Search for: All records

Abstract Most studies assessing rates of phenotypic change focus on population mean trait values, whereas a largely overlooked additional component is changes in population trait variation. Theoretically, eco‐evolutionary dynamics mediated by such changes in trait variation could be as important as those mediated by changes in trait means. To date, however, no study has comprehensively summarised how phenotypic variation is changing in contemporary populations. Here, we explore four questions using a large database: How do changes in trait variances compare to changes in trait means? Do different human disturbances have different effects on trait variance? Do different trait types have different effects on changes in trait variance? Do studies that established a genetic basis for trait change show different patterns from those that did not? We find that changes in variation are typically small; yet we also see some very large changes associated with particular disturbances or trait types. We close by interpreting and discussing the implications of our findings in the context of eco‐evolutionary studies. 

Abstract Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use‐cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next‐generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications. 

Abstract Environmental DNA studies have proliferated over the last decade, with promising data describing the diversity of organisms inhabiting aquatic and terrestrial ecosystems. The recovery of DNA present in the sediment of aquatic systems (sedDNA) has provided short‐ and long‐term data on a wide range of biological groups (e.g., photosynthetic organisms, zooplankton species) and has advanced our understanding of how environmental changes have affected aquatic communities. However, substantial challenges remain for recovering the genetic material of macro‐organisms (e.g., fish) from sediments, preventing complete reconstructions of past aquatic ecosystems, and limiting our understanding of historic, higher trophic level interactions. In this review, we outline the biotic and abiotic factors affecting the production, persistence, and transport of fish DNA from the water column to the sediments, and address questions regarding the preservation of fish DNA in sediment. We identify sources of uncertainties around the recovery of fish sedDNA arising during the sedDNA workflow. This includes methodological issues related to experimental design, DNA extraction procedures, and the selected molecular method (quantitative PCR, digital PCR, metabarcoding, metagenomics). By evaluating previous efforts (published and unpublished works) to recover fish sedDNA signals, we provide suggestions for future research and propose troubleshooting workflows for the effective detection and quantification of fish sedDNA. With further research, the use of sedDNA has the potential to be a powerful tool for inferring fish presence over time and reconstructing their population and community dynamics. 

Abstract Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer. 

Fish stocking has been utilized for over a century to offset extirpations or declines in abundance of many native species. These historical declines and hatchery contributions have led to uncertainty surrounding whether many contemporary populations are native, introgressed with hatchery sources, or entirely of hatchery origin. Such uncertainty is problematic for the conservation of native biodiversity as it hampers management agencies' ability to prioritize the conservation of indigenous locally adapted populations. Fortunately, genetic and genomic tools have allowed researchers to investigate these questions, often through the use of clustering or assignment approaches that are predicated on identifiable and consistent divergence between native populations and hatchery sources. Here, we apply these methods to restriction-site associated DNA (RAD) data from 643 brook trout (Salvelinus fontinalis) originating from 13 wild populations and an exogenous hatchery strain to investigate the extent of historical extirpations, hatchery contributions, and processes affecting population structure in a small area of the previously unglaciated Driftless Area of Wisconsin, USA. The results from these analyses suggest that wild populations in this region are genetically distinct even at small spatial scales, lack strong hydrologically associated population structure, rarely exchange gene flow, and have small effective population sizes. Furthermore, wild populations are substantially diverged from known hatchery strains and show minimal evidence of introgression in clustering analyses. However, we demonstrate through empirically informed simulations that distinct wild populations may potentially be hatchery-founded and have since diverged through rapid genetic drift. Collectively, the apparent lack of hydrological population structure and potential for rapid drift in the Driftless Area suggest that many native populations may have been historically extirpated and refounded by stocking events. If this is the case, then commonly used genomic clustering methods and their associated model selection criteria may result in underestimation of hatchery introgression in the face of rapid drift. 

Oceanographic changes are occurring more rapidly in recent decades, with new implications for ocean ecosystems and adjacent human communities. It is important to bring attention to these changes while they are unfolding rather than after they have occurred. Here we report on a rapid shift toward colder, fresher water in the deep Gulf of Maine that, as of mid-June 2024, has persisted for at least six months. The shift likely represents an influx of Labrador Slope Water and resembles conditions that predated a major warming shift that occurred in 2011–2012. Deep-water oceanographic conditions in the Gulf of Maine have a strong influence on ecosystem dynamics, including the prey of critically endangered North Atlantic right whales, the seasonal and disease dynamics of American lobster, and the distribution and abundance of kelp forest communities, among others. Oceanographic surprises have an important role in this system, and monitoring how this shift unfolds, oceanographically and ecologically, will give new insights into how oceanographic signals can inform our understanding of ecosystem responses. 

