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At least 1,423 records · Page 79Linked to original sources
USGS2026

An approach for identifying drought typologies: Drivers, characteristics, and impacts of streamflow drought across the Delaware River Basin

Connecting drought drivers to drought conditions and drought conditions to consequences are two key components of drought risk assessment. We propose a two-step data-driven approach that contributes to advancing this capability. First, we use machine learning feature selection techniques to transform hydrologic model outputs into calculated indices and determine which features are most predictive of streamflow drought duration and severity. Second, we use the selected features to cluster drought events from 1985–2015 and examine drivers of drought in each cluster, spatial and temporal patterns, frequency over time, event characteristics, and connections to water management metrics. Our approach is implemented in the Delaware River Basin (DRB), a highly managed basin in the northeastern United States with a history of consequential droughts. Feature selection identified 19 features that can predict drought duration and severity better than models fit to all features. K-means clustering identified three distinct drought types: one capturing summer and fall droughts, largely in the lower basin; one capturing winter droughts, concentrated in the upper basin; and one capturing long-duration droughts across regions and seasons. Although annual drought frequency has decreased slightly over the period of record, those declines have not been split equally between clusters. Analysis of water management metrics revealed that soil moisture indices at 3-6 month timescales are the most able to differentiate the more consequential long-duration droughts from other drought types. This work contributes both specific insights for stakeholders in the DRB and a generalizable approach for similar analyses and explorations in other basins.

ESS Open Archive↗
USGS2026

Guide and data requirements for submission of mineral deposit mineral chemistry data in the Critical Minerals in Ores - Mineral Chemistry (CMiO-MIN) database

The Critical Minerals in Ores - Mineral Chemistry (CMiO-MIN) database (Hawkins et al., 2026) is designed to capture ore and ore-related mineral compositional data from critical mineral-bearing deposits across the globe. Samples included within this database must be well-characterised and come from localities that have been sufficiently studied to have a reasonable constraint on their deposit type and environment of formation. As such, only samples analysed by modern geochemical methods, and with certain minimum metadata attribution, can be accepted. Data that is submitted to the CMiO-MIN database will also be published via the Geoscience Australia Portal (portal.ga.gov.au) and Critical Minerals Mapping Initiative Portal (www.criticalminerals.org). The CMiO-MIN database is a companion database for the Critical Minerals in Ores (CMiO) database (Champion et al., 2021) that was first published in 2021. This guide draws heavily from the submission guide for CMiO (Case et al., 2024) to ensure similar processes for each database. For more information about the CMiO database please refer Champion et al. (2021) and Case et al. (2024; 2025).

Report↗
USGS2026

Abandonment of the Upper Devonian Greenland Gap Group and Scherr Formation and revision of the Upper Devonian Brallier and Foreknobs Formations in the central Valley and Ridge Province

This study revises the lithostratigraphic framework of the Upper Devonian interval traditionally assigned to the Greenland Gap Group across the central Appalachian Valley and Ridge Province. The work aims to modernize and standardize lithostratigraphic nomenclature, establish a new reference section and demonstrate how the revised stratigraphy improves edge-matching of 1:24,000 scale geologic maps and supports compilation mapping at scales of 1:100,000 and larger. The revision eliminates the names Greenland Gap Group, Scherr Formation and the Minnehaha Springs Member of the Scherr Formation; reassigns all strata previously designated as Scherr Formation by Dennison (1970) to the upper Brallier Formation; and abandons the basal Mallow Member of the Foreknobs Formation, placing its strata within the upper Brallier as originally defined by Butts (1918). The contact between the Brallier and Foreknobs formations is placed at the base of the first mappable, ridge-forming package of fine- to coarse-grained, cross-bedded, sandstone beds, often containing rounded quartz pebbles with minor interbeds of shale and siltstone. This contact may be gradational in places but, even in absence of good exposure, can usually be distinguished topographically in recently produced lidar-derived imagery as having elevated relief due to the presence of more resistant, compositionally mature coarse-grained sandstone-rich strata. Applying this criterion for mapping the contact between the Brallier and Foreknobs formations has resulted in reconciliation of mismatches of geologic contacts along several 7.5-minute quadrangle boundaries in the states of Virginia, West Virginia, Maryland and Pennsylvania. A new reference section at Baker, West Virginia showcases the contacts between the Harrell Shale, Brallier Formation, Foreknobs Formation and Hampshire Formation. A digital outcrop model of the reference section is provided for future preservation.

