SEARCH · Search USGS

Results for “Conservation Genetics”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45Linked to original sources

USGS2016

Interdrainage morphological and genetic differentiation in the Escambia Map Turtle, Graptemys ernsti

Graptemys ernsti, the Escambia Map Turtle, inhabits the Escambia/Conecuh River, the adjacent Yellow River, and the Pea River further to the east, all of which have been distinct drainage systems since the Pleistocene. We used continuous and meristic morphological and genetic data to compare populations of G. ernsti and found evidence of differences among the three drainages. Frequency of occurrence of a nasal trident differed among the three drainages. Yellow River specimens possessed unique mitochondrial haplotypes while the Conecuh and the Pea shared haplotypes. Five microsatellite loci identified the drainages as being distinct, with the strongest differentiation between the Yellow River and the other two drainages. While these differences do not appear great enough to warrant taxonomic recognition, they do suggest that each population has a distinct evolutionary and demographic history and that they should therefore be managed separately.

Herpetological Conservation and Biology↗

USGS2012

Evidence of local adaptation in westslope cutthroat trout

An understanding of the process of local adaptation would allow managers to better protect and conserve species. Many salmonids are in need of such efforts, and because they often persist in differing, isolated environments, they are useful organisms for studying local adaptation. In addition, the temperature sensitivity of salmonids provides a likely target for natural selection. We studied thermal adaptation in four wild populations and one hatchery stock of westslope cutthroat trout Oncorhynchus clarkii lewisi . The mean summer temperatures of source streams ranged from 6.7°C to 11.2°C. Embryos were collected from the wild, and embryonic development, embryonic survival, and juvenile growth were determined. A significant relationship between median embryonic survival and source stream temperature was detected. Based on a rank test, populations from colder streams had a greater decline in median embryonic survival at warm temperatures than populations from warmer streams. Embryonic development and juvenile growth did not appear to be influenced by source. These findings suggest that populations are thermally adapted to their source streams and this should be considered by managers. However, further study is necessary to sort out the potential confounding factors, whether genetic or epigenetic.

Transactions of the American Fisheries Society↗

USGS1997

Status and management of the PaliIa, an endangered Hawaiian honeycreeper, 1987-1996

A single, relictual population of Palila Loxioides bailleui, a Hawaiian honeycreeper, survives on the slopes of Mauna Kea volcano on the island of Hawai'i, where it feeds principally on flowers and green seeds of the mamane tree Sophora chrysophylla. The Palila was listed as an endangered species by state and federal governments because of continuing damage to its habitat by browsing Feral and Mouflon Sheep Ovis aries and O. musimon and Goats Capra hircus and because of the bird's restricted range and low numbers. Ecology of the Palila was studied from 1987 to 1996. Annual population estimates fluctuated between 1 600 and 5 700 and averaged 3 400 birds. Estimates varied with availability of mamane seeds, which are less abundant in drought years. In drought years, most birds did not attempt to breed, and survival rates were lower because of a shortage of food. Availability of mamane seeds also showed large seasonal variability. While some nests were preyed upon by Owls Asio flammeus, Cats Felis catus and Rats Rattus rattus, losses were high at the end of the season from unexplained death of eggs and chicks. Genetic studies did not implicate inbreeding depression. Neither avian malaria nor avian pox appeared at this site, where the mosquito vector was absent. However, weather and food shortage worsened towards the end of the nesting season. Availability of food and habitat remain the principal factors limiting increase in the Palila population. Recovery efforts now focus on reducing numbers of feral ungulates, fire management, removing mammalian predators, and developing techniques for captive propagation and introduction to currently unoccupied sites within the bird's former range. Reforestation adjacent to the Mauna Kea Forest Reserve would allow the Palila population to expand and grow.

