Search USGS⌕ Search

SEARCH · Search USGS

Results for “Diversity”

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

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

At least 1,351 records · Page 75Linked to original sources
USGS2016

Impacts of the Deepwater Horizon oil spill on deep-sea coral-associated sediment communities

Cold-water corals support distinct populations of infauna within surrounding sediments that provide vital ecosystem functions and services in the deep sea. Yet due to their sedentary existence, infauna are vulnerable to perturbation and contaminant exposure because they are unable to escape disturbance events. While multiple deep-sea coral habitats were injured by the 2010 Deepwater Horizon (DWH) oil spill, the extent of adverse effects on coral-associated sediment communities is unknown. In 2011, sediments were collected adjacent to several coral habitats located 6 to 183 km from the wellhead in order to quantify the extent of impact of the DWH spill on infaunal communities. Higher variance in macrofaunal abundance and diversity, and different community structure (higher multivariate dispersion) were associated with elevated hydrocarbon concentrations and contaminants at sites closest to the wellhead (MC294, MC297, and MC344), consistent with impacts from the spill. In contrast, variance in meiofaunal diversity was not significantly related to distance from the wellhead and no other community metric (e.g. density or multivariate dispersion) was correlated with contaminants or hydrocarbon concentrations. Concentrations of polycyclic aromatic hydrocarbons (PAH) provided the best statistical explanation for observed macrofaunal community structure, while depth and presence of fine-grained mud best explained meiofaunal community patterns. Impacts associated with contaminants from the DWH spill resulted in a patchwork pattern of infaunal community composition, diversity, and abundance, highlighting the role of variability as an indicator of disturbance. These data represent a useful baseline for tracking post-spill recovery of these deep-sea communities.

Marine Ecology Progress Series↗
USGS2017

Food-web dynamics and isotopic niches in deep-sea communities residing in a submarine canyon and on the adjacent open slopes

Examination of food webs and trophic niches provide insights into organisms' functional ecology, yet few studies have examined trophodynamics within submarine canyons, where the interaction of canyon morphology and oceanography influences habitat provision and food deposition. Using stable isotope analysis and Bayesian ellipses, we documented deep-sea food-web structure and trophic niches in Baltimore Canyon and the adjacent open slopes in the US Mid-Atlantic Region. Results revealed isotopically diverse feeding groups, comprising approximately 5 trophic levels. Regression analysis indicated that consumer isotope data are structured by habitat (canyon vs. slope), feeding group, and depth. Benthic feeders were enriched in 13 C and 15 N relative to suspension feeders, consistent with consuming older, more refractory organic matter. In contrast, canyon suspension feeders had the largest and more distinct isotopic niche, indicating they consume an isotopically discrete food source, possibly fresher organic material. The wider isotopic niche observed for canyon consumers indicated the presence of feeding specialists and generalists. High dispersion in δ 13 C values for canyon consumers suggests that the isotopic composition of particulate organic matter changes, which is linked to depositional dynamics, resulting in discrete zones of organic matter accumulation or resuspension. Heterogeneity in habitat and food availability likely enhances trophic diversity in canyons. Given their abundance in the world's oceans, our results from Baltimore Canyon suggest that submarine canyons may represent important havens for trophic diversity.

Baltimore Canyon↗
USGS2009

Evaluating wildlife response to coastal dune habitat restoration in san francisco, california

The vast dune system that once dominated the entire western half of the San Francisco peninsula in California has been reduced to a few fragments that conserve locally threatened plant and animal species. We measured the effects of ongoing restoration efforts on wildlife abundance and diversity on one of the largest of these fragments, Fort Funston in the Golden Gate National Recreation Area. Efforts included removal of non-native species, active restoration of native dune vegetation, and restricted visitor use. We collected data regarding the composition and abundance of vegetation, birds, and ground-dwelling vertebrates on four treatments including an actively restored area with restricted visitor use, an unrestored area where visitor use had been restricted for ten years, an unrestored area where visitor use had been restricted for two years, and an unrestored area with unrestricted visitor use. Results indicated that the diversity and abundance of wildlife species, as well as the richness and cover of native plant species, were greater in the restored area than in all other sampled areas. Restricted visitor use alone had only modest positive effects on the abundance and diversity of wildlife and the richness and cover of native plant species.