Maryland, Pennsylvania, Virginia, West Virginia↗
USGS2026

Report 17—Revisions to the articles of organization and procedure of the Commission on Stratigraphic Nomenclature of the Americas

Several revisions to the Articles of Organization and Procedure for the North American Commission on Stratigraphic Nomenclature have been adopted following the 75th, 79th, and 80th annual meetings of the Commission in 2020, 2024 and 2025, respectively. Of these, the most substantial change was revision of Article III regarding membership composition of the Commission and the addition of new member organizations from Central and South America and the Caribbean region. As a result, the Commission also voted to change its name to be more inclusive of the expanding membership, with approval of the name: Commission on Stratigraphic Nomenclature of the Americas. A corresponding change to the Commission’s fundamental publication was also approved at the 2025 meeting as the Stratigraphic Code of the Americas (formerly the North American Stratigraphic Code). Additional revisions to the Articles include those aimed at ensuring gender neutrality of titles, permission to hold virtual meetings, and processes for designating new Commissioners. Article V was also modified to define quorum for meetings and the nature of a two-thirds majority vote, with the process for making amendments to the Articles modified to specify that a two-thirds majority vote is required. These revisions are reflected in the following bylaws, which otherwise are as adopted by the Commission under its former name (North American Commission on Stratigraphic Nomenclature) at its 62nd annual meeting in 2007 amended by mail ballot, and published by Owen et al. (2009). The amended bylaws printed below became effective at the close of the 80th annual meeting in 2025 and supersede all previous versions (Moore 1947; Hutchinson 1953; Owen et al. 1985; 2009)

Stratigraphy↗
USGS2026

Samoa basin abyssal mapping: Box coring leg

This cruise report describes work from leg three of the NOAA American Samoa Abyssal Mapping effort, OPR-T900-KR-26. Leg one preceded this effort and collected ship-based acoustic data. Leg two collected autonomous underwater vehicle (AUV) data and began before, continued contemporaneously, and finished subsequently to leg three. The USGS field activity number assigned to this expedition is 2026-604-FA. The objective of this expedition was to collect representative box cores to inform prospectivity analyses through the region, and co-located interdisciplinary datasets as practical. USGS personnel directed the sampling locations and took custody of the box cores once recovered shipboard. USGS personnel then photographed and described the cores, subsampled, conducted analyses including wet weights and time sensitive measurements, and preserved subsamples and additional components for future work. Data releases co-released with this report are listed in the section “paired data releases.” NOAA released data from all legs of this effort in near-real time. Details of the preceding legs, the data, and NOAA’s project summary available from NOAA, (2026). This report is an expedition summary with preliminary datasets; remaining data releases and publications will be forthcoming.

EarthArXiv↗
USGS2026

Evaluating treatment methods to control the egg masses of the crop pest Pomacea maculata

