Genomic resources notes accepted 1 October 2014-30 November 2014

This article documents the public availability of (i) RAD sequencing data and validated SNPs for the American mink Neovison vison and (ii) Transcriptome resources for two nonmodel freshwater crustacean species, the copepod Eucyclops serrulatus and the amphipod Echinogammarus veneris.

An integrated study on Gammarus elvirae (Crustacea, Amphipoda): perspectives for toxicology of arsenic-contaminated freshwater

The Italian region Latium is characterized by extensive quaternary volcanic systems that contribute greatly to arsenic (As) contamination of freshwater, including drinking water supplies. However, knowledge of the possible toxic effects in these aquatic environments is, despite being highly relevant to public health, still limited. In this paper, we approach this issue using Gammarus elvirae, an amphipod species that inhabits rivers and streams in central Italy, including Latium. We explored the possibility of using G. elvirae in the toxicology of freshwater by addressing the most relevant issues. First, we tested the usefulness of hemocytes from G. elvirae in determining non-specific DNA damage by means of the Comet assay after exposure (24 h and 7 days) to different river water samples in Latium; second, we provided an interpretative overview of the usefulness of hepatopancreatic epithelial cells of G. elvirae as a means of assessing toxicity after long-term exposure to As and other pollutants; third, the LC (50-240 h) value for G. elvirae was estimated for arsenate, which is usually the dominant arsenic species in surface waters. Our study sheds light on G. elvirae at different levels, providing a background for future toxicological research of freshwater.

Contrasting effects of chloride on growth, reproduction, and toxicant sensitivity in two genetically distinct strains of Hyalella azteca

The strain of Hyalella azteca (Saussure: Amphipoda) commonly used for aquatic toxicity testing in the United States has been shown to perform poorly in some standardized reconstituted waters frequently used for other test species. In 10-d and 42-d experiments, the growth and reproduction of the US laboratory strain of H. azteca was shown to vary strongly with chloride concentration in the test water, with declining performance observed below 15 mg/L to 20 mg/L. In contrast to the chloride-dependent performance of the US laboratory strain of H. azteca, growth of a genetically distinct strain of H. azteca obtained from an Environment Canada laboratory in Burlington, Ontario, Canada, was not influenced by chloride concentration. In acute toxicity tests with the US laboratory strain of H. azteca, the acute toxicity of sodium nitrate increased with decreasing chloride in a pattern similar not only to that observed for control growth, but also to previous acute toxicity testing with sodium sulfate. Subsequent testing with the Burlington strain showed no significant relationship between chloride concentration and the acute toxicity of sodium nitrate or sodium sulfate. These findings suggest that the chloride-dependent toxicity shown for the US laboratory strain may be an unusual feature of that strain and perhaps not broadly representative of aquatic organisms as a whole.

Genetic diversity in Monoporeia affinis at polluted and reference sites of the Baltic Bothnian Bay

The amphipod Monoporeia affinis plays an important role in the Baltic Sea ecosystem as prey and as detritivore. The species is monitored for contaminant effects, but almost nothing is known about its genetics in this region. A pilot screening for genetic variation at the mitochondrial COI gene was performed in 113 individuals collected at six sites in the northern Baltic. Three coastal sites were polluted by pulp mill effluents, PAHs, and trace metals, and two coastal reference sites were without obvious connection to pollution sources. An off-coastal reference site was also included. Contaminated sites showed lower levels of genetic diversity than the coastal reference ones although the difference was not statistically significant. Divergence patterns measured as ΦST showed no significant differentiation within reference and polluted groups, but there was significant genetic divergence between them. The off-coastal sample differed significantly from all coastal sites and also showed lower genetic variation.

Identification of a putatively multixenobiotic resistance related Abcb1 transporter in amphipod species endemic to the highly pristine Lake Baikal