Ecological Restoration↗
USGS2009

Promoting species establishment in a phragmites-dominated great lakes coastal wetland

This study examined efforts to promote species establishment and maintain diversity in a Phragmites-dominated wetland where primary control measures were underway. A treatment experiment was performed at Crane Creek, a drowned-river-mouth wetland in Ottawa National Wildlife Refuge along the shore of western Lake Erie. Following initial aerial spraying of Phragmites with glyphosate, this study tested combinations of cutting, raking, and additional hand spraying of Phragmites with glyphosate as methods to promote growth of other wetland species and increase plant diversity. Percent-cover vegetation data were collected in permanent plots before and after treatments, and follow-up sampling was performed the following year. Increased species richness, species emergence, and relative dominance of non-Phragmites taxa were used as measures of treatment success. We also examined treatment effects on Phragmites cover. Dimensionality of seedbank and soil properties was reduced using principal component analysis. With the exception of nitrogen, soil nutrients affected species establishment, non-Phragmites taxa dominance, and Phragmites cover. A more viable seedbank led to greater species emergence. Treatments had differential effects on diversity depending on elevation and resulting degree of hydrologic inundation. Whereas raking to remove dead Phragmites biomass was central to promoting species establishment in dry areas, spraying had a greater impact in continually inundated areas. For treatment success across elevations into the year following treatments, spraying in combination with cutting and raking had the greatest effect. The results of this study suggest that secondary treatments can produce a short-term benefit to the plant community in areas treated for Phragmites.

Natural Areas Journal↗
USGS2025

Tracing invasion routes of Cuban treefrogs into Louisiana using mitochondrial DNA

Understanding the origin and spread of invasive species is critical for predicting when and where new introductions will establish, and impact native species. However, due to the complexity of contributing factors such as multiple introductions, dispersal method, genetic admixture in founding populations, and variable propagule pressure, genetic patterns observed in invasive species may not always conform to a single theoretical expectation. Cuban treefrogs ( Osteopilus septentrionalis ) are invasive in peninsular Florida and sporadically in the Florida panhandle. Though O. septentrionalis has been occasionally reported in Louisiana since the 1990s, established populations were not present until the discovery of a breeding population in New Orleans in 2017. In this study we investigated the source of this novel population using existing and newly generated cytochrome B (cyt-b) mitochondrial gene sequences from the native and invasive range of O. septentrionalis . We recovered a total of 14 cyt-b haplotypes, nine novel and five previously published. Within the 95 Louisiana invasion samples, we recovered seven haplotypes including five novel haplotypes. The haplotypes most common in Louisiana were shared exclusively with west and east Florida localities in central Florida, indicating a possible source population. The presence of haplotypes private to the Louisiana locality suggests other unsampled localities may also be contributing to the Louisiana settlement. Metrics of genetic diversity across native and invasive localities did not significantly differ. Furthermore, the Louisiana samples had higher genetic diversity than any single location sampled within Florida. Thus, genetic diversity and our haplotype connectivity suggest the Louisiana population is derived from multiple introductions from Florida. Our study highlights how demographic and genetic analyses can be utilized to understand the source and future expansion potential of invasive populations.

Florida, Louisiana↗
USGS2026

Seasonal and hydrologic variation influences habitat and functional structure of stream fish assemblages

Introduction: Hydrologic variability is a key driver of ecological structure in lotic systems, shaping habitat conditions, taxonomic diversity, and the functional traits that mediate species’ persistence and performance (e.g., reproductive success). While many studies examine taxonomic responses to variation in flows, few evaluate how spatiotemporal hydrologic variation influences the functional organization within stream fish communities. Methods: We quantified seasonal habitat structure and functional trait diversity of fish assemblages across six Ozark Plateau headwater streams representing two contrasting flow regimes: Groundwater Flashy and Runoff/Intermittent Flashy. Fish and habitat data were collected seasonally during a dry year (2002) and a wet year (2003). Functional space was constructed using PCoA of morphological, ecological, and life-history traits, and functional diversity was measured using community weighted means (CWMs), functional richness (FRic), functional evenness (FEve), and functional divergence (FDiv). Results: We found that habitat structure differed strongly by flow regime and season, with Runoff/Intermittent streams exhibiting pronounced reductions in depth, area, and velocity, while groundwater streams remained structurally stable. Functional identity of assemblages was similar across flow regimes, dominated by benthic, hydrodynamic taxa with opportunistic and periodic life-history strategies. However, functional structure differed significantly: FEve and FDiv were consistently lower in Runoff/Intermittent Flashy streams in both years, indicating assemblage dominance of species with similar trait combinations and reduced trait partitioning under variable flow. FRic and taxonomic richness remained stable across seasons and flow regimes, suggesting high functional redundancy despite species turnover. Discussion: Together, results show that flow regime mediates both habitat structural stability and functional organization. As climatic warming and extreme drought increase hydrologic instability in headwaters, functional trait approaches provide a sensitive tool for detecting losses of functional roles that may not be evident by using taxonomic metrics alone.

