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USGS2006

Monitoring biological diversity: strategies, tools, limitations, and challenges

Monitoring is an assessment of the spatial and temporal variability in one or more ecosystem properties, and is an essential component of adaptive management. Monitoring can help determine whether mandated environmental standards are being met and can provide an early-warning system of ecological change. Development of a strategy for monitoring biological diversity will likely be most successful when based upon clearly articulated goals and objectives and may be enhanced by including several key steps in the process. Ideally, monitoring of biological diversity will measure not only composition, but also structure and function at the spatial and temporal scales of interest. Although biodiversity monitoring has several key limitations as well as numerous theoretical and practical challenges, many tools and strategies are available to address or overcome such challenges; I summarize several of these. Due to the diversity of spatio-temporal scales and comprehensiveness encompassed by existing definitions of biological diversity, an effective monitoring design will reflect the desired sampling domain of interest and its key stressors, available funding, legal requirements, and organizational goals.

Northwestern Naturalist↗

USGS2013

Predicting the effects of proposed Mississippi River diversions on oyster habitat quality; application of an oyster habitat suitability index model

In an attempt to decelerate the rate of coastal erosion and wetland loss, and protect human communities, the state of Louisiana developed its Comprehensive Master Plan for a Sustainable Coast. The master plan proposes a combination of restoration efforts including shoreline protection, marsh creation, sediment diversions, and ridge, barrier island, and hydrological restoration. Coastal restoration projects, particularly the large-scale diversions of fresh water from the Mississippi River, needed to supply sediment to an eroding coast potentially impact oyster populations and oyster habitat. An oyster habitat suitability index model is presented that evaluates the effects of a proposed sediment and freshwater diversion into Lower Breton Sound. Voluminous freshwater, needed to suspend and broadly distribute river sediment, will push optimal salinities for oysters seaward and beyond many of the existing reefs. Implementation and operation of the Lower Breton Sound diversion structure as proposed would render about 6,173 ha of hard bottom immediately east of the Mississippi River unsuitable for the sustained cultivation of oysters. If historical harvests are to be maintained in this region, a massive and unprecedented effort to relocate private leases and restore oyster bottoms would be required. Habitat suitability index model results indicate that the appropriate location for such efforts are to the east and north of the Mississippi River Gulf Outlet.

Louisiana↗

USGS2025

Simulation of the impacts of spring diversions on streamflow in the Strawberry Creek watershed, San Bernardino County, California, using an integrated hydrological model

The Strawberry Creek watershed, situated in the San Bernardino Mountains of southern California, features a group of natural springs known as Arrowhead Springs that have been augmented with diversions in the form of sub-horizontal borings and tunnels. Understanding the impact of these structures on streamflow through groundwater capture is crucial for managing surface-water resources in this watershed. In this study we constructed the Strawberry Creek integrated hydrological model (SCIHM) to increase this understanding. The SCIHM is an integrated surface runoff and groundwater model that uses the coupled groundwater and surface-water flow model (GSFLOW), which is based on the integration of the precipitation-runoff modeling system (PRMS) and the modular groundwater flow model commonly called MODFLOW, version MODFLOW-2005 software to simulate surface runoff and infiltration and groundwater flow. The model has three layers, 263 rows, and 176 columns. The model area includes the Strawberry Creek and four adjacent watersheds. The PRMS model was calibrated using two streamflow gaging stations and the GSFLOW model was calibrated to reported spring diversion discharge and a sparse number of groundwater-level measurements. The SCIHM was run with and without diversions active and simulated streamflow was compared, finding that in the headwaters of Strawberry Creek about 35 percent of the diversion flow was captured from base flow.

