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At least 379 records · Page 21Linked to original sources
USGS2021

Genetic structure and population history in two critically endangered Kaua‘i honeycreepers

Population sizes of endemic songbirds on Kaua‘i have decreased by an order of magnitude over the past 10–15 years to dangerously low numbers. The primary cause appears to be the ascent of invasive mosquitoes and Plasmodium relictum , the agent of avian malaria, into elevations formerly free of introduced malarial parasites and their vectors. Given that these declines in native bird populations appear to be continuing, last resort measures to save these species from extinction, such as conservation breeding, are being implemented. Using 200–1439 SNPs from across the genome, we assessed kinship among individuals, levels of genetic variation, and extent of population decline in wild birds of the two most critically endangered Kaua‘i endemic species, the ‘akikiki ( Oreomystis bairdi ) and ‘akeke‘e ( Loxops caeruleirostris ). We found relatively high genomic diversity within individuals and little evidence of spatial population genetic structure. Populations displayed genomic signatures of declining population size, but individual inbreeding coefficients were universally negative, likely indicating inbreeding avoidance. Diversity within the founding conservation breeding population largely mirrored that in the wild, indicating that genetic variation in the conservation breeding population is representative of the wild population and suggesting that the current breeding program captures existing variation. Thus, although existing genetic diversity is likely lower than in historical populations, contemporary variation has been retained through high gene flow and inbreeding avoidance. Nonetheless, current effective population size for both species was estimated at fewer than 20 individuals, highlighting the urgency of management actions to protect these species.

Hawaii↗
USGS2020

Genotyping-by-sequencing illuminates high levels of divergence among sympatric forms of coregonines in the Laurentian Great Lakes

Effective resource management depends on our ability to partition diversity into biologically meaningful units. Recent evolutionary divergence, however, can often lead to ambiguity in morphological and genetic differentiation, complicating the delineation of valid conservation units. Such is the case with the "coregonine problem," where recent postglacial radiations of coregonines into lacustrine habitats resulted in the evolution of numerous species flocks, often with ambiguous taxonomy. The application of genomics methods is beginning to shed light on this problem and the evolutionary mechanisms underlying divergence in these ecologically and economically important fishes. Here, we used restriction site-associated DNA (RAD) sequencing to examine genetic diversity and differentiation among sympatric forms in the Coregonus artedi complex in the Apostle Islands of Lake Superior, the largest lake in the Laurentian Great Lakes. Using 29,068 SNPs, we were able to clearly distinguish among the three most common forms for the first time, as well as identify putative hybrids and potentially misidentified specimens. Population assignment rates for these forms using our RAD data were 93%-100% with the only mis-assignments arising from putative hybrids, an improvement from 62% to 77% using microsatellites. Estimates of pairwise differentiation ( F ST : 0.045-0.056) were large given the detection of hybrids, suggesting that reduced fitness of hybrid individuals may be a potential mechanism for the maintenance of differentiation. We also used a newly built C. artedi linkage map to look for islands of genetic divergence among forms and found widespread differentiation across the genome, a pattern indicative of long-term drift, suggesting that these forms have been reproductively isolated for a substantial amount of time. The results of this study provide valuable information that can be applied to develop well-informed management strategies and stress the importance of re-evaluating conservation units with genomic tools to ensure they accurately reflect species diversity.

Wisconsin↗
USGS2015

Conservation genomics reveals multiple evolutionary units within Bell’s Vireo ( Vireo bellii ).

The Bell’s Vireo ( Vireo bellii ) is a widespread North American species of bird that has declined since the mid-1960s primarily due to habitat modification. Throughout its range, Bell’s Vireo populations are regulated under varying degrees of protection; however, the species has never been characterized genetically. Therefore, the current taxonomy used to guide management decisions may misrepresent the true evolutionary history for the species. We sequenced 86 individuals for ND2 and genotyped 48 individuals for genome-wide SNPs to identify distinct lineages within Bell’s Vireo. Phylogenetic analyses uncovered two distinct clades that are separated in the arid southwestern United States, near the border of the Chihuahuan and Sonoran Deserts. These clades diverged from each other approximately 1.11–2.04 mya. The timing of diversification, geographic location, and niche modeling of the east/west divergence suggest vicariance as a mode of diversification for these two lineages. Analyses of the SNP dataset provided additional resolution and indicated the Least Bell’s Vireo populations are a distinct evolutionary lineage. Our genetic evidence, together with information from morphology and behavior, suggests that the Bell’s Vireo complex involves two species, each containing two separate subspecies. This new information has implications for the federal, state and other listing status of Bell’s Vireo throughout its range.