Arkansas, Kansas, Missouri, Oklahoma↗
USGS2019

Global observational needs and resources for marine biodiversity

The diversity of life in the sea is critical to the health of ocean ecosystems that support living resources and therefore essential to the economic, nutritional, recreational, and health needs of billions of people. Yet there is evidence that the biodiversity of many marine habitats is being altered in response to a changing climate and human activity. Understanding this change, and forecasting where changes are likely to occur, requires monitoring of organism diversity, distribution, abundance, and health. It requires a minimum of measurements including productivity and ecosystem function, species composition, allelic diversity, and genetic expression. These observations need to be complemented with metrics of environmental change and socio-economic drivers. However, existing global ocean observing infrastructure and programs often do not explicitly consider observations of marine biodiversity and associated processes. Much effort has focused on physical, chemical and some biogeochemical measurements. Broad partnerships, shared approaches, and best practices are now being organized to implement an integrated observing system that serves information to resource managers and decision-makers, scientists and educators, from local to global scales. This integrated observing system of ocean life is now possible due to recent developments among satellite, airborne, and in situ sensors in conjunction with increases in information system capability and capacity, along with an improved understanding of marine processes represented in new physical, biogeochemical, and biological models.

Frontiers in Marine Science↗
USGS2021

Genetic connectivity of the West Indian manatee in the southern range and limited evidence of hybridization with Amazonian manatees

The Antillean subspecies of the West Indian manatee is classified as endangered by the International Union for the Conservation of Nature (IUCN) Red List. In Brazil, the manatee population is listed as endangered with an estimated population size of 500–1,000. Historic hunting, recent habitat degradation, and fisheries bycatch have decreased the population size. The Amazonian manatee is listed as vulnerable by the IUCN with unknown population sizes within Brazil. The Antillean manatee occurs in sympatry with the Amazonian manatee in Brazil and hybridization has been previously indicated. To provide information on the genetic structure, diversity, and degree of hybridization in the sympatric zone near the Amazon River mouth, the mitochondrial DNA control region and 13 nuclear microsatellite markers were assessed on the two species. Samples were analyzed from the Antillean subspecies across its distribution in Brazil ( n = 78) and from the Amazonian species ( n = 17) at the Amazon River mouth and inland mainstem river. To assess the previously defined evolutionary significant units of Antillean manatees in the area, an additional 11 samples from Venezuela and Guyana were included. The Antillean manatee was found to be a single population in Brazil and had lower than average number of alleles (3.00), expected heterozygosity (0.34), and haplotype diversity (0.15) when compared to many other manatee populations. The low values may be influenced by the small population size and extended pressures from anthropogenic threats. Gene flow was identified with Venezuela/Guyana in admixed Antillean Brazil samples, although the two populations were found to be moderately divergent. The nuclear loci in Venezuela/Guyana Antillean manatee samples indicated high differentiation from the samples collected in the Amazon River ( F ST = 0.35 and R ST = 0.18, p = 0.0001). No indication of nuclear hybridization was found except for a single sample, “Poque” that had been identified previously. The distribution of Antillean manatees in Brazil is extensive and the areas with unique habitat and threats would benefit from independent management and conservation actions. Gene flow, resulting in genetic diversity and long-term population stability, could be improved in the southern range through habitat restoration, and the establishments of travel corridors and protected areas, which are particularly important for successful parturition and neonatal calf survival.