Pacific Conservation Biology↗

USGS2011

Foraging segregation and genetic divergence between geographically proximate colonies of a highly mobile seabird

Foraging segregation may play an important role in the maintenance of animal diversity, and is a proposed mechanism for promoting genetic divergence within seabird species. However, little information exists regarding its presence among seabird populations. We investigated genetic and foraging divergence between two colonies of endangered Hawaiian petrels ( Pterodroma sandwichensis ) nesting on the islands of Hawaii and Kauai using the mitochondrial Cytochrome b gene and carbon, nitrogen and hydrogen isotope values (δ 13 C, δ 15 N and δD, respectively) of feathers. Genetic analyses revealed strong differentiation between colonies on Hawaii and Kauai, with Φ ST = 0.50 ( p < 0.0001). Coalescent-based analyses gave estimates of <1 migration event per 1,000 generations. Hatch-year birds from Kauai had significantly lower δ 13 C and δ 15 N values than those from Hawaii. This is consistent with Kauai birds provisioning chicks with prey derived from near or north of the Hawaiian Islands, and Hawaii birds provisioning young with prey from regions of the equatorial Pacific characterized by elevated δ 15 N values at the food web base. δ 15 N values of Kauai and Hawaii adults differed significantly, indicating additional foraging segregation during molt. Feather δD varied from −69 to 53‰. This variation cannot be related solely to an isotopically homogeneous ocean water source or evaporative water loss. Instead, we propose the involvement of salt gland excretion. Our data demonstrate the presence of foraging segregation between proximately nesting seabird populations, despite high species mobility. This ecological diversity may facilitate population coexistence, and its preservation should be a focus of conservation strategies.

Hawaii↗

USGS2017

Emerging fungal pathogen Ophidiomyces ophiodiicola in wild European snakes

Snake fungal disease (SFD) is an emerging disease of conservation concern in eastern North America. Ophidiomyces ophiodiicola , the causative agent of SFD, has been isolated from over 30 species of wild snakes from six families in North America. Whilst O. ophiodiicola has been isolated from captive snakes outside North America, the pathogen has not been reported from wild snakes elsewhere. We screened 33 carcasses and 303 moulted skins from wild snakes collected from 2010–2016 in Great Britain and the Czech Republic for the presence of macroscopic skin lesions and O. ophiodiicola . The fungus was detected using real-time PCR in 26 (8.6%) specimens across the period of collection. Follow up culture and histopathologic analyses confirmed that both O. ophiodiicola and SFD occur in wild European snakes. Although skin lesions were mild in most cases, in some snakes they were severe and were considered likely to have contributed to mortality. Culture characterisations demonstrated that European isolates grew more slowly than those from the United States, and phylogenetic analyses indicated that isolates from European wild snakes reside in a clade distinct from the North American isolates examined. These genetic and phenotypic differences indicate that the European isolates represent novel strains of O. ophiodiicola . Further work is required to understand the individual and population level impact of this pathogen in Europe.

Scientific Reports↗

USGS2023

Comparing reintroduction strategies for the endangered San Francisco gartersnake (Thamnophis sirtalis tetrataenia) using demographic models

For endangered species persisting in a few populations, reintroductions to unoccupied habitat are a popular conservation action to increase viability in the long term. Identifying the reintroduction strategy that is most likely to result in viable founder and donor populations is essential to optimally use resources available for conservation. The San Francisco gartersnake ( Thamnophis sirtalis tetrataenia ) is an endangered sub-species that persists in a small number of populations in a highly urbanized region of California. Most of the extant populations of San Francisco gartersnakes have low adult abundance and effective population size, heightening the need for establishment of more populations for insurance against the risk of extinction. We used simulations from demographic models to project the probability of quasi-extinction for reintroduced populations of San Francisco gartersnakes based on the release of neonate, juvenile, adult, or mixed-age propagules. Our simulation results indicated that the release of head-started juveniles resulted in the greatest viability of reintroduced populations, and that releases would need to continue for at least 15 years to ensure a low probability of quasi-extinction. Releasing captive-bred juvenile snakes would also have less effect on the viability of the donor population, compared to strategies that require more adult snakes to be removed from the donor population for translocation. Our models focus on snake demography, but the genetic makeup of donor, captive, and reintroduced populations will also be a major concern for any proposed reintroduction plan. This study demonstrates how modeling can be used to inform reintroduction strategies for highly imperiled species.

