Genome assemblies of two species of porcelain crab, Petrolisthes cinctipes and Petrolisthes manimaculis (Anomura: Porcellanidae).

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.

Uncovering the Genomic Basis of Infection Through Co-genomic Sequencing of Hosts and Parasites.

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.

Genetic slippage after sex maintains diversity for parasite resistance in a natural host population.

Although parasite-mediated selection is a major driver of host evolution, its influence on genetic variation for parasite resistance is not yet well understood. We monitored resistance in a large population of the planktonic crustacean Daphnia magna over 8 years, as it underwent yearly epidemics of the bacterial pathogen Pasteuria ramosa. We observed cyclic dynamics of resistance: Resistance increased throughout the epidemics, but susceptibility was restored each spring when hosts hatched from sexual resting stages. Host resting stages collected across the year showed that largely resistant host populations can produce susceptible sexual offspring. A genetic model of resistance developed for this host-parasite system, based on multiple loci and strong epistasis, is in partial agreement with our findings. Our results reveal that, despite strong selection for resistance in a natural host population, genetic slippage after sexual reproduction can be a strong factor for the maintenance of genetic diversity of host resistance.

Modeling the trophic impacts of invasive zooplankton in a highly invaded river.

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.

Zooplankton invasions in the early 21st century: a global survey of recent studies and recommendations for future research.

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.