Pomacea maculata is an invasive aquatic apple snail species that poses serious ecological, agricultural, and public health threats across the southeastern United States. Its spread, particularly in Louisiana, has heavily impacted rice and crayfish farming, an industry producing over 90% of U.S. crayfish and valued at more than $250 million annually. The snail damages seedling rice, clogs crayfish traps, reduces yields, and increases labor for farmers. Moreover, it is a known host of rat lungworm ( Angiostrongylus cantonensis ), a parasite harmful to humans, making its presence in food production environments a public health concern. Controlling P. maculata is challenging due to its life cycle and reproductive strategies. The species lays large clutches of eggs above the waterline, where traditional aquatic molluscicides are ineffective. This study aimed to assess low-cost, practical methods for reducing egg hatch rates, specifically water submersion and vegetable oil application, on newly laid (day 1) and older (day 7) egg clutches. Laboratory trials on 125 egg clutches revealed that water submersion significantly reduced hatch rates and the development of dormant hatchlings, regardless of clutch age. Oil treatment only reduced hatch rates for day 1 clutches and had no effect on dormant hatchlings. These results suggest that water treatment is more broadly effective and feasible for farmers to apply without needing to determine egg age when applied on a routine, weekly basis. While oil showed limited use, its time-sensitive application limits practicality in the field. Water-based approaches offer a scalable solution for reducing P. maculata populations, but do not completely eliminate the potential for hatching and spreading. Without comprehensive control strategies targeting all life stages, the apple snail’s spread and associated impacts are expected to worsen, underscoring the urgency of continued management innovation.

Florida↗
USGS2026

Population densities and trends of landbirds in the National Park of American Samoa

The National Park of American Samoa (NPSA), which protects some of the most intact tropical rainforest in the South Pacific, is exposed to recurring, intense tropical cyclones, including Tropical Cyclone Gita in 2018. In combination with other anthropogenic pressures, cyclones represent a potential source of disturbance to landbird populations, particularly native frugivorous and seed-dispersing species. Long-term monitoring provides a means to evaluate population trajectories following disturbance events and to identify potential management gaps. Landbird surveys were conducted in the Tutuila and Taʻū units of NPSA in 2011, 2018, and 2023 using point-transect distance sampling, with vegetation composition and structure quantified at each sampling station. Species-specific detection functions were fitted to count data to estimate densities by unit, with variance estimated using bootstrap procedures. Comparisons of 2018 and 2023 density estimates using two-sample z-tests indicated that changes in most landbird populations were inconclusive. Since 2018, increases in density were observed for the Pacific Imperial Pigeon ( Ducula pacifica ) and Crimson-crowned Fruit Dove ( Ptilinopus porphyraceus ) on Tutuila, while decreases were observed for the Pacific Kingfisher ( Todiramphus sacer ) on Tutuila, and for the Polynesian Wattled Honeyeater ( Foulehaio carunculatus ), Polynesian Starling ( Aplonis tabuensis ), and Samoan Starling ( Aplonis atrifusca ) on Taʻū. The Many-colored Fruit Dove ( Ptilinopus perousii ) remained rare in both units, and the Manuʻa Shrikebill (Clytorhynchus vitiensis powelli) was narrowly distributed on Taʻū, with insufficient detections of either species to estimate density. The cryptic Spotless Crake ( Zapornia tabuensis ) was detected only in 2018. Changes in tree canopy cover and height did not exhibit patterns clearly associated with a major disturbance event and likely reflected differences in sampling frames among surveys. Invasive non-native plants, most notably Miconia crenata , were widespread in both units. Although many landbird populations in NPSA remain abundant, inference from current monitoring is constrained by limited information on vital rates and species-specific responses to invasive species, disease, habitat change, and extreme weather. As climate change is projected to increase tropical cyclone intensity in the South Pacific, sustained monitoring and targeted management will be important for understanding and conserving landbird populations in American Samoa.

National Park of American Samoa, Ta'u, Tutuila↗
USGS2026

Whitefishes—Coregonus spp.