PLoS ONE↗

USGS2022

Using landscape genomics to delineate future adaptive potential for climate change in the Yosemite toad (Anaxyrus canorus)

An essential goal in conservation biology is delineating population units that maximize the probability of species persisting into the future and adapting to future environmental change. However, future-facing conservation concerns are often addressed using retrospective patterns that could be irrelevant. We recommend a novel landscape genomics framework for delineating future “Geminate Evolutionary Units” (GEUs) in a focal species: (1) identify loci under environmental selection, (2) model and map adaptive conservation units that may spawn future lineages, (3) forecast relative selection pressures on each future lineage, and (4) estimate their fitness and likelihood of persistence using geo-genomic simulations. Using this process, we delineated conservation units for the Yosemite toad ( Anaxyrus canorus ), a U.S. federally threatened species that is highly vulnerable to climate change. We used a genome-wide dataset, redundancy analysis, and Bayesian association methods to identify 24 candidate loci responding to climatic selection ( R 2 ranging from 0.09 to 0.52), after controlling for demographic structure. Candidate loci included genes such as MAP3K5, involved in cellular response to environmental change. We then forecasted future genomic response to climate change using the multivariate machine learning algorithm Gradient Forests. Based on all available evidence, we found three GEUs in Yosemite National Park, reflecting contrasting adaptive optima: YF-North (high winter snowpack with moderate summer rainfall), YF-East (low to moderate snowpack with high summer rainfall), and YF-Low-Elevation (low snowpack and rainfall). Simulations under the RCP 8.5 climate change scenario suggest that the species will decline by 29% over 90 years, but the highly diverse YF-East lineage will be least impacted for two reasons: (1) geographically it will be sheltered from the largest climatic selection pressures, and (2) its standing genetic diversity will promote a faster adaptive response. Our approach provides a comprehensive strategy for protecting imperiled non-model species with genomic data alone and has wide applicability to other declining species.

California↗

USGS2004

Less waste corn, more land in soybeans, and the switch to genetically modified crops: Trends with important implications for wildlife management

American agriculture has provided abundant high-energy foods for migratory and resident wildlife populations since the onset of modern wildlife management. Responding to anecdotal evidence that corn residues are declining in cropland, we remeasured waste corn post-harvest in the Central Platte River Valley (CPRV) of Nebraska during 1997 and 1998 to compare with 1978. Post-harvest waste corn averaged 2.6% and 1.8% of yield in 1997 and 1998, respectively. After accounting for a 20% increase in yield, waste corn in 1997 and 1998 was reduced 24% and 47% from 1978. We also evaluated use of soybeans by spring-staging sandhill cranes ( Crus canadensis ) and waterfowl during spring 1998 and 1999. Despite being widely available in the CPRV, soybeans did not occur in esophageal contents of sandhill cranes ( n= 174), northern pintails ( Anas acuta , n= 139), greater white-fronted geese ( Anser albifrons , n= 198), or lesser snow geese ( Chen caerulescens , n= 208) collected with food in their esophagi. Lack of soybean consumption by cranes and waterfowl in Nebraska in early spring builds upon previously published findings, suggesting that soybeans are poorly suited for meeting nutrient needs of wildlife requiring a high-energy diet. Given evidence that high-energy food and numerous populations of seed-eating species found on farmland are declining, and the enormous potential risk to game and nongame wildlife populations if high-energy foods were to become scarce, a comprehensive research effort to study the problem appears warranted. Provisions under the Conservation Security subtitle of The Farm Security and Rural Investment Act of 2002 offer a potential mechanism to encourage producers to manage cropland in ways that would replace part of the high-energy foods that have been lost to increasing efficiency of production agriculture.