Arizona, California, Missouri, Nebraska, Nevada, O↗
USGS2021

Coalescent methods reconstruct contributions of natural colonization and stocking to origins of Michigan inland Cisco (Coregonus artedi)

Fish population structure in previously glaciated regions is often influenced by natural colonization processes and human-mediated dispersal, including fish stocking. Endemic populations are of conservation interest because they may contain rare and unique genetic variation. While coregonines are native to certain Michigan inland lakes, some were stocked with fish from Great Lakes sources, calling into question the origin of extant populations. While most stocking targeted lake whitefish ( Coregonus clupeaformis ), cisco ( C. artedi ) were also stocked from the Great Lakes to inland waterbodies. We used population genetic data (microsatellite genotypes and mitochondrial (mt)DNA sequences), coalescent modeling, and approximate Bayesian computation to investigate the origins of 12 inland Michigan cisco populations. The spatial distribution of mtDNA haplotypes suggests Michigan is an introgression zone for two ancestral cisco lineages associated with separate glacial refugia. Low levels of genetic diversity and high levels of genetic divergence were observed for populations located well inland of the Great Lakes relative to populations occupying waterbodies near the Great Lakes. Estimates of recent Great Lakes gene flow ranged from 27 to 48% for populations near the Great Lakes shoreline but were substantially lower (under 8%) for populations further inland. Inland lakes with elevated recent gene flow estimates may have been recipients of stocked coregonine fry, including cisco. Low levels of genetic diversity paired with a high likelihood of endemism as indicated by strong genetic divergence and low Great Lakes population inputs suggest the analyzed cisco populations occupying southern Michigan kettle lakes are of elevated conservation interest.

Michigan↗
USGS2022

Scale-dependent influence of the sagebrush community on genetic connectivity of the sagebrush obligate Gunnison sage-grouse

Habitat fragmentation and degradation impacts an organism's ability to navigate the landscape, ultimately resulting in decreased gene flow and increased extinction risk. Understanding how landscape composition impacts gene flow (i.e., connectivity) and interacts with scale is essential to conservation decision-making. We used a landscape genetics approach implementing a recently developed statistical model based on the generalized Wishart probability distribution to identify the primary landscape features affecting gene flow and estimate the degree to which each component influences connectivity for Gunnison sage-grouse ( Centrocercus minimus ). We were interested in two spatial scales: among distinct populations rangewide and among leks (i.e., breeding grounds) within the largest population, Gunnison Basin. Populations and leks are nested within a landscape fragmented by rough terrain and anthropogenic features, although requisite sagebrush habitat is more contiguous within populations. Our best fit models for each scale confirm the importance of sagebrush habitat in connectivity, although the important sagebrush characteristics differ. For Gunnison Basin, taller shrubs and higher quality nesting habitat were the primary drivers of connectivity, while more sagebrush cover and less conifer cover facilitated connectivity rangewide. Our findings support previous assumptions that Gunnison sage-grouse range contraction is largely the result of habitat loss and degradation. Importantly, we report direct estimates of resistance for landscape components that can be used to create resistance surfaces for prioritization of specific locations for conservation or management (i.e., habitat preservation, restoration, or development) or as we demonstrated, can be combined with simulation techniques to predict impacts to connectivity from potential management actions.