Coregonines represent a diverse group of fishes of the Salmonidae subfamily Coregoninae that have ecological, cultural, and economical importance throughout their range. They are prey for other commercially and recreationally important predatory fish and are harvested for human consumption (Cleland 1982). Coregonines are generally cool- and coldwater species distributed across the northern hemisphere. The Laurentian Great Lakes of North America experienced considerable loss of coregonine biodiversity due to overfishing, the effects of nonnative species, and habitat loss (Bunnell et al. 2023). This resulted in the extinction of several species (Deepwater Cisco, Longjaw Cisco, and Kiyi) and local extirpations of other species (Blackfin Cisco, Shortnose Cisco, Shortjaw Cisco, Bloater, and Cisco) across all lakes (Bunnell et al. 2023). Renewed interest in restoring coregonines as the native prey base in the Laurentian Great Lakes prompted the development of a multi-agency restoration framework (Bunnell et al. 2023, 2024), and stocking of hatchery-produced coregonines is one of the management tools being used in this large restoration effort. This chapter focuses on culture methods for Lake Whitefish, Cisco, and Bloater currently being propagated for restoration and reintroduction in the Great Lakes (Bunnell et al. 2023). The techniques used for these species can serve as a starting point for the culture of other cisco species, such as Kiyi, which fisheries managers may consider for restoration stocking. Lake Whitefish, Cisco, and Bloater (Figure 1) are similar in appearance but have distinctively different life histories. They are silvery-white-colored fish and possess an adipose fin. Lake Whitefish are distinguished from Cisco and Bloater by a snout that overhangs the lower jaw (subterminal), whereas Cisco and Bloater have a lower jaw that extends beyond the snout (terminal). Lake Whitefish can reach lengths up to 79 cm (Phillips et al. 1982). Cisco and Bloater are smaller, reaching lengths of 34 and 30 cm, respectively (Eshenroder et al. 2016; Bunnell et al. 2023). Cisco and Bloater are similar in appearance but can be differentiated by head profiles, number of gill rakers (47 for Cisco and 42 for Bloater; Bunnell et al. 2023), and body morphometry. Lake Whitefish spawn from September through January in water depths of 2–4 m (Phillips et al. 1982). Cisco spawn from November through December in water depths of 1–47 m (Paufve et al. 2022), whereas Bloater spawn later in winter (February through May) at depths of 37–92 m (Koelz 1929; Becker 1983; Eshenroder et al. 2016). After eggs of all three species hatch in the spring, larvae feed on zooplankton and then switch to larger invertebrate prey as they grow; some will begin to feed on other fish species as they reach maturity (Warren and Lehman 1988; Brown and Taylor 1992; Breaker et al. 2020; Gatch et al. 2021). All three species typically mature at ages 4–5, with some maturing beginning at age 2 (Beauchamp 2002; Gorman 2012; DeCosta 2016).

Book chapter↗
USGS2026

Culturing emerging, imperiled, and poorly understood fishes

Most fish hatcheries and farms raise fish for food, to supply the bait and ornamental fish trades, or to create or enhance recreational and commercial fishing opportunities. Culture methods for these species are well established and are described in various chapters of this book. However, a growing number of facilities are responsible for cultivation of emerging, imperiled, or lesser-known species in support of rescue or recovery efforts. “Imperiled” may refer to species that have been formally listed as threatened or endangered under the U.S. Endangered Species Act (ESA) or analogous state regulations, or it may refer to populations or other groups that are considered at-risk for other reasons (e.g., fish living in drought-affected areas). The USFWS defines an endangered species as one that is in danger of extinction throughout all or a significant portion of its range, while a threatened species is one that is likely to become endangered in the foreseeable future (USFWS 2016b). There is often limited information available regarding the biology and propagation of these species. Many have never been propagated in captivity, and conventional hatchery techniques are not necessarily suited to their dietary needs, feeding habits, flow preferences, reproductive requirements, stress management, tank preferences, and use of structure (Rakes et al. 1999). To successfully maintain and propagate these fish, the fish culturist must identify the water quality, health and nutrition, spawning, and habitat needs of the species in question. Success often demands a painstaking process of mimicking natural conditions in the hatchery until suitable modifications can be developed or individuals can be habituated to more conventional rearing conditions. Rearing lesser-known species requires dedication and creativity as well as the application of new, sometimes experimental culture techniques to ensure a safe environment that provides for the well-being of imperiled species while in captivity.