Nebraska↗

USGS2018

Intraspecific niche models for ponderosa pine (Pinus ponderosa) suggest potential variability in population-level response to climate change

Unique responses to climate change can occur across intraspecific levels, resulting in individualistic adaptation or movement patterns among populations within a given species. Thus, the need to model potential responses among genetically distinct populations within a species is increasingly recognized. However, predictive models of future distributions are regularly fit at the species level, often because intraspecific variation is unknown or is identified only within limited sample locations. In this study, we considered the role of intraspecific variation to shape the geographic distribution of ponderosa pine ( Pinus ponderosa ), an ecologically and economically important tree species in North America. Morphological and genetic variation across the distribution of ponderosa pine suggest the need to model intraspecific populations: the two varieties (var. ponderosa and var. scopulorum ) and several haplotype groups within each variety have been shown to occupy unique climatic niches, suggesting populations have distinct evolutionary lineages adapted to different environmental conditions. We utilized a recently-available, geographically-widespread dataset of intraspecific variation (haplotypes) for ponderosa pine and a recently-devised lineage distance modeling approach to derive additional, likely intraspecific occurrence locations. We confirmed the relative uniqueness of each haplotype-climate relationship using a niche-overlap analysis, and developed ecological niche models (ENMs) to project the distribution for two varieties and eight haplotypes under future climate forecasts. Future projections of haplotype niche distributions generally revealed greater potential range loss than predicted for the varieties. This difference may reflect intraspecific responses of distinct evolutionary lineages. However, directional trends are generally consistent across intraspecific levels, and include a loss of distributional area and an upward shift in elevation. Our results demonstrate the utility in modeling intraspecific response to changing climate and they inform management and conservation strategies, by identifying haplotypes and geographic areas that may be most at risk, or most secure, under projected climate change.

Systematic Biology↗

USGS1999

Hybridization and the phylogenetic relationship between polecats and domestic ferrets in Britain

Ferrets ( Mustela furo ) were domesticated from polecats ( M. putorius, M. eversmannii ) over 2000 years ago. Following their introduction to Britain, they escaped and hybridized with native European polecats ( M. putorius ). Native polecats declined to the point of near extinction prior to World War I, but have recently begun to expand from a Welsh refugium. Concern has arisen as to the extent of polecat/ferret introgression, and in particular, whether the expanding population is of mainly hybrid origin. Therefore, mitochondrial DNA sequencing was used to investigate polecat genetic diversity in Britain. Two geographically distinct lineages were found, where one may be ancestral to the British polecat, and the other to the domestic ferret. The ancestral distribution of each lineage, or assortative mating is sufficient to explain the observed pattern. A further comparison between the distribution of the polecat phenotype and mitochondrial haplotype implies that the current population expansion may be mediated by dispersing male polecats hybridizing with female feral ferrets. However, the wild source of the ferret remains obscure. Relatively recent speciation from European mink ( M. lutreola ) and black-footed ferrets ( M. nigripes ), and/or the effects of hybridization result in an unresolved molecular phylogeny.

Biological Conservation↗

USGS2004

Migration stopover ecology of western avian populations: A southwestern migration workshop