The fauna of Lake Baikal in Eastern Siberia, the largest freshwater body on Earth, is characterized by high degrees of biodiversity and endemism. Amphipods, a prominent taxon within the indigenous fauna, occur in an exceptionally high number of endemic species. Considering the specific water chemistry of Lake Baikal with extremely low levels of potentially toxic natural organic compounds, it seems conceivable that certain adaptions to adverse environmental factors are missing in endemic species, such as cellular defense mechanisms mitigating toxic effects of chemicals. The degree to which the endemic fauna is affected by the recently occurring anthropogenic water pollution of Lake Baikal may depend on the existence of such cellular defense mechanisms in those species. We here show that endemic amphipods express transcripts for Abcb1, a major component of the cellular multixenobiotic resistance (MXR) defense against toxic chemicals. Based on a partial abcb1 cDNA sequence from Gammarus lacustris, an amphipod species common across Northern Eurasia but only rarely found in Lake Baikal, respective homologous sequences were cloned from five amphipods endemic to Lake Baikal, Eulimnogammarus verrucosus, E. vittatus, E. cyaneus, E. marituji, and Gmelinoides fasciatus, confirming that abcb1 is transcribed in those species. The effects of thermal (25 °C) and chemical stress (1-2 mg L(-1) phenanthrene) in short-term exposures (up to 24 h) on transcript levels of abcb1 and heat shock protein 70 (hsp70), used as a proxy for cellular stress in the experiments, were exemplarily examined in E. verrucosus, E. cyaneus, and Gammarus lacustris. Whereas increases of abcb1 transcripts upon treatments occurred only in the Baikalian species E. verrucosus and E. cyaneus but not in Gammarus lacustris, changes of hsp70 transcript levels were seen in all three species. At least for species endemic to Lake Baikal, the data thus indicate that regulation of the identified amphipod abcb1 is triggered within the general cellular stress response. This is the first report presenting molecular data on a MXR transporter in amphipods, an ecotoxicologically important but with regard to gene sequence data comparatively little explored taxon.

Identification of the first neuropeptides from the Amphipoda (Arthropoda, Crustacea)

Despite being used as models in the field of ecotoxicology, including use in studies of endocrine disruption, little is known about the hormonal systems of amphipods, particularly their peptidergic signaling systems. Here, transcriptome shotgun assembly (TSA) sequences were used to predict the structures of the first neuropeptides from members of this crustacean order. Using a well-established workflow, BLAST searches of the extant amphipod TSA data were conducted for putative peptide-encoding transcripts. The pre/preprohormones deduced from the identified TSA sequences were then used to predict the mature structures of amphipod neuropeptides. In total, 43 putative peptide-encoding transcripts were identified from three amphipods, Echinogammarus veneris, Hyalella azteca and Melita plumulosa. Collectively, 139 distinct mature peptides (110 from E. veneris alone) were predicted from these TSA sequences. The identified peptides included members of the adipokinetic hormone/red pigment concentrating hormone, allatostatin A, allatostatin B, allatostatin C, bursicon α, bursicon β, crustacean hyperglycemic hormone, diuretic hormone 31, FLRFamide, molt-inhibiting hormone, myosuppressin, neuroparsin, neuropeptide F, orcokinin, pigment dispersing hormone (PDH), proctolin, RYamide, SIFamide, sulfakinin and tachykinin-related peptide families. Of particular note were the identifications of orcokinins possessing SFDEIDR- rather than the typical NFDEIDR- amino-termini, e.g. SFDEINRSNFGFN, a carboxyl-terminally amidated orcokinin, i.e. SFDEINRSNFGFSamide, PDHs longer than the stereotypical 18 amino acids, e.g. NSELLNTLLGSKSLAALRAAamide, and a 13 rather than 12 amino acid long SIFamide, i.e. GPYRKPPFNGSIFamide. These data not only provide the first descriptions of native amphipod neuropeptides, but also represent a new resource for initiating investigations of peptidergic signaling in the Amphipoda.

454 pyrosequencing-based analysis of gene expression profiles in the amphipod Melita plumulosa: transcriptome assembly and toxicant induced changes

