies to highlight research trends, knowledge gaps, and emergent principles, organized around their genetic, demographic, spatial, environmental, and implementation features. We identify the phenomena that most significantly influence model predictions, discuss limitations of …

Pronghorn Survival And Resource Selection In Western Nebraska's Agriculturally Dominated Landscape, Katie Piecora

School of Natural Resources: Dissertations, Theses, and Student Research

Nebraska’s pronghorn population has been stable over the last decade, yet their presence on the landscape remains a contentious subject amongst private landowners. Conversion of grassland for crop production and increased anthropogenic activity has drastically altered pronghorn behavior throughout their current range, however basic ecology and resource use by pronghorn in Nebraska remains poorly understood. Establishing baseline population metrics and seasonal patterns of resource use for this population at the eastern periphery of the species range is critical to guide management actions. We deployed GPS collars on 110 adult pronghorn to quantify survival, mortality risk, and seasonal resource selection in …

2023 Coordinated Spring Survey Of Mid-Continent Sandhill Cranes, Terry Liddick

United States Fish and Wildlife: Staff Publications

The aerial transect portion of the coordinated spring survey of mid-continent Sandhill cranes was conducted on March 22, 2023 in Nebraska’s Central Platte and North Platte River valleys (United States). The 2023 photo-corrected aerial estimate is 1,259,000 birds. Outside the traditional aerial transect portion, observers conducted ground surveys during the period March 20–22. From these regions, observers in the Official Survey Area (OSA) of Nebraska, Kansas, Texas, Oklahoma, and Wyoming reported an additional 25,363 cranes. The 2023 total estimate (1,284,500) increased 43.1% from 2022. The current three-year average (2021–2023 with no photo correction in 2021), based on photo corrected estimates …

Nou Spring Field Days And Annual Meeting. Valentine, May 5-7, 2023

Nebraska Bird Review

The NOU Annual Meeting and Spring Field Days was held in Valentine on May 5-7, 2023, with 50 in attendance. Our meetings and meals took place in the Niobrara Lodge. Field trips were led by Robin Harding, William Flack, T. J. Walker, Dave Heidt, Mark Brogie and Don and Janis Paseka. Destinations included Thomas Creek WMA, Cub Creek Recreation Area, the Niobrara Valley Preserve (TNC Property), the river road from Meadville (SW of Springview) to Norden, the Valentine City Park, Valentine Fish Hatchery, Ft. Niobrara NWR, Anderson Bridge WMA, the Minnechaduza Creek crossing north of Kilgore, Steer Creek, Merritt Reservoir, …

Spring Field Report, March - May 2023, W. Ross Silcock

Nebraska Bird Review

First off, I want to reiterate that reports compiled for this Spring Seasonal Report are evaluated against current knowledge as presented in Birds of Nebraska-Online (“BONO”; https://birds.outdoornebraska.gov/). Species whose reports do not add new information on distribution, early or late dates, etc., are listed as having “Routine reports”. Please let me know at silcock@rosssilcock.com if you have information that is not in BONO, or if you have additions and/or corrections of information in BONO. Another reminder: if evidence of breeding is observed, please enter the appropriate descriptor in your eBird checklist under “Breeding and Behavior Code”. These descriptors can be …

The Nebraska Bird Review: A Magazine Of Ornithology Of The Nebraska Region. Volume 91 June 2023 Number 2

Nebraska Bird Review

Spring Field Report, March - May 2023 by W. Ross Silcock …46

Correction to 2022-2023 Christmas Bird Count tally ….70

Rethinking the Status and Temporal Occurrence of the American Woodcock in Nebraska because of its Unusual Life History by Joel G. Jorgensen and Stephen J. Brenner …71

NOU Spring Field Days and Annual Meeting in Valentine, May 5-7, 2023 …..84

Subscription and Organization Information …91

Rethinking The Status And Temporal Occurrence Of The American Woodcock In Nebraska Because Of Its Unusual Life History, Joel G. Jorgensen, Stephen J. Brenner

Nebraska Bird Review

Historical distribution and range expansion -- We reviewed existing information to evaluate conclusions by previous authors (e.g., Sharpe et al. 2001, Silcock and Jorgensen 2023) that woodcock have expanded their range west since settlement of Nebraska by Euro-Americans. We also provide additional context about the species’ distribution over time using regional resources.

Temporal occurrence and abundance -- We used data from woodcock outfitted with satellite transmitters 2021-2022 and compared it with occurrence data from two sources, eBird (eBird.org 2023) from all years through 2022 and the SFRs in the Nebraska Bird Review 1994–2019. We chose not to use SFR data …

Feral Swine As Indirect Indicators Of Environmental Anthrax Contamination And Potential Mechanical Vectors Of Infectious Spores, Rachel M. Maison, Maggie R. Priore, Vienna R. Brown, Michael Bodenchuk, Bradley R. Borlee, Richard Bowen, Angela M. Bosco-Lauth

USDA Wildlife Services: Staff Publications

U.S. government work

Mechanistic Examination Of Protist-Mediated Plant Growth Through The Comparative Development Of Medicago Truncatula, Shane Connolly

University Scholar Projects

Protists are known to increase plant growth through two main mechanisms: the microbial loop and the alteration of the root microbiome. The microbial loop is a nutrient recycling method in which protists provide inorganic nitrogen ions to the plant. Alteration of root microbiome leads to the removal of plant pathogens and shifting communities towards plant growth-promoting bacteria (PGPB). This study aimed to elicit which mechanism could produce the largest boost in shoot weight for Medicago truncatula. A series of microcosm experiments were explored in which M. truncatula was grown with variable microbiome structures to allow for mechanism differentiation. The …

Optimal R&D Investment In The Management Of Invasive Species, William Haden Chomphosy, Dale T. Manning, Stephanie A. Shwiff, Stephan Weiler

USDA Wildlife Services: Staff Publications

Invasive alien species (IAS) threaten world biodiversity, ecosystem services, and economic welfare. While existing literature has characterized the optimal control of an established IAS, it has not considered how research and development (R&D) into new removal methods or technologies can affect management decisions and costs over time. R&D can lower the costs of control in a management plan and creates an intertemporal trade-off between quick but costly control and gradual but cheaper removal over time. In this paper, we develop and solve a continuous time dynamic optimization model to study how investment in R&D influences the optimal control of an …

Analysis Of The Population Structure And Migration Habits Of The Northern Leopard Frog (Lithobates Pipiens) At Midewin National Tallgrass Prairie, Gretchen A. Brinkman

Honors Program Projects

Massive amphibian declines of recent years have pushed researchers to pursue population genetics surveys and assess the status of these essential components of many ecosystems. The Northern Leopard Frog (Lithobates pipiens) has continuously experienced population declines across the continental United States due to a combination of habitat losses and environmental changes. Midewin National Tallgrass Prairie houses a considerable portion of L. pipiens in Illinois, and the two creek watersheds studied within this location provide ideal conditions to support these animals. Because this prairie restoration project is a relatively recent development, further assessments regarding the population structure and degree …