EarthArXiv↗

USGS2011

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

Gulf Of Mexico↗

USGS2021

Distribution, abundance, and genomic diversity of the endangered antioch dunes evening primrose (Oenothera deltoides subsp. howellii) surveyed in 2019

Sand dune ecosystems are highly dynamic landforms found along coastlines and riverine deltas where a supply of sand-sized material is available to be delivered by aquatic and wind environments. These unique ecosystems provide habitat for a variety of endemic and rare plant and animal species. Sand dunes have been affected by human development, sand mining, and shoreline stabilization from invasive weeds. This report provides a summary of a comprehensive literature review, field survey, and genomic analysis for the Antioch Dunes evening primrose ( Oenothera deltoides subsp. howellii , hereafter howellii ), an endemic species to the San Francisco Bay-Delta, California, which was listed as a federally endangered subspecies in 1978. Howellii is found on a historic dune sheet (the Antioch sand sheet) near the confluence of the Sacramento and San Joaquin Rivers. The Antioch sand sheet has been greatly altered by sand mining and land conversion into agriculture and urban development. In chapter A, we describe results of the literature review and field survey. We found howellii at eight locations with over 90 percent of the adult population and nearly 99 percent of juveniles observed on the Antioch Dunes National Wildlife Refuge. We measured a negative relationship between howellii numbers and invasive weed cover, illustrating the importance of mobilized open sand for this species. In chapter B, we describe the genomic study results. We surveyed genomic diversity by using double-digest restriction-site associated sequencing to estimate population genetic structure and levels of diversity across all surveyed occurrences. The genomic analyses included outgroup samples of the closely related Oenothera deltoides subsp. cognata and three occurrences of an unknown taxon with intermediate morphology to cognata and howellii , which also occurs on the Antioch sand sheet, east of the Antioch Dunes National Wildlife Refuge. These three morphologically distinctive groups formed genetically distinctive clusters and well-supported monophyletic clades in clustering and phylogenetic analyses, respectively. There was no indication of recent hybridization among any of the groups. Among howellii occurrences, the Antioch Dunes National Wildlife Refuge contained the greatest genetic diversity. Our approach, which combined field surveys, habitat assessments, and genetic analyses, can provide useful information for the conservation and management of rare and at-risk plant species and highlights the uniqueness of the Antioch sand sheet floral diversity through the discovery of a putative new taxon within the bird-cage evening primrose species complex.

California↗

USGS2025

Water-budget analysis of the Medina and Diversion Lake system, with estimated recharge to the Edwards aquifer and the upper zone of the Trinity aquifer, Bandera, Bexar, and Medina Counties, Texas, 1955–2022

The U.S. Geological Survey—in cooperation with the San Antonio Water System and the Edwards Aquifer Authority—used data collected during four different periods (March 1955–August 1964, October 1995–September 1996, March 2001–June 2002, and March 2017–October 2022) as part of a new study to refine previously derived relations between the altitude of the water surface of Medina Lake and recharge to the Edwards aquifer and the upper zone of the Trinity aquifer in the form of seepage losses from Medina Lake and the immediately downstream Diversion Lake. Any seepage losses that occur within the conservation pools of Medina and Diversion Lakes infiltrate the Edwards aquifer and the upper zone of the Trinity aquifer as recharge. To quantify recharge to the Edwards aquifer and the upper zone of the Trinity aquifer from Medina and Diversion Lakes, daily water budgets were used to calculate monthly and annual recharge (method 1). A new statistical analysis culminated in a new log-log weighted least-squares (WLS) regression equation that relates recharge from Medina and Diversion Lakes to the Medina Lake stage. Recharge estimates obtained by using the new log-log WLS regression equation (method 2), as well as the recharge estimated by using a method published in 1978 (referred to as the “Puente method”) (method 3), were compared with the calculated recharge during March 2017–September 2022. During March 2017–September 2022, the WLS estimated recharge was 224,310 acre-feet, 0.5 percent less than the calculated recharge of 225,400 acre-feet. The Puente method estimated recharge was 342,080 acre-feet, about 52 percent more than the calculated recharge. The analysis of the three methods indicates that WLS estimated recharge provides a more accurate accounting of actual recharge to the Edwards aquifer and the upper zone of the Trinity aquifer compared to the Puente method.