Next generation sequencing using Roche's 454 pyrosequencing platform can be used to generate genomic information for non-model organisms, although there are bioinformatic challenges associated with these studies. These challenges are compounded by a lack of a standardized protocol to either assemble data or to evaluate the quality of a de novo transcriptome. This study presents an assembly of the control and toxicant responsive transcriptome of Melita plumulosa, an Australian amphipod commonly used in ecotoxicological studies. RNA was harvested from control amphipods, juvenile amphipods, and from amphipods exposed to either metal or diesel contaminated sediments. This RNA was used as the basis for a 454 based transcriptome sequencing effort. Sequencing generated 1.3 million reads from control, juvenile, metal-exposed and diesel-exposed amphipods. Different read filtering and assembly protocols were evaluated to generate an assembly that (i) had an optimal number of contigs; (ii) had long contigs; (iii) contained a suitable representation of conserved genes; and (iv) had long ortholog alignment lengths relative to the length of each contig. A final assembly, generated using fixed-length trimming based on the sequence quality scores, followed by assembly using the MIRA algorithm, produced the best results. The 26,625 contigs generated via this approach were annotated using Blast2GO, and the differential expression between treatments and control was determined by mapping with BWA followed by DESeq. Although the mapping generated low coverage, many differentially expressed contigs, including some with known developmental or toxicological function, were identified. This study demonstrated that 454 pyrosequencing is an effective means of generating reference transcriptome information for organisms, such as the amphipod M. plumulosa, that have no genomic information available in databases or in closely related sequenced species. It also demonstrated how optimization of read filtering protocols and assembly approaches changes the utility of results obtained from next generation sequencing studies, and establishes criteria to determine the quality of a de novo assembly in species lacking a reference genome. This new transcriptomic knowledge provides the genomic foundation for the creation of microarray and qPCR assays, serving as a reference transcriptome in future RNAseq studies, and allowing both the biology and ecotoxicology of this organism to be better understood. This approach will allow genomics-based methodology to be applied to a wider range of environmentally relevant species.

Vitellogenin is not an appropriate biomarker of feminisation in a crustacean

The expression of the yolk protein vitellogenin (Vtg) has been used as a biomarker of feminisation in multiple fish species throughout the world. Since the late 1990s, researchers have attempted to develop similar biomarkers to address whether reproductive endocrine disruption also occurs in the males of invertebrate groups such as the Crustacea. To date, the vast majority of studies investigating Vtg induction in male Crustacea have resulted in negative or inconclusive results, leading researchers to question the utility of Vtg expression as a biomarker in this taxon. This study measured the expression of Vtg genes in two intersex phenotypes (termed internal and external) found in the male amphipod, Echinogammarus marinus, and compared them with those of normal males and females. Males presenting the external intersex phenotype are infected with known feminising parasites and display a variety of feminised traits including oviduct structures on their testes and external female brood plates (oostegites). The internal intersex male phenotype, that displays a pronounced oviduct structure on the testes without the external intersex characteristics, is not parasite infected and it is thought to be a result of environmental contamination. Given their morphology, these phenotypes might be considered highly 'feminised' or 'de-masculinised' and can be utilised to test the suitability of feminisation biomarkers. The E. marinus transcriptome was searched for genes resembling Vtg and two sequences were revealed, that we subsequently refer to as Vtg1 and Vtg2. Results from a high-throughput transcriptomic sequencing screen of gonadal cDNA libraries suggested that very low expression (in this manuscript gene transcription is taken to represent gene expression, although it is acknowledged that in addition to transcription, translation, transcript processing, mRNA stability and protein stability can regulate gene expression) of Vtg1 and Vtg2 in normal males (ESTs=1 and 0 for Vtg1 and Vtg2, respectively), internal intersex males (ESTs=0 for both Vtg sequences) and external intersex males (ESTs=5 and 0 for Vtg1 and Vtg2, respectively). In contrast, the sequencing suggested notable levels of expression of both Vtg genes in females (ESTs=1133 and 84 for Vtg1 and Vtg2, respectively). Subsequent qPCR analysis validates these expression levels, with the signal for Vtg1 and Vtg2 transcripts in all male phenotypes being indistinguishable from that caused by contamination of trace levels of genomic DNA or the low-level amplification non-target sequences. These findings suggest that Vtg expression is not notably induced in highly feminised amphipods and is therefore not an appropriate biomarker of feminisation/de-masculination in crustaceans. We discuss our findings in the context of previous attempts to measure Vtg in male crustaceans and suggest a requirement for more appropriate taxon-specific biomarkers to monitor feminisation in these groups.

Dissolved and particulate copper exposure induces differing gene expression profiles and mechanisms of toxicity in the deposit feeding amphipod Melita plumulosa

Uptake of metals via ingestion is an important route of exposure for many invertebrates, and it has been suggested that the toxic response to metals accumulated via food differs from that of metals accumulated via the dissolved phase. To test this hypothesis, the deposit-feeding epibenthic amphipod Melita plumulosa was exposed to nontoxic or reproductively toxic concentrations of copper via the overlying water, via ingestion of sediment, or via a combination of the two. Rates of copper uptake from the two exposure routes were predicted using a biokinetic model. Gene expression profiles were measured via microarray analysis and confirmed via quantitative polymerase chain reaction. Differences in expression profiles were related to the exposure route more than to individual or combined rates of copper uptake. Chitinase and digestive protease transcript expression levels correlated to the copper uptake rate from sediment, rather than from the dissolved phase or combined total uptake rate. Overall, this study supports the hypothesis that metals accumulated via ingestion have a different mode of toxic action than metals taken up from water. Consequently, guidelines that only consider dissolved metal exposure, including equilibrium-partitioning-based guidelines, may underestimate the potential effects from deposited or resuspended metal-contaminated sediments.