Frontiers in Marine Science↗
USGS2016

Municipal solid waste landfills harbor distinct microbiomes

Landfills are the final repository for most of the discarded material from human society and its “built environments.” Microorganisms subsequently degrade this discarded material in the landfill, releasing gases (largely CH 4 and CO 2 ) and a complex mixture of soluble chemical compounds in leachate. Characterization of “landfill microbiomes” and their comparison across several landfills should allow the identification of environmental or operational properties that influence the composition of these microbiomes and potentially their biodegradation capabilities. To this end, the composition of landfill microbiomes was characterized as part of an ongoing USGS national survey studying the chemical composition of leachates from 19 non-hazardous landfills across 16 states in the continental U.S. The landfills varied in parameters such as size, waste composition, management strategy, geography, and climate zone. The diversity and composition of bacterial and archaeal populations in leachate samples were characterized by 16S rRNA gene sequence analysis, and compared against a variety of physical and chemical parameters in an attempt to identify their impact on selection. Members of the Epsilonproteobacteria, Gammaproteobacteria, Clostridia, and candidate division OP3 were the most abundant. The distribution of the observed phylogenetic diversity could best be explained by a combination of variables and was correlated most strongly with the concentrations of chloride and barium, rate of evapotranspiration, age of waste, and the number of detected household chemicals. This study illustrates how leachate microbiomes are distinct from those of other natural or built environments, and sheds light on the major selective forces responsible for this microbial diversity.

Frontiers in Microbiology↗
USGS2024

Genotypic clustering of H5N1 avian Influenza viruses in North America evaluated by ordination analysis

The introduction of HPAI H5N1 clade 2.3.4.4b viruses to North America in late 2021 resulted in avian influenza outbreaks in poultry, mortality events in many wild bird species, and spillover into many mammalian species. Reassortment events with North American low pathogenic virus were identified as early as February 2022 and over 100 genotypes have been characterized. Such diversity increases the complexity and time required for monitoring virus evolution. Here, we performed ordination and clustering analyses on sequence data from H5N1 viruses identified in North America between January 2020 to December 2023 to visualize virus genotypic diversity in poultry and wildlife populations. Our results reveal that ordination and cluster-based approaches can complement traditional phylogenetic analyses specifically for the preliminary assignment of H5N1 viruses to genotypic groups or to identify novel genotypes. Our study expands current knowledge on genotype diversity of H5N1 viruses in North America and describes a rapid approach for early virus genotype assignment.

Viruses↗
USGS2017

A culture-based survey of fungi in soil from bat hibernacula in the eastern United States and its implications for detection of Geomyces destructans, the causal agent of bat white-nose syndrome

The recent emergence of white-nose syndrome (WNS), a fungal disease causing unprecedented mortality among hibernating bats of eastern North America, has revealed a knowledge gap regarding fungal communities associated with bats and their hibernacula. We used culture-based techniques to investigate the diversity of fungi in soil samples collected from 24 bat hibernacula in the eastern United States. Ribosomal RNA regions (internal transcribed spacer and partial intergenic spacer) were sequenced to preliminarily characterize isolates. Geomyces species were one of the most abundant and diverse groups cultured, representing approximately 33% of all isolates. Geomyces destructans was isolated from soil samples from three hibernacula in states where WNS is known to occur, and many of the other cultured Geomyces isolates likely represent undescribed taxa. Further characterization of the diversity of fungi that occur in hibernacula will both facilitate an improved understanding of the ecology of G. destructans within this complex fungal community and provide an opportunity to identify characteristics that differentiate G. destructans from non-pathogenic relatives.

Mycologia↗
USGS2017

Differences in breeding bird assemblages related to reed canary grass cover cover and forest structure on the Upper Mississippi River

Floodplain forest of the Upper Mississippi River provides habitat for an abundant and diverse breeding bird community. However, reed canary grass Phalaris arundinacea invasion is a serious threat to the future condition of this forest. Reed canary grass is a well-known aggressive invader of wetland systems in the northern tier states of the conterminous United States. Aided by altered flow regimes and nutrient inputs from agriculture, reed canary grass has formed dense stands in canopy gaps and forest edges, retarding tree regeneration. We sampled vegetation and breeding birds in Upper Mississippi River floodplain forest edge and interior areas to 1) measure reed canary grass cover and 2) evaluate whether the breeding bird assemblage responded to differences in reed canary grass cover. Reed canary grass was found far into forest interiors, and its cover was similar between interior and edge sites. Bird assemblages differed between areas with more or less reed canary grass cover (.53% cover breakpoint). Common yellowthroat Geothlypis trichas , black-capped chickadee Parus atricapillus , and rose-breasted grosbeak Pheucticus ludovicianus were more common and American redstart Setophaga ruticilla , great crested flycatcher Myiarchus crinitus , and Baltimore oriole Icterus galbula were less common in sites with more reed canary grass cover. Bird diversity and abundance were similar between sites with different reed canary grass cover. A stronger divergence in bird assemblages was associated with ground cover ,15%, resulting from prolonged spring flooding. These sites hosted more prothonotary warbler Protonotaria citrea , but they had reduced bird abundance and diversity compared to other sites. Our results indicate that frequently flooded sites may be important for prothonotary warblers and that bird assemblages shift in response to reed canary grass invasion.