Book chapter↗
USGS2026

Is "weediness" and "invasiveness" of weeds a function of the plant microbiome?

Over the past several decades, the extent to which microbes enhance plant development and health has become clearer; however, this has not been explored in terms of the aggressiveness and hardiness of weedy plants. In this review, we explore the hypothesis that many features of weeds and invasive plants are related to the activities of plant microbiomes. Microbes contribute to weed growth, fecundity, and fitness. They also play roles in soils, and in plants as endophytes, where they modulate plant development and protect the host from pathogens, insects, animals, and abiotic stresses. In addition, the adaptability and hardiness of weeds partly stem from the effects of endophytes on plant gene expression and genetic diversity. Weed control often involves multiple applications of herbicides or other treatments that can be costly and destructive. Weed and invasive plant control for agriculture and environment goes beyond monetary costs to negative impacts on people, animals and environment. However, with a more complete knowledge of the roles played by microbes, their symbiotic interactions may be altered to diminish aggressive traits less expensively and with fewer non target effects on environmental, human and animal health.

Grass Research↗
USGS2026

Satellite tracking of Galapagos Petrel Pterodroma phaeopygia reveals distribution and movements during chick rearing

We tracked 19 adult Galapagos Petrels Pterodroma phaeopygia during the chick-rearing seasons in 2009 and 2010 (Santa Cruz Island [ n = 16] and Floreana Island [ n = 3]) in the Galápagos Islands, Ecuador. Eight petrels performed 27 complete foraging trips lasting 0.6 to 18.8 days. Short trips (3.2 ± 2.1 days; 785 km; max displacement 671 km) and long trips (10.8 ± 3.9 days; 2,856 km; max displacement 1,034 km) resulted in concentrated use of waters off southern and western Isabela Island and within the Galápagos Marine Reserve (GMR). Less concentrated time extended farther southwest and eastward, in that case toward mainland Ecuador. Total distance covered among all completed trips, independent of duration, was strongly correlated with trip duration ( R ² = 0.92), indicating a strategy favoring active searching and foraging over commuting. Petrels ranged across Ecuador's exclusive economic zone (EEZ), as well as other countries' (Colombia, Costa Rica, Perú), and waters beyond; they spent 46%, 27%, and 34% of their time in the GMR during short, long, and apparent (incomplete) trips, respectively. However, overlap with EEZs or marine protected areas (MPAs) does not necessarily confer protection, because commercial tuna fishing, including legal fishing historically permitted inside the GMR, occurs within these waters. Including all complete and incomplete trips, petrels spent 37% of their time in high-seas waters without formal protection, outside both MPAs and EEZs. While some hot spots overlapped Galápagos MPAs, the far-ranging nature of chick-provisioning petrels underscores the importance for this species of also having coordinated, multinational protection of the high seas.

Floreana Island, Galápagos Islands, Santa Cruz Isl↗
USGS2026

Subaerially exposed Iceberg Lake sediments: An exceptional record of historical subaqueous earthquake disturbance at the eastern edge of the Alaskan-Aleutian subduction zone

Paleoseismic records are limited in the Yakutat Terrane (eastern edge of the Alaskan-Aleutian subduction zone) due to the extensive ice cover that hinders traditional methods such as trenching of the faults, but lacustrine sediments offer an alternative archive. We investigated lakebed sediments exposed after recent outburst floods (1999 CE) at Iceberg Lake, a glacier-dammed basin whose stratigraphy was revealed after the lake drained and partially eroded. We logged outcrops across the basin and sampled their sediments. Between annually laminated background deposits, we identified sediment gravity flow beds and in-situ soft-sediment deformation structures (convolutions, sand blows, and fractures) interpreted to be earthquake-induced. Our age model links some of the uppermost depositional and deformational events to the 1958, 1964 and 1979 CE earthquakes. These results demonstrate that Iceberg Lake was a sensitive recorder of seismic shaking and its sediments hold strong potential for producing a paleoseismic record for the northern Yakutat Terrane.

