Mark J. Bagley

Genetic patterns across multiple introductions of the globally invasive crab genus Carcinus

The European green crab Carcinus maenas is one of the worlds most successful aquatic invaders, having established populations on every continent with temperate shores. Here we describe patterns of genetic diversity across both the native and introduced ranges of C. maenas and its sister species, C. aestuarii, including all known non‐native populations. The global data set includes sequences from the mitochondrial cytochrome c oxidase subunit I gene, as well as multilocus genotype data from nine polymorphic nuclear microsatellite loci. Combined phylogeographic and population genetic analyses clarify the global colonization history of C. maenas, providing evidence of multiple invasions to Atlantic North America and South Africa, secondary invasions to the northeastern Pacific, Tasmania, and Argentina, and a strong likelihood of C. maenas × C. aestuarii hybrids in South Africa and Japan. Successful C. maenas invasions vary broadly in the degree to which they retain genetic diversity, although populations with the least variation typically derive from secondary invasions or from introductions that occurred more than 100 years ago.

Population genetic diversity and fitness in multiple environments

BackgroundWhen a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations to adapt to altered environments. However, it is not clear how much genetic diversity within populations may be lost before populations are put at significant risk. Development of tools to evaluate this relationship would be a valuable contribution to conservation biology. To address these issues, we have created an experimental system that uses laboratory populations of an estuarine crustacean, Americamysis bahia with experimentally manipulated levels of genetic diversity. We created replicate cultures with five distinct levels of genetic diversity and monitored them for 16 weeks in both permissive (ambient seawater) and stressful conditions (diluted seawater). The relationship between molecular genetic diversity at presumptive neutral loci and population vulnerability was assessed by AFLP analysis.ResultsPopulations with very low genetic diversity demonstrated reduced fitness relative to high diversity populations even under permissive conditions. Population performance decreased in the stressful environment for all levels of genetic diversity relative to performance in the permissive environment. Twenty percent of the lowest diversity populations went extinct before the end of the study in permissive conditions, whereas 73% of the low diversity lines went extinct in the stressful environment. All high genetic diversity populations persisted for the duration of the study, although population sizes and reproduction were reduced under stressful environmental conditions. Levels of fitness varied more among replicate low diversity populations than among replicate populations with high genetic diversity. There was a significant correlation between AFLP diversity and population fitness overall; however, AFLP markers performed poorly at detecting modest but consequential losses of genetic diversity. High diversity lines in the stressful environment showed some evidence of relative improvement as the experiment progressed while the low diversity lines did not.ConclusionsThe combined effects of reduced average fitness and increased variability contributed to increased extinction rates for very low diversity populations. More modest losses of genetic diversity resulted in measurable decreases in population fitness; AFLP markers did not always detect these losses. However when AFLP markers indicated lost genetic diversity, these losses were associated with reduced population fitness.

Assessing Macroinvertebrate Biodiversity in Freshwater Ecosystems: Advances and Challenges in DNA-based Approaches

Assessing the biodiversity of macroinvertebrate fauna in freshwater ecosystems is an essential component of both basic ecological inquiry and applied ecological assessments. Aspects of taxonomic diversity and composition in freshwater communities are widely used to quantify water quality and measure the efficacy of remediation and restoration efforts. The accuracy and precision of biodiversity assessments based on standard morphological identifications are often limited by taxonomic resolution and sample size. Morphologically based identifications are laborious and costly, significantly constraining the sample sizes that can be processed. We suggest that the development of an assay platform based on DNA signatures will increase the precision and ease of quantifying biodiversity in freshwater ecosystems. Advances in this area will be particularly relevant for benthic and planktonic invertebrates, which are often monitored by regulatory agencies. Adopting a genetic assessment platform will alleviate some of the current limitations to biodiversity assessment strategies. We discuss the benefits and challenges associated with DNA-based assessments and the methods that are currently available. As recent advances in microarray and next-generation sequencing technologies will facilitate a transition to DNA-based assessment approaches, future research efforts should focus on methods for data collection, assay platform development, establishing linkages between DNA signatures and well-resolved taxonomies, and bioinformatics.

Incorporation of DNA barcoding into a large-scale biomonitoring program: opportunities and pitfalls

Abstract Taxonomic identification of benthic macroinvertebrates is critical to protocols used to assess the biological integrity of aquatic ecosystems. The time, expense, and inherent error rate of species-level morphological identifications has necessitated use of genus- or family-level identifications in most large, statewide bioassessment programs. Use of coarse-scale taxonomy can obscure signal about biological condition, particularly if the range of species tolerances is large within genera or families. We hypothesized that integration of deoxyribonucleic acid (DNA) barcodes (partial cytochrome c oxidase subunit I sequences) into bioassessment protocols would provide greater discriminatory ability than genus-level identifications and that this increased specificity could lead to more sensitive assessments of water quality and habitat. Analysis of DNA barcodes from larval specimens of Ephemeroptera, Plecoptera, and Trichoptera (EPT) taxa collected as part of Marylands Biological Stream Survey (MBSS) revealed ∼2 to 3× as many DNA-barcode groups or molecular operational taxonomic units (mOTUs) as morphologically identified genera. As expected, geographic distributions for several mOTUs were tighter than for the parent genus, but few mOTUs showed closer associations with water-quality variables or physical-habitat features than did the genus in which they belonged. The need for improved protocols for the consistent generation of DNA barcodes is discussed.