Colorado, Utah↗
USGS2015

Genetic signatures of historical dispersal of fish threatened by biological invasions: the case of galaxiids in South America

Aim The ecological effects of biological invasions are well documented, but little is known about the effects of invaders on the genetic structure of native species. We examined the phylogeography, genetic variation and population structuring of two galaxiid fishes, Aplochiton zebra and A. taeniatus , threatened by non-native salmonids, and whose conservation is complicated by misidentification and limited knowledge of their genetic diversity. Location Chile and the Falkland Islands. Methods We combined microsatellite and mitochondrial DNA (16S rDNA and COI) markers to compare genetic diversity, effective population size and gene flow of Aplochiton spp. populations differentially affected by salmonid presence. Results We identified two 16S rDNA haplotypes among A. zebra – one dominant in coastal populations and another dominant in inland populations. Populations living on the island of Chiloé displayed a mixture of coastal and inland haplotypes, as well as high microsatellite diversity, as one would expect if the island had been a refugium during the Last Glacial Maximum, or a contact zone among populations. Microsatellite data revealed strong population structuring, indicative of current isolation patterns, and a negative correlation between the genetic diversity of A. zebra and the relative abundance of invasive salmonids. Main conclusions Our study indicates that population structuring of A. zebra reflects the influence of historical patterns of migration, but also the current levels of reduced gene flow among watersheds. Invasive salmonids, known to compete with and prey on native galaxiids, may have had negative impacts on the genetic diversity of Aplochiton spp. The low genetic variation found in some populations, coupled with potential biases in abundance estimates due to species misidentification, highlight the urgent need for more research into the conservation status of the two species of Aplochiton .

Journal of Biogeography↗
USGS2024

Wintering grounds leave their mark: Where birds winter influences genomic structure in Arctic nesting common eiders

Information about the distribution of genomic variation within and between nesting locations of waterfowl can aid in defining populations and conservation plans and inform harvest management. Identification of locations where shifts in allelic diversity occur is particularly important for Arctic nesting species nesting, a region currently experiencing rapid change associated with climate and other factors. Here, we build upon previous investigations on spatial patterns of genetic variation in a largely migratory, circumpolar breeding sea duck, the common eider ( Somateria mollissima ) through inclusion of additional sample locations and genomic markers. We analyzed double-digest restriction site-associated DNA sequences from 309 common eiders to estimate genetic variation within, and differentiation among, 21 nesting locations across North America. Our results corroborate previous evidence of four genetic groups that coincide with colonies that share similar winter areas. We found deeper genomic differences between common eiders wintering in the west (Pacific Ocean) versus the east (Atlantic Ocean and Hudson Bay). We also identified subtle structure, not previously recognized, within Hudson Bay nesting common eiders. Our findings add to evidence linking wintering areas and genomic differentiation in waterfowl, offering further insights for management of this culturally important sea duck species.

Conservation Genetics↗
USGS2024

Environmental DNA

The widespread adoption of environmental DNA (eDNA) detection tools for biodiversity monitoring has led to the need for universal data standards to inform principled eDNA data applications. Improvements in understanding the meaning and possible uncertainty of eDNA data can minimize erroneous conclusions, increase confidence in eDNA data, and maximize conservation outcomes. -Environmental DNA (eDNA) is the genetic material left by organisms in the environment. -eDNA is increasingly being used to detect the presence of species and assess biodiversity, but broad-scale best practices are still being developed. -This affects the quality, accessibility, and usefulness of data. -Non-invasive eDNA sampling can complement or enhance conventional approaches, as it can be a highly sensitive, rapid, and cost-effective tool for biodiversity monitoring. -Creating unified eDNA data best practices and developing DNA reference libraries will ensure eDNA detection methods are applied consistently to accurately inform conservation and wildlife management.

Report↗
USGS2020

Characterization of the genetic structure of four sucker species in the Klamath River. Final Report