Upper Mississippi River↗
USGS2016

Fire effects on wildlife in Central Hardwoods and Appalachian regions

Fire is being prescribed and used increasingly to promote ecosystem restoration (e.g., oak woodlands and savannas) and to manage wildlife habitat in the Central Hardwoods and Appalachian regions, USA. However, questions persist as to how fire affects hardwood forest communities and associated wildlife, and how fire should be used to achieve management goals. We provide an up-to-date review of fire effects on various wildlife species and their habitat in the Central Hardwoods and Appalachians. Documented direct effects (i.e., mortality) on wildlife are rare. Indirect effects (i.e., changes in habitat quality) are influenced greatly by light availability, fire frequency, and fire intensity. Unless fire intensity is great enough to kill a portion of the overstory, burning in closed-canopy forests has provided little benefit for most wildlife species in the region because it doesn’t result in enough sunlight penetration to elicit understory response. Canopy reduction through silvicultural treatment has enabled managers to use fire more effectively. Fire intensity must be kept low in hardwoods to limit damage to many species of overstory trees. However, wounding or killing trees with fire benefits many wildlife species by allowing increased sunlight to stimulate understory response, snag and subsequent cavity creation, and additions of large coarse woody debris. In general, a fire-return interval of 2 yr to 7 yr benefits a wide variety of wildlife species by providing a diverse structure in the understory; increasing browse, forage, and soft mast; and creating snags and cavities. Historically, dormant-season fire was most prevalent in these regions, and it still is when most prescribed fire is implemented in hardwood systems as burn-days are relatively few in the growing season of May through August because of shading from leaf cover and high fuel moisture. Late growing-season burning increases the window for burning, and better control on woody composition is possible. Early growing-season fire may pose increased risk for some species, especially herpetofauna recently emerged from winter hibernacula (April) or forest songbirds that nest in the understory (May to June). However, negative population-level effects are unlikely unless the burned area is relatively large and early growing-season fire is used continually. We did not find evidence that fire is leading to population declines for any species, including Endangered Species Act (ESA)-listed species (e.g., Indiana bat [ Myotis sodalis Mill. Allen] or northern long-eared bat [ M. septentrionalis Trouess.]). Instead, data indicate that fire can enhance habitat for bats by increasing suitability of foraging and day-roost sites. Similarly, concern over burning and displacement of woodland salamanders (Plethodontidae), another taxa of heightened conservation concern, is alleviated when fire is prescribed along ecologically appropriate aspect and slope gradients and not forced into mesic, high site index environments where salamanders are most common. Because topography across the Central Hardwoods and Appalachians is diverse, we contend that applying fire on positions best suited for burning is an effective approach to increase regional landscape heterogeneity and biological diversity. Herein, we offer prescriptive concepts for burning for various wildlife species and guilds in the Central Hardwoods and Appalachians.

Appalachian region, Central Hardwoods region↗
USGS2017

Impacts of mastication fuel treatments on California, USA, chaparral vegetation structure and composition

Mechanical fuel treatments are a primary pre-fire strategy for potentially mitigating the threat of wildland fire, yet there is limited information on how they impact shrubland ecosystems. Our goal was to assess the impact of mechanical mastication fuel treatments on chaparral vegetation and to determine the extent to which they emulate early post-fire succession. Mastication treatments significantly reduced the height and cover of woody vegetation and increased herbaceous cover and diversity. Non-native cover, density, and diversity were also significantly higher in masticated treatments. Comparisons with post-fire data from two studies showed that certain ephemeral post-fire endemics were absent or of limited occurrence from masticated plots in comparison to their abundance on adjacent burned plots. Structurally, masticated sites differed in the dense woody debris cover, whereas burned sites had little such ground cover. Regional comparison of masticated plots to previously published post-fire studies found that burned sites had greater cover, density, and diversity of native species. However, masticated sites and burned sites were broadly similar in distribution of different growth forms. Results from our study show that the use of mastication fuel treatments in chaparral are not in alignment with some resource conservation goals, but in some cases it is recognized that such sacrifice of natural resources may be an acceptable tradeoff to potentially mitigating fire hazard.