Spatial and Temporal Genetic Analyses Show High Gene Flow Among European Corn Borer (Lepidoptera: Crambidae) Populations Across the Central U.S. Corn Belt

ABSTRACT European corn borer, Ostrinia nubilalis (Hübner), adults were sampled at 13 sites along two perpendicular 720-km transects intersecting in central Iowa and for the following two generations at four of the same sites separated by 240 km in the cardinal directions. More than 50 moths from each sample location and time were genotyped at eight microsatellite loci. Spatial analyses indicated that there is no spatial genetic structuring between European corn borer populations sampled 720 km apart at the extremes of the transects and no pattern of genetic isolation by distance at that geographic scale. Although these results suggest high gene flow over the spatial scale tested, it is possible that populations have not had time to diverge since the central Corn Belt was invaded by this insect ≈60 yr ago. However, temporal analyses of genetic changes in single locations over time suggest that the rate of migration is indeed very high. The results of this study suggest that the geographic dimensions of European corn borer populations are quite large, indicating that monitoring for resistance to transgenic Bt corn at widely separated distances is justified, at least in the central Corn Belt. High gene flow further implies that resistance to Bt corn may be slow to evolve, but once it does develop, it may spread geographically with such speed that mitigation strategies will have to be implemented quickly to be effective.

Genetic diversity and species diversity of stream fishes covary across a land-use gradient

Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture–forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems.

Development of codominant markers for identifying species hybrids

Herein we describe a simple method fordeveloping species-diagnostic markers thatwould permit the rapid identification of hybridindividuals. Our method relies on amplifiedlength polymorphism (AFLP) and single strandconformation polymorphism (SSCP) technologies,both of which can be performed in any molecularbiology facility using standard laboratoryequipment. We demonstrate the utility of theAFLP-SSCP method by developing threetaxon-specific markers that will be suitablefor monitoring introgression in endangeredKlamath basin suckers.

Chapter 23 USEPA biomonitoring and bioindicator concepts needed to evaluate the biological integrity of aquatic systems

Abstract This chapter presents the current uses, concepts and anticipated future directions of biomonitoring and bioindicators in the regulatory and research programs of the United States Environmental Protection Agency (USEPA). The chapter provides a historical look on how biomonitoring and bioindicators evolved in the USEPA or its predecessor agencies from the 1960s – 1980s, then describes two current key biomonitoring and bioindicator programmes, the USEPA Office of Research and Developments Environmental Monitoring and Assessment Programme (EMAP) and USEPAs Office of Waters Biocriteria Programme. The remainder of the chapter is organized hierarchically beginning with concepts and monitoring approaches using fish, macroinvertebrates, and periphyton assemblages, and functional ecosystem measures. The assemblage approaches are followed by current research and regulatory use of whole organism toxicity testing assessments for measuring contamination in aquatic environments and remediation assessment. The chapter includes existing and proposed activities in the use of real-time biomonitoring to assess biological exposures to contaminants and other environmental changes. A new approach that uses small and large adult whole fish tissue as a bioindicator for assessing potential contaminant exposures to wildlife is presented, followed by a description of new research in molecular approaches to biomonitoring and bioindicators through measures of gene expression, use of microarrays and measures of genetic diversity.

Genetic structure and gene flow among European corn borer populations from the Great Plains to the Appalachians of North America

1 Earlier population genetic spatial analysis of European corn borer Ostrinia nubilalis (Hübner) indicated no genetic differentiation even between locations separated by 720 km. This result suggests either high dispersal resulting in high gene flow or that populations are not in migration–drift equilibrium subsequent to their invasion of the central U.S.A. in the 1940s. 2 To discriminate among these two possibilities, samples were collected at 12 locations in eight states from New York to Colorado, a geographic scale that is three‐fold greater than previously tested. Eight microsatellite markers were employed to estimate genetic differentiation and gene flow among these populations, and to test for isolation‐by‐distance. 3 Although pairwise FST estimates were very low, there was a significant isolation‐by‐distance relationship. 4 Wrights neighbourhood area (i.e. the surface area covered by a panmictic group of individuals within a larger continuous distribution) was calculated as 433 km2, and the radius indicates that approximately 13% of O. nubilalis adults disperse a net distance >12 km per generation from their natal source. 5 Analyses indicated significant differentiation between the north‐eastern region (New York and Pennsylvania) and the region combining sample locations from Ohio to Colorado, suggesting the potential for isolation of populations by topographic barriers in the Northeast. 6 Taken together, the results suggest that O. nubilalis exhibits substantial gene flow over long distances and that the lack of genetic differentiation between populations across hundreds of kilometres is not simply a result of migration–drift disequilibrium arising from the recent range expansion.