Four species of suckers (family Catostomidae) inhabit the Klamath River Basin of Oregon and California: Lost River suckers (LRS; Deltistes luxatus), shortnose suckers (SNS; Chasmistes brevirostris), Klamath largescale suckers (KLS; Catostomus snyderi), and Klamath smallscale suckers (KSS; Catostomus rimiculus). All but Klamath smallscale suckers are endemic and restricted to the Klamath River Basin where they occur sympatrically in large lakes and reservoirs, including the Lost River and Klamath Lake subbasins (Figure 1; USFWS 2012). Population declines, primarily due to loss or degradation of spawning, rearing, and adult habitat, have resulted in Lost River and shortnose suckers being listed as endangered throughout their entire range under the U.S. Endangered Species Act (USFWS 1988). Continued population declines coupled with failed adult recruitment prompted the USFWS to initiate an assisted rearing program in 2015 as a part of their recovery strategy (Childress et al. 2019). The program was designed to maintain as much genetic diversity as possible while improving recruitment by averting high early life stage mortality (Day et al. 2017). However, while assisted rearing efforts are targeted towards endangered LRS and SNS, species differentiation of larval and juvenile suckers is problematic in the Klamath River Basin. This, in turn, complicates the management of these species as well as the population modeling used to evaluate recovery efforts. Maintaining as much as possible of the genetic resources, or “evolutionary legacy” of a species is a goal common to conservation and endangered species recovery strategies. Inappropriate assumptions regarding species’ evolutionary lineages, and genetic characteristics may lead to the mismanagement of an endangered species through a failure to recognize and appropriately manage species boundaries and genetic population structure. Despite a considerable amount of research, the partitioning of genetic diversity within and among the four species of suckers in the Klamath River Basin remains unclear. Previously developed genetic markers are effective at differentiating some species, but fail to effectively differentiate all four species of suckers in the basin (Tranah et al. 2001; Wagman 2003; Tranah and May 2006; Hoy and Ostberg 2015; Dowling et al. 2016). Peer-reviewed publications describing the morphological characteristics of (Markle et al. 2005) and genetic relationships among (Dowling et al. 2016; Tranah and May 2006) Klamath River Basin suckers have not resolved uncertainties regarding the systematic relationships among the four currently recognized taxa. Specifically, genetic and morphological data generally support LRS and KSS as being distinct entities, but genetic evidence does not support a distinction between KLS and SNS. All three publications above refer to unpublished information regarding ecological differences between KLS and SNS as evidence to support the existence of two entities. However, the authors also acknowledge that overlap in morphological characters (Markle et al. 2005) and a lack of genetic differentiation (Dowling et al. 2016; Tranah and May 2006) between KLS and SNS raises the question of their specific identity. This is particularly problematic in the Lost River subbasin, where overlap in morphological characters between KLS and SNS is greatest. In our opinion, the basis of the strong genetic similarity between KLS and SNS has not been resolved. Morphological characters mostly support the existence of two distinct species, while genetic characters do not (i.e., genetic divergence between KLS and SNS is less than divergence among populations of each species; (Smith et al. 2015). Some have suggested that introgressive hybridization may have resulted in a lack of genetic differentiation between KLS and SNS and a breakdown of monophyletic species (Dowling et al. 2016; Tranah and May 2006), and that this hybridization may be an important process in

California, Oregon↗
USGS2005

Population genetics of Gunnison sage-grouse: Implications for management

The newly described Gunnison sage-grouse ( Centrocercus minimus ) is a species of concern for management because of marked declines in distribution and abundance due to the loss and fragmentation of sagebrush habitat. This has caused remaining populations to be unusually small and isolated. We utilized mitochondrial DNA sequence data and data from 8 nuclear microsatellites to assess the extent of population subdivision among Gunnison sage-grouse populations in southwestern Colorado and southeastern Utah, USA. We found a high degree of population structure and low amounts of gene flow among all pairs of populations except the geographically adjacent Gunnison and Curecanti populations. Population structure for Gunnison sage-grouse was significantly higher than has been reported for greater sage-grouse ( C. urophasianus ). Further, we documented low levels of genetic diversity in some populations (particularly Dove Creek/Monticello and Piñon Mesa with an average of only 3.00 and 2.13 alleles per locus respectively) indicating that translocations from larger, more genetically diverse populations may be warranted. Bayesian analysis identified 3 potential migrants (involving San Miguel, Dove Creek/Monticello, Crawford, and Curecanti). Further, this analysis showed that 4 individuals from Cerro/Cimarron were more closely related to birds from San Miguel than to its geographically closer neighbors Gunnison and Curecanti. This suggests the Cerro/Cimarron area may act as a stepping stone for gene flow between San Miguel and Gunnison and that habitat restoration and protection in areas between these 2 basins should be a priority in an attempt to facilitate natural movement among these populations. Conservation plans should include monitoring and maintaining genetic diversity, preventing future habitat loss and fragmentation, enhancing existing habitat, and restoring converted sagebrush communities.