Alaska↗
USGS2026

Improving offshore 3D splay fault geometries and slip histories using seismic data reprocessing and structural modeling

The goal of this project as written in the CRESCENT seed grant proposal was as follows: 1) reprocess selected profiles along strike from 45° to 48°N from the CASIE21 crustal-scale seismic data to obtain higher-resolution and higher-quality imaging of the uppermost 1-2 km of the accretionary wedge; 2) convert high-resolution USGS sparker seismic data from the time to depth domain to constrain near-surface fault geometries; 3) use kinematic modeling in the MOVE software to derive individual fault slip rates and per-event-displacements; and 4) work with the CFM group to create updated 3D models of identified faults based on the new data sources. At this stage, we have begun the reprocessing of the CASIE21 seismic reflection data (Carbotte et al., 2023). The time-migration reprocessing of the CASIE21 dataset has improved imaging of the near-surface structure by incorporating usable frequencies up to ~220 Hz, in contrast to the ~50 Hz maximum usable content in the currently available pre-stack depth migrated (PSDM) profiles (Fig. 1C). An example of the image quality gained through reprocessing is shown in Fig. 1, where the dominant wavelength of each reflector is reduced to ~10 m (Fig. 1B) from ~20 m in the existing PSDM product (Fig. 1A). The reprocessing work is still currently in progress. While the imaging in the shallow section has been much improved, reprocessing below the first multiple is still needed to create a seamless image from the plate boundary to the surface.

Final Report↗
USGS2026

Extrinsic factors similarly affect nest survival of a threatened shorebird in natural and human-created habitats

Knowledge of factors that influence nest survival can inform effective conservation management for imperiled avian species. Habitat availability and quality are common priorities of conservation efforts, and climate and interspecific associations can also affect survival rates. In the lower Platte River system of eastern Nebraska, USA, Piping Plovers ( Charadrius melodus , hereafter plovers) nest on river sandbars and different types of human-created off-river sites (i.e., sand and gravel mines, housing developments, and transitional sites) that are unique within the Northern Great Plains breeding population. However, off-river habitat may not be suitable for plover nesting long-term because of reduced habitat availability on both river sandbars and off-river sites. We evaluated plover nest survival at off-river and sandbar sites using data from 2008 to 2023 (n = 285). In addition, we examined the effects of extreme temperatures, proximity to conspecific and Interior Least Tern ( Sternula antillarum athalassos , hereafter tern) nests, and temporal factors on nest survival. Plover nest survival did not differ between off-river sites and sandbars or amongst different off-river site types. Daily nest survival was 0.9818 (95% CI = 0.9729–0.9878) from 2008 to 2013 (unexclosed; n = 87) and 0.9950 (0.9918–0.9970) from 2014 to 2023 (exclosed; n = 198). Nest survival increased with the proportion of above average temperature days, increased with proximity to neighboring tern nests, and decreased with later nest initiation dates. Therefore, prioritizing early season nests, recognizing the benefits terns provide to plover nest survival, and monitoring the effect of climatic trends may aid future conservation efforts. Finally, as nest survival at off-river sites is comparable to sandbars, the predicted decline of habitat provided at off-river sites may reduce the overall breeding productivity and abundance of plovers in the lower Platte River system with ramifications to broader population viability.

Nebraska↗
USGS2026

King Rails in southeastern Arkansas are majority resident

King Rails ( Rallus elegans ), a declining species of secretive marsh bird, have a mixed migratory strategy, with some individuals migrating and some being year-round residents. Determining the distribution of migratory versus resident King Rails is critical to guiding habitat management and assessing risks to populations. We examined the migratory status of adult King Rails at the Choctaw West Wildlife Management Area in southeastern Arkansas, the only known site in Arkansas with multiple breeding pairs. Of the 23 adult King Rails we tagged in 2022 and 2023, two birds migrated away from the local area, one in each year. One migrated 145 km, and the other 450 km. Our findings suggest that the line between the migratory and resident range of Arkansas King Rails could be north of our site.