The importance of migration stopover sites in ensuring that migratory birds successfully accomplish their journeys between breeding and non-breeding ranges has come to the forefront of avian research. Migratory birds that breed in western United States (US) and Canada and overwinter primarily in western Mexico migrate across the arid region of northern Mexico and southwestern US. Many of these migrants use lowland riparian stopover habitats, which comprise less than 0.1% of the western U.S. landscape. These habitats represent a significant conservation priority. Recognizing the importance of migration stopover habitats in the arid southwest, the U.S. Fish and Wildlife Service (USFWS) Region 6 partnered with the U.S. Geological Survey (USGS) to support a project---“Migration stopover ecology of western avian populations: patterns of geographic and habitat distribution.” A primary objective of the project was to convene a workshop for avian researchers, conservation professionals, and land managers involved in stopover needs of migratory birds that breed in western North America. The workshop included presentations on our current state of knowledge regarding passerine migration in western North America, techniques and technologies potentially useful in researching migration, and efforts that agencies and other partners are conducting within the realm of migration. Workshop presentations provided a backdrop for subsequent discussions, the goals of which were to identify research needs and initiate a coordinated approach to research of western migration stopover ecology. Workshop presentations spanned a wide range of concerns and interests. Highlights included indications that mid- and high-elevation riparian and montane shrubland habitats may be as crucial to western migrants in fall migration as lowland riparian habitats are in spring migration. Comparisons of eastern versus western migration systems elucidated large differences in stopover habitats used and the intensity with which certain types are used, underscoring the potential need to develop separate management approaches for eastern and western stopover sites. Presentations on techniques and technology for migration research revealed that rate of lipid deposition can serve as an indicator of habitat quality; that genetics and stable isotope analyses of feathers can be valuable tools to elucidate linkages between breeding and wintering areas; that radar imagery can be used to track large-scale movement patterns and habitat use; and that there are analytical options for combining multiple sources of information. Other presentations focused on partnership perspectives (USFWS and Sonoran Joint Venture), the genesis of a western migration monitoring network, premises of Coordinated Bird Monitoring, and how collaborative efforts could benefit migration research (e.g., combined bird and bat migration studies; linking avian researchers with fluvial geomorphologists; linking research throughout western North America; linking surveys and banding). Priority research needs and questions identified during the open discussions fell into three main categories: (1) habitat/landscape/climate relationships, (2) en route bird distribution patterns, and (3) general migration ecology. Tasks within these categories included: define the relative importance of various habitat types to migrants in spring and fall, determine what distinguishes high- from poor-quality stopover habitat; determine geographic patterns of loss in stopover habitats; model landscape attributes associated with species richness and abundance; identify effects of climate change and current climate anomalies on plant phonologies, associated insect flushes, and timing of migration; and determine effects of hydrologic changes on riparian vegetation, food availability, and stopover habitat quality. Workshop participants discussed a coordinated approach for addressing immediate research needs regarding migration patterns and crucial stopover sites and types. They envisioned a three-tiered, coordinated approach: (1) long-term research to address effects of climate change and other large-scale patterns, (2) intensive, short-term survey and monitoring efforts using a stratified random design within habitats of interest to elucidate regional patterns of distribution and habitat use, and (3) research conducted at existing survey and banding sites to address more in-depth questions (e.g., rates of lipid deposition, microhabitat use, isotope analyses). There was considerable interest in developing common research proposals to blend the broad expertise represented at this workshop. A second meeting is recommended to build on the momentum of these discussions, to facilitate collaborations, and further the goals of integrated approaches to broadscale research on migration stopover ecology.

Open-File Report↗

USGS2002

History of pronghorn population monitoring, research, and management in Yellowstone National Park

Pronghorn antelope in Yellowstone National Park (YNP) persist in a small population that historically has experienced recurrent, sometimes dramatic declines. They apparently are isolated from other pronghorns, depend partly on private lands for winter range, experience heavy predation of fawns, and concentrate during winter in a relatively small area, thereby increasing their vulnerability to factors like disease or locally extreme weather. Overall, the situation raises serious concerns about the long-term viability of this population. Although such concerns are not new, evidence of a dramatic population decline since 1991 and continued poor recruitment has created a renewed sense of urgency. Recent efforts to revitalize pronghorn research in YNP began with fawn recruitment and habitat use studies, initiated in 1999 and 2000. With those studies drawing to a close, YNP is reviewing the status and direction of its pronghorn program. The Yellowstone Pronghorn Conservation Assessment Workshop was convened in YNP in January, 2002, to appraise the current state of knowledge about this pronghorn population and make recommendations about future management and research needs. A review of pronghorn population change, management, and research in YNP was commissioned in May, 2001, to provide historical background for workshop participants. Following is a written summary of that review. The process of locating materials for this review was limited to 3 months. Not all relevant materials were discovered or reviewed in that time. In particular, it was not possible to find and review all original sources of information. Also, except for occasional anecdotal accounts, weather records were not reviewed, leaving a potentially serious gap in our understanding of the forces driving changes in pronghorn population counts and estimates 2 over time. Despite these deficiencies, considerable information was reviewed, earlier summaries of population classification and count data were updated, and previously uncited sources of information were identified that challenge important aspects of previous interpretations of the history of pronghorns and pronghorn management in YNP. Information is grouped into 4 major subject areas: distribution and habitat use, demographics and management, genetics, and disease.