California↗
USGS2015

Collaborative decision-analytic framework to maximize resilience of tidal marshes to climate change

Decision makers that are responsible for stewardship of natural resources face many challenges, which are complicated by uncertainty about impacts from climate change, expanding human development, and intensifying land uses. A systematic process for evaluating the social and ecological risks, trade-offs, and cobenefits associated with future changes is critical to maximize resilience and conserve ecosystem services. This is particularly true in coastal areas where human populations and landscape conversion are increasing, and where intensifying storms and sea-level rise pose unprecedented threats to coastal ecosystems. We applied collaborative decision analysis with a diverse team of stakeholders who preserve, manage, or restore tidal marshes across the San Francisco Bay estuary, California, USA, as a case study. Specifically, we followed a structured decision-making approach, and we using expert judgment developed alternative management strategies to increase the capacity and adaptability to manage tidal marsh resilience while considering uncertainties through 2050. Because sea-level rise projections are relatively confident to 2050, we focused on uncertainties regarding intensity and frequency of storms and funding. Elicitation methods allowed us to make predictions in the absence of fully compatible models and to assess short- and long-term trade-offs. Specifically we addressed two questions. (1) Can collaborative decision analysis lead to consensus among a diverse set of decision makers responsible for environmental stewardship and faced with uncertainties about climate change, funding, and stakeholder values? (2) What is an optimal strategy for the conservation of tidal marshes, and what strategy is robust to the aforementioned uncertainties? We found that when taking this approach, consensus was reached among the stakeholders about the best management strategies to maintain tidal marsh integrity. A Bayesian decision network revealed that a strategy considering sea-level rise and storms explicitly in wetland restoration planning and designs was optimal, and it was robust to uncertainties about management effectiveness and budgets. We found that strategies that avoided explicitly accounting for future climate change had the lowest expected performance based on input from the team. Our decision-analytic framework is sufficiently general to offer an adaptable template, which can be modified for use in other areas that include a diverse and engaged stakeholder group.

California↗
USGS2025

Comparison of two benthic assemblage sampling gears for use on intertidal oyster reefs in Louisiana

Background Estuarine biodiversity plays a vital role in supporting ecosystem functions yet remains threatened by climate change and anthropogenic activity. Tracking and identifying estuarine biodiversity trends helps management ensure long-term provisions of human and environmental benefits by contributing to the estimation of habitat loss and the monitoring of restoration and conservation progress. However, the sampling gear and biodiversity metric used may indicate different conclusions, which can lead to uncertainty in the actual state of the ecosystem-level biodiversity. Sampling benthic biodiversity in complex estuarine habitats, such as oyster reefs, is particularly challenging because no one gear type captures entire target assemblages, and differences in gear efficiency on these complex habitats make comparisons across gear types challenging. Methods We investigated how estimates of oyster reef-associated benthic taxa abundance, richness, Pielou’s evenness, and Shannon-Wiener diversity differed across three Crassostrea virginica reefs in Louisiana between suction sampler and substrate tray sampling gears ( n = 6), and how gear influenced comparisons across reefs (3 reefs × 6 replicates × 2 gears). Results Abundance and richness were higher, and Pielou’s evenness was lower, in trays compared to suction samples at all reefs. Shannon-Wiener diversity was similar in suction samples and trays at two out of three reefs. Amphipod taxa were numerically dominant in trays, skewing the distribution of abundances and driving the reef assemblage differences between gears. Abundance and Shannon-Wiener diversity were similar across reefs within each gear. However, there were significant differences in richness across reefs in tray samples only, while evenness differed across reefs only in suction samples. Our results highlight that gear choices, along with biodiversity metrics tracked, can result in different conclusions in biodiversity trends, ultimately affecting conservation decisions and management.