Assessing mechanisms of toxicant response in the amphipod Melita plumulosa through transcriptomic profiling

This study describes the function of transcripts with altered abundance in the epibenthic amphipod, Melita plumulosa, following whole-sediment exposure to a series of common environmental contaminants. M. plumulosa were exposed for 48 h to sediments spiked and equilibrated with the following contaminants at concentrations predicted to cause sublethal effects to reproduction: porewater ammonia 30 mg L(-1); bifenthrin at 100 μg kg(-1); fipronil at 50 μg kg(-1); 0.6% diesel; 0.3% crude oil; 250 mg Cu kg(-1); 400 mg Ni kg(-1); and 400 mg Zn kg(-1). RNA was extracted and hybridized against a custom Agilent microarray developed for this species. Although the microarray represented a partial transcriptome and not all features on the array could be annotated, unique transcriptomic profiles were generated for each of the contaminant exposures. Hierarchical clustering grouped the expression profiles together by contaminant class, with copper and zinc, the petroleum products and nickel, and the pesticides each forming a distinct cluster. Many of the transcriptional changes observed were consistent with patterns previously described in other crustaceans. The changes in the transcriptome demonstrated that contaminant exposure caused changes in digestive function, growth and moulting, and the cytoskeleton following metal exposure, whereas exposure to petroleum products caused changes in carbohydrate metabolism, xenobiotic metabolism and hormone cycling. Functional analysis of these gene expression profiles can provide a better understanding of modes of toxic action and permits the prediction of mixture effects within contaminated ecosystems.

Screening differentially expressed genes in an amphipod (Hyalella azteca) exposed to fungicide vinclozolin by suppression subtractive hybridization

Vinclozolin, a dicarboximide fungicide, is an endocrine disrupting chemical that competes with an androgenic endocrine disruptor compound. Most research has focused on the epigenetic effect of vinclozolin in humans. In terms of ecotoxicology, understanding the effect of vinclozolin on non-target organisms is important. The expression profile of a comprehensive set of genes in the amphipod Hyalella azteca exposed to vinclozolin was examined. The expressed sequence tags in low-dose vinclozolin-treated and -untreated amphipods were isolated and identified by suppression subtractive hybridization. DNA dot blotting was used to confirm the results and establish a subtracted cDNA library for comparing all differentially expressed sequences with and without vinclozolin treatment. In total, 494 differentially expressed genes, including hemocyanin, heatshock protein, cytochrome, cytochrome oxidase and NADH dehydrogenase were detected. Hemocyanin was the most abundant gene. DNA dot blotting revealed 55 genes with significant differential expression. These genes included larval serum protein 1 alpha, E3 ubiquitin-protein ligase, mitochondrial cytochrome c oxidase, mitochondrial protein, proteasome inhibitor, hemocyanin, zinc-finger-containing protein, mitochondrial NADH-ubiquinone oxidoreductase and epididymal sperm-binding protein. Vinclozolin appears to upregulate stress-related genes and hemocyanin, related to immunity. Moreover, vinclozolin downregulated NADH dehydrogenase, related to respiration. Thus, even a non-lethal concentration of vinclozolin still has an effect at the genetic level in H. azteca and presents a potential risk, especially as it would affect non-target organism hormone metabolism.

Effect of test duration and feeding on relative sensitivity of genetically distinct clades of Hyalella azteca

The amphipod Hyalella azteca is widely used in ecotoxicology laboratories for the assessment of chemical risks to aquatic environments, and it is a cryptic species complex with a number of genetically distinct strains found in wild populations. While it would be valuable to note differences in contaminant sensitivity among different strains collected from various field sites, those findings would be influenced by acclimation of the populations to local conditions. In addition, potential differences in metabolism or lipid storage among different strains may confound assessment of sensitivity in unfed acute toxicity tests. In the present study, our aim was to assess whether there are genetic differences in contaminant sensitivity among three cryptic provisional species of H. azteca. Therefore, we used organisms cultured under the same conditions, assessed their ability to survive for extended periods without food, and conducted fed and unfed acute toxicity tests with two anions (nitrate and chloride) whose toxicities are not expected to be altered by the addition of food. We found that the three genetically distinct clades of H. azteca had substantially different responses to starvation, and the presence/absence of food during acute toxicity tests had a strong role in determining the relative sensitivity of the three clades. In fed tests, where starvation was no longer a potential stressor, significant differences in sensitivity were still observed among the three clades. In light of these differences in sensitivity, we suggest that ecotoxicology laboratories consider using a provisional species in toxicity tests that is a regionally appropriate surrogate.