Wyoming↗

USGS2025

A molecular specimen bank for contemporary and future study captures landscape-scale biodiversity baselines before Klamath River dam removal

Global restoration and conservation of freshwater biodiversity are represented in practice by works such as the Klamath River Renewal Project (KRRP), the largest dam removal and river restoration in the United States, which has reconnected 640 river kilometers. With dam removals, many biological outcomes remain understudied due to a lack of pre-impact data and complex ecosystem recovery timeframes. To avoid this, we created the KRRP molecular library, an environmental specimen bank, for long-term curation of environmental nucleic acids collected from the restoration project. We used these initial samples, environmental DNA metabarcoding, and generalized linear mixed-effects models to evaluate patterns of pre-dam removal fish richness and diversity. Demonstrating the suitability to resolve biological differences, the baseline shows that tributary and mainstem streams had greater native fish diversity and 2.3–10.7 times greater native fish species richness than reservoirs. These and future sampling efforts should, at a minimum, allow tracking of fish community response to ecosystem restoration. Anticipating the acceleration of omics innovation, we preserved samples for long-term storage and identified requisite phases for sustained function and adaptation of the molecular library: securing a physical storage facility for genetic material, establishing a governance structure, and confirming support for archive management.

California, Oregon↗

USGS2015

Mechanisms and timescales of generating eruptible rhyolitic magmas at Yellowstone caldera from zircon and sanidine geochronology and geochemistry

We constrain the physical nature of the magma reservoir and the mechanisms of rhyolite generation at Yellowstone caldera via detailed characterization of zircon and sanidine crystals hosted in three rhyolites erupted during the (ca. 170 – 70 ka) Central Plateau Member eruptive episode – the most recent post-caldera magmatism at Yellowstone. We present 238U-230Th crystallization ages and trace-element compositions of the interiors and surfaces (i.e., unpolished rims) of individual zircon crystals from each rhyolite. We compare these zircon data to 238U- 230Th crystallization ages of bulk sanidine separates coupled with chemical and isotopic data from single sanidine crystals. Zircon age and trace-element data demonstrate that the magma reservoir that sourced the Central Plateau Member rhyolites was long-lived (150 – 250 kyr) and genetically related to the preceding episode of magmatism, which occurred ca. 256 ka. The interiors of most zircons in each rhyolite were inherited from unerupted material related to older stages of Central Plateau Member magmatism or the preceding late Upper Basin Member magmatism (i.e., are antecrysts). Conversely, most zircon surfaces crystallized near the time of eruption from their host liquids (i.e., are autocrystic). The repeated recycling of zircon interiors from older stages of magmatism demonstrates that sequentially erupted Central Plateau Member rhyolites are genetically related. Sanidine separates from each rhyolite yield 238U-230Th crystallization ages at or near the eruption age of their host magmas, coeval with the coexisting zircon surfaces, but are younger than the coexisting zircon interiors. Chemical and isotopic data from single sanidine crystals demonstrate that the sanidines in each rhyolite are in equilibrium with their host melts, which considered along with their near-eruption crystallization ages suggests that nearly all CPM sanidines are autocrystic. The paucity of antecrystic sanidine crystals relative to antecrystic zircons require a model where eruptible rhyolites are generated by extracting melt and zircons from a long-lived mush of immobile crystal-rich magma. In this process the larger sanidine crystals remain trapped in the locked crystal network. The extracted melts (plus antecrystic zircon) amalgamate into a liquid dominated (i.e., eruptible) magma body that is maintained as a physically distinct entity relative to the bulk of the long-lived crystal mush. Zircon surfaces and sanidines in each rhyolite crystallize after melt extraction/amalgamation and their ages constrain the residence time of eruptible magmas at Yellowstone. Residence times of the large volume rhyolites (~40 – 70 km3) are ≤ 1 kyr (conservatively < 6 kyr), which suggests that large volumes of rhyolite can be generated rapidly by extracting melt from a crystal mush. Because the lifespan of the crystal mush that sourced the Central Plateau Member rhyolites is two orders of magnitude longer than the residence time of eruptible magma bodies within the reservoir, it is apparent that the Yellowstone magma reservoir spends most of its time in a largely-crystalline (i.e., uneruptible) state, similar to the present-day magma reservoir, and that eruptible magma bodies are ephemeral features.