Louisiana↗
USGS2019

Relative abundance and molecular evolution of Lake Sinai Virus (Sinaivirus) clades

Lake Sinai Viruses (Sinaivirus) are commonly detected in honey bees ( Apis mellifera ) but no disease phenotypes or fitness consequences have yet been demonstrated. This viral group is genetically diverse, lacks obvious geographic structure, and multiple lineages can co-infect individual bees. While phylogenetic analyses have been performed, the molecular evolution of LSV has not been studied extensively. Here, I use LSV isolates from GenBank as well as contigs assembled from honey bee Sequence Read Archive (SRA) accessions to better understand the evolutionary history of these viruses. For each ORF, substitution rate variation, codon usage, and tests of positive selection were evaluated. Outlier regions of high or low diversity were sought with sliding window analysis and the role of recombination in creating LSV diversity was explored. Phylogenetic analysis consistently identified two large clusters of sequences that correspond to the current LSV1 and LSV2 nomenclature, however lineages sister to LSV1 were the most frequently detected in honey bee SRA accessions. Different expression levels among ORFs suggested the occurrence of subgenomic transcripts. ORF1 and RNA-dependent RNA polymerase had higher evolutionary rates than the capsid and ORF4. A hypervariable region of the ORF1 protein-coding sequence was identified that had reduced selective constraint, but a site-based model of positive selection was not significantly more likely than a neutral model for any ORF. The only significant recombination signals detected between LSV1 and LSV2 initiated within this hypervariable region, but assumptions of the test (single-frame coding and independence of substitution rate by site) were violated. LSV codon usage differed strikingly from that of honey bees and other common honey-bee viruses, suggesting LSV is not strongly co-evolved with that host. LSV codon usage was significantly correlated with that of Varroa destructor , however, despite the relatively weak codon bias exhibited by the latter. While codon usage between the LSV1 and LSV2 clusters was similar for three ORFs, ORF4 codon usage was uncorrelated between these clades, implying rapid divergence of codon use for this ORF only. Phylogenetic placement and relative abundance of LSV isolates reconstructed from SRA accessions suggest that detection biases may be over-representing LSV1 and LSV2 in public databases relative to their sister lineages.

PeerJ↗
USGS2020

An updated genetic marker for detection of Lake Sinai Virus and metagenetic applications

Background Lake Sinai Viruses (LSV) are common RNA viruses of honey bees ( Apis mellifera ) that frequently reach high abundance but are not linked to overt disease. LSVs are genetically heterogeneous and collectively widespread, but despite frequent detection in surveys, the ecological and geographic factors structuring their distribution in A. mellifera are not understood. Even less is known about their distribution in other species. Better understanding of LSV prevalence and ecology have been hampered by high sequence diversity within the LSV clade. Methods Here we report a new polymerase chain reaction (PCR) assay that is compatible with currently known lineages with minimal primer degeneracy, producing an expected 365 bp amplicon suitable for end-point PCR and metagenetic sequencing. Using the Illumina MiSeq platform, we performed pilot metagenetic assessments of three sample sets, each representing a distinct variable that might structure LSV diversity (geography, tissue, and species). Results The first sample set in our pilot assessment compared cDNA pools from managed A. mellifera hives in California ( n = 8) and Maryland ( n = 6) that had previously been evaluated for LSV2, confirming that the primers co-amplify divergent lineages in real-world samples. The second sample set included cDNA pools derived from different tissues (thorax vs. abdomen, n = 24 paired samples), collected from managed A. mellifera hives in North Dakota. End-point detection of LSV frequently differed between the two tissue types; LSV metagenetic composition was similar in one pair of sequenced samples but divergent in a second pair. Overall, LSV1 and intermediate lineages were common in these samples whereas variants clustering with LSV2 were rare. The third sample set included cDNA from individual pollinator specimens collected from diverse landscapes in the vicinity of Lincoln, Nebraska. We detected LSV in the bee Halictus ligatus (four of 63 specimens tested, 6.3%) at a similar rate as A. mellifera (nine of 115 specimens, 7.8%), but only one H. ligatus sequencing library yielded sufficient data for compositional analysis. Sequenced samples often contained multiple divergent LSV lineages, including individual specimens. While these studies were exploratory rather than statistically powerful tests of hypotheses, they illustrate the utility of high-throughput sequencing for understanding LSV transmission within and among species.

California, Maryland, Nebraska↗