The common ecotoxicology laboratory strain of Hyalella azteca is genetically distinct from most wild strains sampled in eastern North America

The amphipod Hyalella azteca is commonly used as a model for determining safe concentrations of contaminants in freshwaters. The authors sequenced the mitochondrial cytochrome c oxidase subunit I (COI) gene for representatives of 38 populations of this species complex from US and Canadian toxicology research laboratories and eastern North American field sites to determine their genetic relationships. With 1 exception, all US and Canadian laboratory cultures sampled were identified as conspecific. In 22 wild populations spanning 5 US states and 1 Canadian province, the commonly occurring laboratory species was found only in northern Florida, USA. Therefore, the diversity of the H. azteca species complex detected in the wild is not accurately represented in North American laboratories, questioning the reliability of H. azteca cultures currently in use to accurately predict the responses of wild populations in ecotoxicological assays. The authors also examined the utility of different COI nucleotide fragments presently in use to determine phylogenetic relationships in this group and concluded that saturation in DNA sequences leads to inconsistent relationships between clades. Amino acid sequences for COI were not saturated and may allow a more accurate phylogeny estimate. Hyalella azteca is crucial for developing water-quality regulations; therefore, laboratories should know and standardize the strain(s) they use to confidently compare toxicity tests across laboratories and determine whether they are an appropriate surrogate for their regions.

Can environment predict cryptic diversity? The case of Niphargus inhabiting Western Carpathian groundwater

In the last decade, several studies have shown that subterranean aquatic habitats harbor cryptic species with restricted geographic ranges, frequently occurring as isolated populations. Previous studies on aquatic subterranean species have implied that habitat heterogeneity can promote speciation and that speciation events can be predicted from species’ distributions. We tested the prediction that species distributed across different drainage systems and karst sectors comprise sets of distinct species. Amphipods from the genus Niphargus from 11 caves distributed along the Western Carpathians (Romania) were investigated using three independent molecular markers (COI, H3 and 28S). The results showed that: 1) the studied populations belong to eight different species that derive from two phylogenetically unrelated Niphargus clades; 2) narrow endemic species in fact comprise complexes of morphologically similar species that are indistinguishable without using a molecular approach. The concept of monophyly, concordance between mitochondrial and nuclear DNA, and the value of patristic distances were used as species delimitation criteria. The concept of cryptic species is discussed within the framework of the present work and the contribution of these species to regional biodiversity is also addressed.

Genetic and morphological divergences in the cosmopolitan deep-sea amphipod Eurythenes gryllus reveal a diverse abyss and a bipolar species

Eurythenes gryllus is one of the most widespread amphipod species, occurring in every ocean with a depth range covering the bathyal, abyssal and hadal zones. Previous studies, however, indicated the existence of several genetically and morphologically divergent lineages, questioning the assumption of its cosmopolitan and eurybathic distribution. For the first time, its genetic diversity was explored at the global scale (Arctic, Atlantic, Pacific and Southern oceans) by analyzing nuclear (28S rDNA) and mitochondrial (COI, 16S rDNA) sequence data using various species delimitation methods in a phylogeographic context. Nine putative species-level clades were identified within E. gryllus. A clear distinction was observed between samples collected at bathyal versus abyssal depths, with a genetic break occurring around 3,000 m. Two bathyal and two abyssal lineages showed a widespread distribution, while five other abyssal lineages each seemed to be restricted to a single ocean basin. The observed higher diversity in the abyss compared to the bathyal zone stands in contrast to the depth-differentiation hypothesis. Our results indicate that, despite the more uniform environment of the abyss and its presumed lack of obvious isolating barriers, abyssal populations might be more likely to show population differentiation and undergo speciation events than previously assumed. Potential factors influencing species' origins and distributions, such as hydrostatic pressure, are discussed. In addition, morphological findings coincided with the molecular clades. Of all specimens available for examination, those of the bipolar bathyal clade seemed the most similar to the 'true' E. gryllus. We present the first molecular evidence for a bipolar distribution in a macro-benthic deep-sea organism.

