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The lower Columbia River (Washington and Oregon, USA) has been heavily invaded by a large number of planktonic organisms including the invasive copepod Pseudodiaptomus forbesi and the planktonic juveniles of the invasive clam, Corbicula fluminea . In order to assess the ecological impacts of these highly abundant invaders, we developed a multivariate auto-regressive (MAR) model of food web dynamics based upon a 12-year time-series of plankton community and environmental data from the Columbia River. Our model results indicate that plankton communities in the lower Columbia River are strongly impacted by the copepod P . forbesi at multiple trophic levels. We observed different ecological effects across different life stages of P . forbesi , with nauplii negatively impacting ciliates and autotrophs, and copepodite stages negatively impacting Daphnia and cyclopoid copepods. Although juvenile C . fluminea were highly abundant in the summer and autumn of each year, our best fit MAR model did not show significant C . fluminea impacts. Our results illustrate the strong ecological impact that some zooplankton invaders may cause within rivers and estuarine systems, and highlight the need for further research on the feeding ecology of the planktonic life-stage of C . fluminea . Overall, our study demonstrates the manner in which long-term, high resolution data sets can be used to better understand the ecological impacts of invasive species among complex and highly dynamic communities.

We present the first comprehensive analysis of the Pacific Northwest estuaries (PNWE) zooplankton time series, which encompasses 38 estuaries distributed across more than 1000 km of the North American Pacific Coast. With observations spanning more than 20 yr, we here examine biogeographic trends among zooplankton communities, patterns of biological invasion across the region, and environmental correlates with dominant native and invasive taxa. Our results show that some estuaries across the region are invaded by multiple zooplankton species and that the geographic extent of invasion is far greater than previously reported for at least five species of copepods: Pseudodiaptomus inopinus, Pseudodiaptomus forbesi, Oithona davisae, Limnoithona sinensis, Sinocalanus doerrii, and the cladoceran Bosmina coregoni. Some of these species appear to be rapidly spreading across the region, while others have occupied a relatively static geographic range for decades. The copepod, P. inopinus, is by far the most abundant and geographically widespread of these invaders, comprising more than 90% of all zooplankton abundance at some sites. We propose that the geographic distribution of these invaders is strongly constrained by geomorphic characteristics that define the salinity and mixing regimes in these estuaries, reflecting the strong role that physical forces play in structuring estuarine zooplankton communities.

It has been widely proposed that increasing global temperatures will promote the geographic spread of invasive species, yet few studies have examined the effects of increasing temperatures on existing populations of invaders. Here, we examine temperature trends across a 70‐year series of daily records from the lower Columbia River (Washington and Oregon), and assess the correlation between interannual water temperature variability and the abundance of several native and invasive zooplankton species using a 12‐year series of monthly zooplankton samples from a nearby station. Our results show a clear pattern of increasing temperatures in the river, with a negative correlation between elevated late summer temperatures and the abundance of all examined native taxa, but none of the examined invasive taxa. Our study supports the hypothesis that anthropogenic climate change may promote conditions more favorable to previously established populations of invasive zooplankton species.

Abstract Understanding the genomic basis of infectious disease is a fundamental objective in co-evolutionary theory with relevance to healthcare, agriculture, and epidemiology. Models of host-parasite co-evolution often assume that infection requires specific combinations of host and parasite genotypes. Co-evolving host and parasite loci are, therefore, expected to show associations that reflect an underlying infection/resistance allele matrix, yet little evidence for such genome-to-genome interactions has been observed among natural populations. We conducted a study to search for this genomic signature across 258 linked host (Daphnia magna) and parasite (Pasteuria ramosa) genomes. Our results show a clear signal of genomic association between multiple epistatically interacting loci in the host genome, and a family of genes encoding for collagen-like protein in the parasite genome. These findings are supported by laboratory-based infection trials, which show strong correspondence between phenotype and genotype at the identified loci. Our study provides clear genomic evidence of antagonistic co-evolution among wild populations.