Texas↗

USGS2026

Simulation of the impacts of spring diversions on streamflow in the Strawberry Creek watershed, San Bernardino County, California, using an integrated hydrological model

The Strawberry Creek watershed, in the San Bernardino Mountains of southern California, features a group of natural springs known as Arrowhead Springs that have been augmented with diversions in the form of sub-horizontal borings and tunnels. Understanding the effects of these structures on streamflow through groundwater capture is crucial for managing surface-water resources in this watershed. In this study, we constructed the Strawberry Creek integrated hydrological model to increase this understanding. The Strawberry Creek integrated hydrological model is an integrated surface runoff and groundwater model, GSFLOW to simulate surface runoff and infiltration and groundwater flow. The model has 263 rows and 176 columns in each of its three layers. The model area includes the Strawberry Creek and four adjacent watersheds. The precipitation-runoff modeling system was calibrated using two streamflow gaging stations, and the groundwater and surface-water flow model was calibrated to the reported spring diversion discharge and a sparse number of groundwater-level measurements. The Strawberry Creek integrated hydrological model was run with and without diversions active, and simulated streamflow was compared, indicating that in the headwaters of Strawberry Creek, about 35 percent of the diversion flow was captured from base flow.

California↗

USGS2012

Palynological composition of a Lower Cretaceous South American tropical sequence: Climatic implications and diversity comparisons with other latitudes.

Premise of the study : Reconstruction of floristic patterns during the early diversification of angiosperms is impeded by the scarce fossil record, especially in tropical latitudes. Here we collected quantitative palynological data from a stratigraphic sequence in tropical South America to provide floristic and climatic insights into such tropical environments during the Early Cretaceous. Methods : We reconstructed the floristic composition of an Aptian-Albian tropical sequence from central Colombia using quantitative palynology (rarefied species richness and abundance) and used it to infer its predominant climatic conditions. Additionally, we compared our results with available quantitative data from three other sequences encompassing 70 floristic assemblages to determine latitudinal diversity patterns. Key results : Abundance of humidity indicators was higher than that of aridity indicators (61% vs. 10%). Additionally, we found an angiosperm latitudinal diversity gradient (LDG) for the Aptian, but not for the Albian, and an inverted LDG of the overall diversity for the Albian. Angiosperm species turnover during the Albian, however, was higher in humid tropics. Conclusions : There were humid climates in northwestern South America during the Aptian-Albian interval contrary to the widespread aridity expected for the tropical belt. The Albian inverted overall LDG is produced by a faster increase in per-sample angiosperm and pteridophyte diversity in temperate latitudes. However, humid tropical sequences had higher rates of floristic turnover suggesting a higher degree of morphological variation than in temperate regions.

American Journal of Botany↗

USGS2016

Is the impact of eutrophication on phytoplankton diversity dependent on lake volume/ecosystem size?

Research focusing on biodiversity responses to the interactions of ecosystem size and anthropogenic stressors are based mainly on correlative gradient studies, and may therefore confound size-stress relationships due to spatial context and differences in local habitat features across ecosystems. We investigated how local factors related to anthropogenic stressors ( e.g., eutrophication) interact with ecosystem size to influence species diversity. In this study, constructed lake mesocosms (with two contrasting volumes: 1020 (shallow mesocosms) and 2150 (deep mesocosms) litres) were used to simulate ecosystems of different size and manipulated nutrient levels to simulate mesotrophic and hypertrophic conditions. Using a factorial design, we assessed how the interaction between ecosystem size and nutrients influences phytoplankton diversity. We assessed community metrics (richness, diversity, evenness and total biovolumes) and multivariate community structure over a growing season (May to early November 2011). Different community structures were found between deep and shallow mescosoms with nutrient enrichment: Cyanobacteria dominated in the deep and Charophyta in the shallow mesocosms. In contrast, phytoplankton communities were more similar to each other in the low nutrient treatments; only Chlorophyta had generally a higher biovolume in the shallow compared to the deep mesocosms. These results suggest that ecosystem size is not only a determinant of species diversity, but that it can mediate the influence of anthropogenic effects on biodiversity. Such interactions increase the uncertainty of global change outcomes, and should therefore not be ignored in risk/impact assessment and management.