Idaho, Wyoming↗

USGS2022

Genomic divergence, local adaptation, and complex demographic history may inform management of a popular sportfish species complex

The Neosho Bass ( Micropterus velox ), a former subspecies of the keystone top-predator and globally popular Smallmouth Bass ( M. dolomieu ), is endemic and narrowly restricted to small, clear streams of the Arkansas River Basin in the Central Interior Highlands (CIH) ecoregion, USA. Previous studies have detected some morphological, genetic, and genomic differentiation between the Neosho and Smallmouth Basses; however, the extent of neutral and adaptive divergence and patterns of intraspecific diversity are poorly understood. Furthermore, lineage diversification has likely been impacted by gene flow in some Neosho populations, which may be due to a combination of natural biogeographic processes and anthropogenic introductions. We assessed: (1) lineage divergence, (2) local directional selection (adaptive divergence), and (3) demographic history among Smallmouth Bass populations in the CIH using population genomic analyses of 50,828 single-nucleotide polymorphisms (SNPs) obtained through ddRAD-seq. Neosho and Smallmouth Bass formed monophyletic clades with 100% bootstrap support. We identified two major lineages within each species. We discovered six Neosho Bass populations (two nonadmixed and four admixed) and three nonadmixed Smallmouth Bass populations. We detected 29 SNPs putatively under directional selection in the Neosho range, suggesting populations may be locally adapted. Two populations were admixed via recent asymmetric secondary contact, perhaps after anthropogenic introduction. Two other populations were likely admixed via combinations of ancient and recent processes. These species comprise independently evolving lineages, some having experienced historical and natural admixture. These results may be critical for management of Neosho Bass as a distinct species and may aid in the conservation of other species with complex biogeographic histories.

Ecology and Evolution↗

USGS2013

Fluvial rainbow trout contribute to the colonization of steelhead ( Oncorhynchus mykiss ) in a small stream

Life history polymorphisms provide ecological and genetic diversity important to the long term persistence of species responding to stochastic environments. Oncorhynchus mykiss have complex and overlapping life history strategies that are also sympatric with hatchery populations. Passive integrated transponder (PIT) tags and parentage analysis were used to identify the life history, origin (hatchery or wild) and reproductive success of migratory rainbow/steelhead for two brood years after barriers were removed from a small stream. The fluvial rainbow trout provided a source of wild genotypes to the colonizing population boosting the number of successful spawners. Significantly more parr offspring were produced by anadromous parents than expected in brood year 2005, whereas significantly more parr offspring were produced by fluvial parents than expected in brood year 2006. Although hatchery steelhead were prevalent in the Methow Basin, they produced only 2 parr and no returning adults in Beaver Creek. On average, individual wild steelhead produced more parr offspring than the fluvial or hatchery groups. Yet, the offspring that returned as adult steelhead were from parents that produced few parr offspring, indicating that high production of parr offspring may not be related to greater returns of adult offspring. These data in combination with other studies of sympatric life histories of O. mykiss indicate that fluvial rainbow trout are important to the conservation and recovery of steelhead and should be included in the management and recovery efforts.