The bridle shiner (Notropis bifrenatus) is a small cyprinid native to the eastern United States and Canada. Bridle shiner populations have declined across their range, and the species now receives concern status or legal protection in 13 states and two provinces. Bridle shiners were historically found in southern and western Maine in densely vegetated, shallow habitats along the shorelines of streams and ponds. We surveyed areas of Maine that supported historical bridle shiner populations using environmental DNA (eDNA) and traditional seine netting methods, and then used eDNA sampling to survey areas with unknown bridle shiner presence. We rediscovered bridle shiner populations at 11 of 32 historically occupied waterbodies and documented bridle shiners in four additional waterbodies. We determined that both eDNA and seine net surveys are viable options for monitoring bridle shiners in Maine and identified ways to streamline the eDNA methods used in this study to reduce the time and cost of future surveys. 

Advancements in genetic technology and processing allows for the presence of loose genetic material in the environment to become a resource, capable of assisting habitat and wildlife management efforts by providing information about organisms in a region without having to disturb or disrupt the organisms and environment. This use of environmental DNA has gained traction across biomes, with researchers continuing to test extraction and processing of DNA from various environmental media. However, the high variability in media quality, characteristics, and taxonomic knowledge means that the tested capabilities of eDNA vary wildly depending on the application and species of interest. In this thesis, I focus on the use of eDNA metabarcoding in freshwater streams in Maine, examining the ability and existing libraries of two genetic loci to identify Maine fish and macroinvertebrate species. eDNA results are compared against a traditional specimen-based surveying method utilized by the Maine Department of Environmental Protection and the Penobscot Nation’s Department of Natural Resources, and over time to monitor the success of stream restoration initiatives. While eDNA samples successfully detected fish and invertebrate species in both datasets, no strong correlation was found between benthic macroinvertebrate abundance counts and detected sequence variants. Furthermore, eDNA detection led to highly different community survey results than the specimen-based survey method, and limitations of available reference sequences indicate a strong need for localized references for future eDNA work. While eDNA was able to identify ASVs at a higher clarity than the specimen-based survey method, only 4 taxonomic families were shared between the survey method categorization and eDNA detection. However, eDNA was successful when applied to a broader range of taxa for presence-absence detection and community composition detection, and found that stream communities did change significantly based on installment of large wood addition projects. 

Invasive species are organisms moved from one region to another by humans. Although they are not always harmful to the recipient community, their lack of evolutionary history with their new community can set the stage for destruction. In a world of increasing interconnectivity and warming waters, we expect invasive species will continue to be introduced and that their ranges will expand as more areas become suitable habitats. At this critical point in our planet’s natural history, the need to understand where invasive species can survive and how to detect them are important. Here, I begin with a review of invasive species physiology measurements using species identified as invasive through the Marine Invader Monitoring and Information Collaborative. These data points highlight inconsistencies in measurement technique as well as the importance that acclimation temperature and life stage play on thermal thresholds. Based on the noise in the data, I recommend laboratory experiments to understand the absolute maximum and minimum survivable temperatures for each species, followed by field observations of temperatures needed to grow and reproduce. Then, using a newer invader to Maine Hemigrapsus sanguineus, I measured thermal thresholds for summer and winter-acclimated crabs and found shifts in thermal thresholds as well as evidence that winter temperatures are stressful for these crabs. Lastly, to effectively detect invasive species early, I tested and designed assays for environmental DNA (eDNA) detection of 9 invasive or nuisance species in the Gulf of Maine. Using laboratory experiments and a two-year time series in a local tide pool, I found that not all of the studied invertebrate species can be detected equally. Some organisms with soft, exposed tissues shed eDNA consistently with their abundance, while organisms with exoskeletons or shells do not. This trend does not hold true for all of the studied taxa, but this premise alongside an understanding of natural history and morphology helps clarify the observed trends. Thus, eDNA techniques should not be applied equally across all taxa for management purposes without a clear understanding of the message of the signal. Overall, I made recommendations to better predict suitable habitats for invasive species, characterized thresholds for an understudied invasive species in New England, and continued building upon the challenges of detecting invertebrates with eDNA.