Journal of Limnology↗

USGS2014

Comparisons of genetic diversity in captive versus wild populations of the federally endangered Quino checkerspot butterfly ( Euphydryas editha quino Behr; Lepidoptera: Nymphalidae)

Captive populations can play a significant role in threatened and endangered species management. An important consideration when developing and managing captive populations, however, is the maintenance of genetic diversity to ensure that adequate variation exists to avoid the negative consequences of inbreeding. In this investigation, we compared genetic diversity patterns within captive and wild populations of the federally endangered Quino checkerspot butterfly (Euphydryas editha quino Behr [Lepidoptera: Nymphalidae]), a taxon with a restricted distribution to chaparral and sage shrublands within Riverside and San Diego counties, California. Our analyses revealed that medium to high-frequency alleles from the wild populations were also present in the captive populations. While there was no significant difference in genetic diversity as quantified by expected heterozygosity, the captive populations showed tendencies toward significantly lower allelic richness than their wild counterparts. Given that alleles from the wild populations were occasionally not detected in captive populations, periodic incorporation of new wild specimens into the captive population would help ensure that allelic diversity is maintained to the extent possible. If performed in advance, genetic surveys of wild populations may provide the clearest insights regarding the number of individuals needed in captivity to adequately reflect wild populations.

California↗

USGS2023

Assessing arthropod diversity metrics derived from stream environmental DNA: Spatiotemporal variation and paired comparisons with manual sampling

Background Benthic invertebrate (BI) surveys have been widely used to characterize freshwater environmental quality but can be challenging to implement at desired spatial scales and frequency. Environmental DNA (eDNA) allows an alternative BI survey approach, one that can potentially be implemented more rapidly and cheaply than traditional methods. Methods We evaluated eDNA analogs of BI metrics in the Potomac River watershed of the eastern United States. We first compared arthropod diversity detected with primers targeting mitochondrial 16S (mt16S) and cytochrome c oxidase 1 (cox1 or COI) loci to that detected by manual surveys conducted in parallel. We then evaluated spatial and temporal variation in arthropod diversity metrics with repeated sampling in three focal parks. We also investigated technical factors such as filter type used to capture eDNA and PCR inhibition treatment. Results Our results indicate that genus-level assessment of eDNA compositions is achievable at both loci with modest technical noise, although database gaps remain substantial at mt16S for regional taxa. While the specific taxa identified by eDNA did not strongly overlap with paired manual surveys, some metrics derived from eDNA compositions were rank-correlated with previously derived biological indices of environmental quality. Repeated sampling revealed statistical differences between high- and low-quality sites based on taxonomic diversity, functional diversity, and tolerance scores weighted by taxon proportions in transformed counts. We conclude that eDNA compositions are efficient and informative of stream condition. Further development and validation of scoring schemes analogous to commonly used biological indices should allow increased application of the approach to management needs.

PeerJ↗

USGS1988

Patterns of relative diversity within riparian small mammal communities, Platte River Watershed, Colorado

Relative diversity within and between small mammal assemblages of riparian and upland vegetation was evaluated at 6 study areas across an elevational gradient. In contrast to avian diversity analyses conducted at the same sites, species richness, relative diversity, and faunal similarity of small mammals were greater among upland rather than riparian communities across the cline. Beta diversity between riparian and upland small mammal communities is greater at higher elevations within the watershed. These higher elevation portions of watersheds must be emphasized in management strategies to conserve regional integrity of native small mammal faunas.

Colorado↗

USGS2020

Species and genetic diversity in Lake Huron in 2018

Fish community objectives (FCOs) for species and genetic diversity (DesJardine et al. 1995) complement the species- or genera-specific objectives by recognizing that diversity within and among species can improve ecosystem resiliency through portfolio effects (DuFour et al. 2015). In Lake Huron, native species (such as Lake Trout and Lake Whitefish), and non-native species (such as Alewife and Pacific salmon) play important roles in the ecosystem. The FCOs recognize the importance of genetic diversity within all fish populations to ensure their long-term sustainability. This section summarizes the current state of species diversity and recent genetic analyses of important biota in the fish community.