Journal of Wildlife Management↗
USGS2014

Identification of evolutionary hotspots based on genetic data from multiple terrestrial and aquatic taxa and gap analysis of hotspots in protected lands encompassed by the South Atlantic Landscape Conservation Cooperative.

The southeastern United States is a recognized hotspot of biodiversity for a variety of aquatic taxa, including fish, amphibians, and mollusks. Unfortunately, the great diversity of the area is accompanied by a large proportion of species at risk of extinction . Gap analysis was employed to assess the representation of evolutionary hotspots in protected lands w h ere an evolutionary hotspot was defined as an area with high evolutionary potential and measured by atypical patterns of genetic divergence, genetic diversity, and to a lesser extent genetic similarity across multiple terrestrial or aquatic taxa. A survey of the primary literature produced 16 terrestrial and 14 aquatic genetic datasets for estimation of genetic divergence and diversity. Relative genetic diversity and divergence values for each terrestrial and aquatic dataset were used for interpolation of multispecies genetic surfaces and subsequent visualization using ArcGIS. The multispecies surfaces interpolated from relative divergences and diversity data identified numerous evolutionary hotspots for both terrestrial and aquatic taxa , many of which were afforded some current protection. For instance, 14% of the cells identified as hotspots of aquatic diversity were encompassed by currently protected areas. Additionally, 25% of the highest 1% of terrestrial diversity cells were afforded some level of protection. In contrast, areas of high and low divergence among species, and areas of high variance in diversity were poorly represented in the protected lands. Of particular interest were two areas that were consistently identified by several different measures as important from a conservation perspective. These included an area encompassing the panhandle of Florida and southern Georgia near the Apalachicola National Forest (displaying varying levels of genetic divergence and greater than average levels of genetic diversity) and a large portion of the coastal regions of North and South Carolina (displaying low genetic divergence and greater than average levels of genetic diversity) . Our results show the utility o f genetic data sets for identifying cross - species patterns of genetic diversity and divergence (i.e., evolutionary hotspots) in aquatic and terrestrial environments for use in conservation design and delivery across the southeastern United States.

Alabama, Florida, Georgia, North Carolina, South C↗
USGS2015

Generic reclassification and species boundaries in the rediscovered freshwater mussel ‘Quadrula’ mitchelli (Simpson in Dall, 1896)

The Central Texas endemic freshwater mussel, Quadrula mitchelli (Simpson in Dall, 1896), had been presumed extinct until relict populations were recently rediscovered. To help guide ongoing and future conservation efforts focused on Q . mitchelli we set out to resolve several uncertainties regarding its evolutionary history, specifically its unknown generic position and untested species boundaries. We designed a molecular matrix consisting of two loci ( cytochrome c oxidase subunit I and internal transcribed spacer I ) and 57 terminal taxa to test the generic position of Q . mitchelli using Bayesian inference and maximum likelihood phylogenetic reconstruction. We also employed two Bayesian species validation methods to test five a priori species models (i.e. hypotheses of species delimitation). Our study is the first to test the generic position of Q. mitchelli and we found robust support for its inclusion in the genus Fusconaia. Accordingly, we introduce the binomial, Fusconaia mitchelli comb. nov., to accurately represent the systematic position of the species. We resolved F. mitchelli individuals in two well supported and divergent clades that were generally distinguished as distinct species using Bayesian species validation methods, although alternative hypotheses of species delineation were also supported. Despite strong evidence of genetic isolation within F. mitchelli , we do not advocate for species-level status of the two clades as they are allopatrically distributed and no morphological, behavioral, or ecological characters are known to distinguish them. These results are discussed in the context of the systematics, distribution, and conservation of F. mitchelli .