Arkansas↗
USGS2026

Columbia Basin pygmy rabbit recovery planning through structured decision making

The endangered Columbia Basin pygmy rabbit (CBPR) faces multiple threats, particularly increasing risk of larger and more intense wildfires due to climate change, emerging disease, and sagebrush habitat loss due to agriculture and development. Through the use of conservation breeding, the CBPR wild population grew from a low of 16 individuals captured in 2001 to over 100 individuals in two subpopulations in 2024. However, these subpopulations are geographically proximate, with potential risk that both subpopulations could be affected by a single wildfire or disease event. Additionally, a succession of setbacks in the breeding program has prompted a natural re-evaluation point for the CBPR conservation program. We undertook a structured decision-making (SDM) process with participants from both Washington Department of Fish and Wildlife (WDFW) and US Fish and Wildlife Service (USFWS) to develop a strategy that is sustainable and implementable for guiding management in the coming decades across the range of the CBPR, taking into account changing conditions and updated information. A population model that incorporated both demographic and high impact event uncertainties was developed to test how alternative strategies – defined by conservation breeding program, vaccination, and translocation components – affect CBPR population growth and cost objectives. Based on analysis of the model results, we identified the following actions that appear to have the greatest potential to allow WDFW and USFWS to meet their conservation objectives for CBPR: Continue conservation breeding program, and possibly expand to include an island subpopulation (an isolated, unfenced area that can serve as a source for rabbits while requiring fewer management inputs) Continue Rabbit Hemorrhagic Disease Virus (RHDV2) annual vaccinations in both breeding and wild populations When juveniles are available for translocation, prioritize recovery areas that are in the establishing phase In addition, while not analyzed explicitly in the model, discussions during the SDM process led to the identification of the following actions, which the group considered to have potential to benefit the CBPR either directly or indirectly: Increase the amount of suitable habitat available to pygmy rabbits Increase protections for existing and potential recovery areas Design future monitoring to better estimate survival and reproduction, with an emphasis on understanding how these vital rates vary between wild and semi-captive individuals, between vaccinated and unvaccinated individuals, and as a function of habitat factors

BioRxiv↗
USGS2026

A genomic tool to tackle cryptic diversity demonstrates the potential for off-target use of GT-seq panels

A comprehensive understanding of life history is vital to successful species conservation and management. When different life history stages are accompanied by considerable morphological or cryptic variation, such as the egg and larval phases exhibited by most fishes, genomic tools are essential for identifying species so that early-life ecology questions can be studied. Genotyping-in-thousands by sequencing (GT-seq) has recently emerged as a targeted and efficient approach for species identification. We leveraged existing genomic and transcriptomic data to develop a GT-seq panel capable of differentiating the members of the Coregonus artedi complex, a radiation of salmonids in the Laurentian Great Lakes whose members are indistinguishable with mitochondrial DNA barcoding loci and are the focus of bi-national conservation initiatives. Our panel of 494 loci was able to assign fishes in the C. artedi complex to species and lake. We examined cross-amplification in other coregonines with overlapping distributions and found that congeneric Lake Whitefish ( C. clupeaformis ) cross-amplified at 94% of loci and confamilial Round and Pygmy Whitefish ( Prosopium spp.) cross-amplified at 42% and 38% of loci, respectively. We adapted bioinformatic probes to account for Prosopium -specific variants including 22 new SNPs and developed a whitelist of 428 SNPs capable of distinguishing these whitefishes. Finally, we demonstrated performance by identifying 3,066 coregonine larvae and juveniles collected in spring 2019-2021 from Lake Superior. These results hold promise for future insights into the species-specific ecology of early life coregonines and demonstrate the flexibility of GT-seq panels, which may cross-amplify hundreds of informative genome-wide loci in related taxa.

BioRxiv↗