Lake Huron↗

USGS2006

Linking the concept of scale to studies of biological diversity: evolving approaches and tools.

Although the concepts of scale and biological diversity independently have received rapidly increasing attention in the scientific literature since the 1980s, the rate at which the two concepts have been investigated jointly has grown much more slowly. We find that scale considerations have been incorporated explicitly into six broad areas of investigation related to biological diversity: (1) heterogeneity within and among ecosystems, (2) disturbance ecology, (3) conservation and restoration, (4) invasion biology, (5) importance of temporal scale for understanding processes, and (6) species responses to environmental heterogeneity. In addition to placing the papers of this Special Feature within the context of brief summaries of the expanding literature on these six topics, we provide an overview of tools useful for integrating scale considerations into studies of biological diversity. Such tools include hierarchical and structural-equation modelling, kriging, variable-width buffers, k -fold cross-validation, and cascading graph diagrams, among others. Finally, we address some of the major challenges and research frontiers that remain, and conclude with a look to the future.

Diversity and Distributions↗

USGS2022

As the goose flies: Migration routes and timing influence patterns of genetic diversity in a circumpolar migratory herbivore

Migration schedules and the timing of other annual events (e.g., pair formation and molt) can affect the distribution of genetic diversity as much as where these events occur. The greater white-fronted goose ( Anser albifrons ) is a circumpolar goose species, exhibiting temporal and spatial variation of events among populations during the annual cycle. Previous range-wide genetic assessments of the nuclear genome based on eight microsatellite loci suggest a single, largely panmictic population despite up to five subspecies currently recognized based on phenotypic differences. We used double digest restriction-site associated DNA (ddRAD-seq) and mitochondrial DNA (mtDNA) sequence data to re-evaluate estimates of spatial genomic structure and to characterize how past and present processes have shaped the patterns of genetic diversity and connectivity across the Arctic and subarctic. We uncovered previously undetected inter-population differentiation with genetic clusters corresponding to sampling locales associated with current management groups. We further observed subtle genetic clustering within each management unit that can be at least partially explained by the timing and directionality of migration events along with other behaviors during the annual cycle. The Tule Goose ( A. a. elgasi ) and Greenland subspecies ( A. a. flavirostris ) showed the highest level of divergence among all sampling locales investigated. The recovery of previously undetected broad and fine-scale spatial structure suggests that the strong cultural transmission of migratory behavior restricts gene flow across portions of the species’ range. Our data further highlight the importance of re-evaluating previous assessments conducted based on a small number of highly variable genetic markers in phenotypically diverse species.

Circumpolar Arctic↗

USGS2016

Ungulate browsers promote herbaceous layer diversity in logged temperate forests

Ungulates are leading drivers of plant communities worldwide, with impacts linked to animal density, disturbance and vegetation structure, and site productivity. Many ecosystems have more than one ungulate species; however, few studies have specifically examined the combined effects of two or more species on plant communities. We examined the extent to which two ungulate browsers (moose [ Alces americanus ]) and white-tailed deer [ Odocoileus virginianus ]) have additive (compounding) or compensatory (opposing) effects on herbaceous layer composition and diversity, 5–6 years after timber harvest in Massachusetts, USA. We established three combinations of ungulates using two types of fenced exclosures – none (full exclosure), deer (partial exclosure), and deer + moose (control) in six replicated blocks. Species composition diverged among browser treatments, and changes were generally additive. Plant assemblages characteristic of closed canopy forests were less abundant and assemblages characteristic of open/disturbed habitats were more abundant in deer + moose plots compared with ungulate excluded areas. Browsing by deer + moose resulted in greater herbaceous species richness at the plot scale (169 m 2 ) and greater woody species richness at the subplot scale (1 m 2 ) than ungulate exclusion and deer alone. Browsing by deer + moose resulted in strong changes to the composition, structure, and diversity of forest herbaceous layers, relative to areas free of ungulates and areas browed by white-tailed deer alone. Our results provide evidence that moderate browsing in forest openings can promote both herbaceous and woody plant diversity. These results are consistent with the classic grazing-species richness curve, but have rarely been documented in forests.