Conservation Genetics↗
USGS2018

Integrative taxonomy resolves taxonomic uncertainty for freshwater mussels being considered for protection under the U.S. Endangered Species Act

Objectively delimiting species boundaries remains an important challenge in systematics and becomes urgent when unresolved taxonomy complicates conservation and recovery efforts. We examined species boundaries in the imperiled freshwater mussel genus Cyclonaias (Bivalvia: Unionidae) using morphometrics, molecular phylogenetics, and multispecies coalescent models to help guide pending conservation assessments and legislative decisions. Congruence across multiple lines of evidence indicated that current taxonomy overestimates diversity in the C. pustulosa species complex. The only genetically and morphologically diagnosable species in the C. pustulosa species complex were C. pustulosa and C. succissa and we consider C. aurea , C. houstonensis, C. mortoni , and C. refulgens to be synonyms of C. pustulosa . In contrast, all three species in the C. nodulata complex ( C. necki , C. nodulata , and C. petrina ) were genetically, geographically, and morphologically diagnosable. Our findings have important conservation and management implications, as three nominal species ( C. aurea , C. houstonensis , and C. petrina ) are being considered for protection under the Endangered Species Act.

Scientific Reports↗
USGS2021

Genetic and morphological characterization of the freshwater mussel clubshell species complex (Pleurobema clava and Pleurobema oviforme) to inform conservation planning

The shell morphologies of the freshwater mussel species Pleurobema clava (federally endangered) and Pleurobema oviforme (species of concern) are similar, causing considerable taxonomic confusion between the two species over the last 100 years. While P. clava was historically widespread throughout the Ohio River basin and tributaries to the lower Laurentian Great Lakes, P. oviforme was confined to the Tennessee and the upper Cumberland River basins. We used two mitochondrial DNA (mtDNA) genes, 13 novel nuclear DNA microsatellite markers, and shell morphometrics to help resolve this taxonomic confusion. Evidence for a single species was apparent in phylogenetic analyses of each mtDNA gene, revealing monophyletic relationships with minimal differentiation and shared haplotypes. Analyses of microsatellites showed significant genetic structuring, with four main genetic clusters detected, respectively, in the upper Ohio River basin, the lower Ohio River and Great Lakes, and upper Tennessee River basin, and a fourth genetic cluster, which included geographically intermediate populations in the Ohio and Tennessee river basins. While principal components analysis (PCA) of morphometric variables (i.e., length, height, width, and weight) showed significant differences in shell shape, only 3% of the variance in shell shape was explained by nominal species. Using Linear Discriminant and Random Forest (RF) analyses, correct classification rates for the two species' shell forms were 65.5% and 83.2%, respectively. Random Forest classification rates for some populations were higher; for example, for North Fork Holston (HOLS), it was >90%. While nuclear DNA and shell morphology indicate that the HOLS population is strongly differentiated, perhaps indicative of cryptic biodiversity, we consider the presence of a single widespread species the most likely biological scenario for many of the investigated populations based on our mtDNA dataset. However, additional sampling of P. oviforme populations at nuclear loci is needed to corroborate this finding.

Indiana, Kentucky, Ohio, Pennsylvania, Tennessee, ↗
USGS2022

Gene pool boundaries for the Yosemite toad (Anaxyrus canorus) reveal asymmetrical migration within meadow neighborhoods

The Yosemite toad ( Anaxyrus [ Bufo ] canorus ) is a federally threatened species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. The species is one of the first amphibians to undergo a large demographic collapse that was well-documented, and is reputed to remain in low abundance throughout its range. Recent phylogeographic work has demonstrated that Pleistocene toad lineages diverged and then admixed to differing extents across an elevational gradient. Although lineage divisions may have significant effects on evolutionary trajectories over large spatial and temporal scales, present-day population dynamics must be delineated in order to manage and conserve the species effectively. In this study, we used a double-digest RADseq dataset to address three primary questions: (1) Are single meadows or neighborhoods of nearby meadows most correlated with population boundaries? (2) Does asymmetrical migration occur among neighborhoods of nearby meadows? (3) What topographic or hydrological variables predict such asymmetrical migration in these meadow neighborhoods? Hierarchical STRUCTURE and AMOVA analyses suggested that populations are typically circumscribed by a single meadow, although 84% of meadows exist in neighborhoods of at least two meadows connected by low levels of migration, and over half (53%) of neighborhoods examined display strong asymmetrical migration. Meadow neighborhoods often contain one or more large and flat “hub” meadows that experience net immigration, surrounded by smaller and topographically rugged “satellite” meadows with net emigration. Hubs tend to contain more genetic diversity and could be prioritized for conservation and habitat management and as potential sources for reestablishment efforts.