Washington↗

USGS2020

A multifaceted reconstruction of the population structure and life history expressions of a remnant metapopulation of Bonneville Cutthroat Trout: Implications for maintaining intermittent connectivity

Fishes that evolutionarily demonstrated a fluvial life history expression and migrated to spawning and rearing habitat by using lotic corridors are increasingly impacted by fragmentation. The overall goal of this study was to identify the contemporary importance of main-stem connectivity and tributaries for maintaining life history expression, population structure, and viability of a large metapopulation of Bonneville Cutthroat Trout (BCT) Oncorhynchus clarkii utah persisting in the highly fragmented Weber River, Utah. We used a multifaceted approach, including active sampling, mark–recapture, passive PIT tag detection, otolith microchemistry, and genetics. We collected BCT in all tributaries and the main stem, encountering age-0 fish in three tributaries, indicating successful reproduction. In tributaries, the size structure was bimodal and consisted of smaller fish that were classified as resident and larger fish that were deemed to be fluvial, whereas all sizes and ages (age ≥ 1) were present in the main stem. We identified up to eight age-classes; tributaries were dominated by ages 2 and 8, and the main stem was dominated by ages 2, 5, 6, and 7. Tributary BCT had lower growth rates than BCT in the main stem. We observed a surprising degree of fluvial life history expression, and fish also demonstrated very complex movement patterns across their life span. Average apparent survival (33%) was within the range estimated in similar studies for BCT, and the resight rate was best explained by angler management regulations. The fact that BCT in the Weber River and tributaries still reproduce successfully in most years and are still able to grow into large, fluvial fish suggests that connectivity must be occasionally available despite considerable fragmentation. Therefore, this metapopulation may need little further human intervention if barriers to fish passage can be removed, thereby improving connectivity, and it represents a high-priority metapopulation for conservation, thus highlighting the utility of our approach.

Utah↗

USGS2019

Environmental DNA (eDNA) detection of nonnative bullseye snakehead in southern Florida

Bullseye Snakehead Channa marulius (Hamilton 1822) was first detected in the southern Florida town of Tamarac in 2000 and has been expanding its geographic range since. Environmental DNA (eDNA) analysis is a newly-developed technique used to noninvasively detect cryptic or low-density species or those that are logistically difficult-to-study. Genetic material shed into the environment through tissue and body fluids is concentrated from water samples and analyzed for the presence of target species eDNA. To help delineate Bullseye Snakehead’s geographic range, we developed and validated a species-specific eDNA assay for both quantitative and droplet digital PCR (ddPCR). We then used ddPCR to assess 16 locations in southeast Florida using 222 water samples collected from 2015 to 2018. Positive eDNA detections were obtained at all six locations that were within the known geographic range of Bullseye Snakehead. Furthermore, eDNA was detected in six of 10 locations that were previously thought to be outside the periphery of the range but hydrologically connected through the extensive canal system. Over the four years of sampling, estimated occurrence rates (ψ) remained stable and relatively high (ψ = 0.67 [95% credible interval (CI) 0.33–0.95]) near Tamarac, Florida, as compared to the most southern sampling locations (ψ = 0.0–0.37). Bulls- eye Snakehead eDNA estimated occurrence rates in the middle region increased between 2016 (0.28 [95% CI 0.03–0.94]) and 2017 (0.66 [95% CI 0.24–0.98]), potentially reflecting eDNA detections related to a growing or expanding population. Bullseye Snakehead eDNA was detected at low concentrations on the northern and eastern borders of Everglades National Park, which is an important conservation area and UNESCO World Heritage Site. Despite extensive sampling via electrofishing, no Bullseye Snakehead were visually detected in several locations that yielded positive eDNA samples. It is unclear whether eDNA was transported through flowing water or another vector. To date, collection records for this species are confined to urban canals; however, Bullseye Snakehead may use the interconnected system of canals to disperse to natural conservation areas such as Everglades National Park, Big Cypress National Preserve, and Water Conservation Areas, where it may impact native species via predation and competition.

Florida↗