Ecology and Evolution↗

USGS2019

Changes in genetic diversity and differentiation in Red‐cockaded woodpeckers (Dryobates borealis) over the past century

Red‐cockaded woodpeckers (RCW; Dryobates borealis ) declined after human activities reduced their fire‐maintained pine ecosystem to <3% of its historical range in the southeastern United States and degraded remaining habitat. An estimated 1.6 million RCW cooperative breeding groups declined to about 3,500 groups with no more than 10,000 birds by 1978. Management has increased RCW population abundances since they were at their lowest in the 1990s. However, no range‐wide study has been undertaken since then to investigate the impacts of this massive bottleneck or infer the effects of conservation management and recent demographic recoveries. We used mitochondrial DNA sequences (mtDNA) and nine nuclear microsatellite loci to determine if range‐wide demographic declines resulted in changes to genetic structure and diversity in RCW by comparing samples collected before 1970 (mtDNA data only), between 1992 and 1995 (mtDNA and microsatellites), and between 2010 and 2014 (mtDNA and microsatellites). We show that genetic diversity has been lost as detected by a reduction in the number of mitochondrial haplotypes. This reduction was apparent in comparisons of pre‐1970 mtDNA data with data from the 1992–1995 and 2010–2014 time points, with no change between the latter two time points in mtDNA and microsatellite analyses. The mtDNA data also revealed increases in range‐wide genetic differentiation, with a genetically panmictic population present throughout the southeastern United States in the pre‐1970s data and subsequent development of genetic structure that has remained unchanged since the 1990s. Genetic structure was also uncovered with the microsatellite data, which like the mtDNA data showed little change between the 1992–1995 and 2010–2014 data sets. Temporal haplotype networks revealed a consistent, star‐like phylogeny, suggesting that despite the overall loss of haplotypes, no phylogenetically distinct mtDNA lineages were lost when the population declined. Our results may suggest that management during the last two decades has prevented additional losses of genetic diversity.

Alabama, Arkansas, Florida, Georgia, Kentucky, Lou↗

USGS2019

Effects of invasive plants on fire regimes and postfire vegetation diversity in an arid ecosystem

We assessed the impacts of co‐occurring invasive plant species on fire regimes and postfire native communities in the Mojave Desert, western USA. We analyzed the distribution and co‐occurrence patterns of three invasive annual grasses (Bromus rubens, Bromus tectorum, and Schismus spp.) known to alter fuel conditions and community structure, and an invasive forb (Erodium cicutarium) which dominates postfire sites. We developed species distribution models (SDMs) for each of the four taxa and analyzed field plot data to assess the relationship between invasives and fire frequency, years postfire, and the impacts on postfire native herbaceous diversity. Most of the Mojave Desert is highly suitable for at least one of the four invasive species, and 76% of the ecoregion is predicted to have high or very high suitability for the joint occurrence of B. rubens and B. tectorum and 42% high or very high suitability for the joint occurrence of the two Bromus species and E. cicutarium. Analysis of cover from plot data indicated two or more of the species occurred in 77% of the plots, with their cover doubling with each additional species. We found invasive cover in burned plots increased for the first 20 years postfire and recorded two to five times more cover in burned than unburned plots. Analysis also indicated that native species diversity and evenness as negatively associated with higher levels of relative cover of the four invasive taxa. Our findings revealed overlapping distributions of the four invasives; a strong relationship between the invasives and fire frequency; and significant negative impacts of invasives on native herbaceous diversity in the Mojave. This suggests predicting the distributions of co‐occurring invasive species, especially transformer species, will provide a better understanding of where native‐dominated communities are most vulnerable to transformations following fire or other disturbances.

California, Nevada↗