California↗
USGS2018

Use of non-invasive genetics to generate core-area population estimates of a threatened predator in the Superior National Forest, USA

Canada lynx (Lynx canadensis) are found in boreal forests of Canada and Alaska and range southward into the contiguous United States. Much less is understood about lynx in their southern range compared to northern populations. Because lynx are currently listed as threatened under the US Endangered Species Act but have recently been recommended for delisting, information on their southern populations is important for lynx recovery, conservation, and management. We used non-invasive, genetic data collected during lynx snowtracking surveys from 2012-2017 to generate core-area estimates of abundance, trend and density in selected core areas of the Superior National Forest of Minnesota, USA. Lynx abundance estimates averaged 41.8 (SD=14.7, range=24-67) during 2012-2017 in the smaller core areas and averaged 52.3 (SD=8.3, range=43-59) during 2015-2017 in the larger core areas. We found no evidence for a decrease or increase in abundance during either period. Lynx density estimates were approximately 7-10 times lower than densities of lynx in northern populations at the low of the snowshoe hare (Lepus americanus) population cycle. To our knowledge, our results are the first attempt to estimate abundance, trend and density of lynx in Minnesota using non-invasive genetic capture-mark-recapture. Estimates such as ours provide useful benchmarks for future comparisons by providing a context with which to assess 1) potential changes in forest management that may affect lynx recovery and conservation, and 2) possible effects of climate change on the depth, density, and duration of annual snow cover and correspondingly, potential effects on snowshoe hares as well.

Minnesota↗
USGS2009

The needs of salmon and steelhead in balancing their conservation and use

Over the past 100 years, Pacific salmon Oncorhynchus spp. and steelhead trout O. mykiss populations in the Pacific Northwest have experienced dramatic declines as a result of human population growth and associated development of the region's natural resources. Any strategy to reverse those declines will depend on achieving consensus among a diverse group of stakeholders willing to (1) restore damaged habitats and watersheds; (2) consider the biological needs of salmonid fishes; and (3) understand, conserve, and manage existing levels of biodiversity within an ecosystem context. The objective of this chapter is to review and summarize the needs of Pacific salmon and steelhead trout from perspectives that promote their sustainability and perpetuity, and, within that context, provide a framework, for the development of a sustainable fisheries strategy. Although volumes of information are available on the life histories and habitat requirements of Pacific salmonids, new concepts have begun to address the importance of habitat complexity, genetic diversity among locally adapted populations, and the need for appropriate units of conservation. Habitat variability and complexity are the templates that produce diverse, locally adapted populations of Pacific salmon and steelhead trout. Molded by conditions in the environments they colonized, salmon and steelhead have unique adaptations they may have taken hundred i?? perhaps thousands i?? of years to evolve. Any strategy to reverse the declines of salmon and steelhead must focus on conserving both current levels of genetic diversity as well as restoration and maintenance of habitats compatible with the specific needs of individual populations. An argument can be made that we know enough already about the needs of our salmon and steelhead to allow us to make appropriate decisions. There is strong need to integrate what we know about local salmonid adaptations and habitat needs with conservation and management strategies that address the problems we have created. It may be possible to have healthy, sustainable salmonid populations coastwide if we do not wait too long to make up our minds.

Book chapter↗
USGS2023

Data mining reveals tissue-specific expression and host lineage-associated forms of Apis mellifera filamentous virus

Apis mellifera filamentous virus (AmFV) is a large double-stranded DNA virus of uncertain phylogenetic position that infects honey bees ( Apis mellifera ). Little is known about AmFV evolution or molecular aspects of infection. Accurate annotation of open-reading frames (ORFs) is challenged by weak homology to other known viruses. This study was undertaken to evaluate ORFs (including coding-frame conservation, codon bias, and purifying selection), quantify genetic variation within AmFV, identify host characteristics that covary with infection rate, and examine viral expression patterns in different tissues.

PeerJ↗