We present a comprehensive survey of the scientific literature pertaining to non-indigenous and invasive zooplankton published across the first decades of the twenty-first century (i.e., 2000–2018). We provide a concise summary of the manner in which the scientific community has allocated its efforts to this issue in recent decades, and to illuminate trends that emerge from the literature. Our search yielded 620 publications encompassing 139 invasive zooplankton species, with invasive zooplankton reported from every region of the planet—including the Arctic and Antarctic. Most taxa were reported in a small number of publications, with the majority being mentioned in only a single paper. In contrast, approximately half of the surveyed publications concerned just four species: Bythotrephes longimanus, Mnemioposis leidyi, Cercopagis pengoi, and Daphnia lumholtzi. Our survey reveals strong geographic patterns among the literature, with most publications arising from economically developed western nations. We found that the majority of publications pertained to holoplanktonic organisms from freshwater habitats, especially from the North American Great Lakes. Based on these results, we present several recommendations for future research topics that may hold considerable opportunity for growth in our understanding of the invasion process.

Crabs are a large subtaxon of the Arthropoda, the most diverse and species-rich metazoan group. Several outstanding questions remain regarding crab diversification, including about the genomic capacitors of physiological and morphological adaptation, that cannot be answered with available genomic resources. Physiologically and ecologically diverse Anomuran porcelain crabs offer a valuable model for investigating these questions and hence genomic resources of these crabs would be particularly useful. Here, we present the first two genome assemblies of congeneric and sympatric Anomuran porcelain crabs, Petrolisthes cinctipes and Petrolisthes manimaculis from different microhabitats. Pacific Biosciences high-fidelity sequencing led to genome assemblies of 1.5 and 0.9 Gb, with N50s of 706.7 and 218.9 Kb, respectively. Their assembly length difference can largely be attributed to the different levels of interspersed repeats in their assemblies: The larger genome of P. cinctipes has more repeats (1.12 Gb) than the smaller genome of P. manimaculis (0.54 Gb). For obtaining high-quality annotations of 44,543 and 40,315 protein-coding genes in P. cinctipes and P. manimaculis, respectively, we used RNA-seq as part of a larger annotation pipeline. Contrarily to the large-scale differences in repeat content, divergence levels between the two species as estimated from orthologous protein-coding genes are moderate. These two high-quality genome assemblies allow future studies to examine the role of environmental regulation of gene expression in the two focal species to better understand physiological response to climate change, and provide the foundation for studies in fine-scale genome evolution and diversification of crabs.

Nonindigenous aquatic species are becoming increasingly common in coastal and inland waters, largely due to the global transport of zooplankton via commercial shipping and recreational boating. The cost of mitigation and lost income due to invasive zooplankton is estimated in the billions of dollars annually, yet we know little about the temporal dynamics of these invaders. Analysis of an 8.5-year (June 2005–December 2013) zooplankton time series from the Columbia River revealed contrasting patterns of invasion dynamics between species, cyclical periods of community invasion, and key environmental variables that constrain populations of invasive zooplankton. We identified four seasonal zooplankton communities (autumn/invaded, winter/barren, spring/rotifer, and transitional) that are strongly correlated with changes in chlorophyll content and water temperature, with peak abundances of invasive zooplankters occurring during periods of maximum water temperature. Additionally, we observed contrasting patterns of phenology between persistent and ephemeral invasive populations, with successful invaders exhibiting delayed annual peaks in population abundance. Two invasive zooplankters—the copepod Pseudodiaptomus forbesi and larval Asian clam Corbicula fluminea—dominate the zooplankton community in late summer and early autumn. Likewise, our results support conclusions from a growing body of literature that delayed phenology may be a key functional trait for successful invaders.

The rate of aquatic invasions by planktonic organisms has increased considerably in recent decades. In order to effectively direct funding and resources to control the spread of such invasions, a methodological framework for identifying high-risk transport vectors, as well as ruling out vectors of lesser concern will be necessary. A number of estuarine ecosystems on the North American Pacific Northwest coast have experienced a series of high impact planktonic invasions that have slowly unfolded across the region in recent decades, most notably, that of the planktonic copepod crustacean Pseudodiaptomus inopinus. Although introduction of P. inopinus to the United States almost certainly occurred through the discharge of ballast water from commercial vessels originating in Asia (the species’ native range), the mechanisms and patterns of subsequent spread remain unknown. In order to elucidate the migration events shaping this invasion, we sampled the genomes of copepods from seven invasive and two native populations using restriction-site associated DNA sequencing. This genetic data was evaluated against spatially-explicit genetic simulation models to evaluate competing scenarios of invasion spread. Our results indicate that invasive populations of P. inopinus exhibit a geographically unstructured genetic composition, likely arising from infrequent and large migration events. This pattern of genetic patchiness was unexpected given the linear geographic structure of the sampled populations, and strongly contrasts with the clear invasion corridors observed in many aquatic systems.