Hidden biodiversity in an ecologically important freshwater amphipod: differences in genetic structure between two cryptic species

Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species.

Phylogeny as a proxy for ecology in seagrass amphipods: which traits are most conserved?

Increasingly, studies of community assembly and ecosystem function combine trait data and phylogenetic relationships to gain novel insight into the ecological and evolutionary constraints on community dynamics. However, the key to interpreting these two types of information is an understanding of the extent to which traits are phylogenetically conserved. In this study, we develop the necessary framework for community phylogenetics approaches in a system of marine crustacean herbivores that play an important role in the ecosystem functioning of seagrass systems worldwide. For 16 species of amphipods and isopods, we (1) reconstructed phylogenetic relationships using COI, 16S, and 18S sequences and Bayesian analyses, (2) measured traits that are potentially important for assembling species between and within habitats, and (3) compared the degree to which each of these traits are evolutionarily conserved. Despite poor phylogenetic resolution for the order Amphipoda as a whole, we resolved almost all of the topology for the species in our system, and used a sampling of ultrametric trees from the posterior distribution to account for remaining uncertainty in topology and branch lengths. We found that traits varied widely in their degree of phylogenetic signal. Body mass, fecundity, and tube building showed very strong phylogenetic signal, and temperature tolerance and feeding traits showed much less. As such, the degree of signal was not predictable based on whether the trait is related to environmental filtering or to resource partitioning. Further, we found that even with strong phylogenetic signal in body size, (which may have large impacts on ecosystem function), the predictive relationship between phylogenetic diversity and ecosystem function is not straightforward. We show that patterns of phylogenetic diversity in communities of seagrass mesograzers could lead to a variety of interpretations and predictions, and that detailed study of trait similarities and differences will be necessary to interpret these patterns.

The maternal transcriptome of the crustacean Parhyale hawaiensis is inherited asymmetrically to invariant cell lineages of the ectoderm and mesoderm

BACKGROUND

The embryo of the crustacean Parhyale hawaiensis has a total, unequal and invariant early cleavage pattern. It specifies cell fates earlier than other arthropods, including Drosophila, as individual blastomeres of the 8-cell stage are allocated to the germ layers and the germline. Furthermore, the 8-cell stage is amenable to embryological manipulations. These unique features make Parhyale a suitable system for elucidating germ layer specification in arthropods. Since asymmetric localization of maternally provided RNA is a widespread mechanism to specify early cell fates, we asked whether this is also true for Parhyale. A candidate gene approach did not find RNAs that are asymmetrically distributed at the 8-cell stage. Therefore, we designed a high-density microarray from 9400 recently sequenced ESTs (1) to identify maternally provided RNAs and (2) to find RNAs that are differentially distributed among cells of the 8-cell stage.

RESULTS

Maternal-zygotic transition takes place around the 32-cell stage, i.e. after the specification of germ layers. By comparing a pool of RNAs from early embryos without zygotic transcription to zygotic RNAs of the germband, we found that more than 10% of the targets on the array were enriched in the maternal transcript pool. A screen for asymmetrically distributed RNAs at the 8-cell stage revealed 129 transcripts, from which 50% are predominantly expressed in the early embryonic stages. Finally, we performed knockdown experiments for two of these genes and observed cell-fate-related defects of embryonic development.

CONCLUSIONS

In contrast to Drosophila, the four primary germ layer cell lineages in Parhyale are specified during the maternal control phase of the embryo. A key step in this process is the asymmetric distribution of a large number of maternal RNAs to the germ layer progenitor cells.

Linkage of genomic biomarkers to whole organism end points in a Toxicity Identification Evaluation (TIE)

Aquatic organisms are exposed to many toxic chemicals and interpreting the cause and effect relationships between occurrence and impairment is difficult. Toxicity Identification Evaluation (TIE) provides a systematic approach for identifying responsible toxicants. TIE relies on relatively uninformative and potentially insensitive toxicological end points. Gene expression analysis may provide needed sensitivity and specificity aiding in the identification of primary toxicants. The current work aims to determine the added benefit of integrating gene expression end points into the TIE process. A cDNA library and a custom microarray were constructed for the marine amphipod Ampelisca abdita. Phase 1 TIEs were conducted using 10% and 40% dilutions of acutely toxic sediment. Gene expression was monitored in survivors and controls. An expression-based classifier was developed and evaluated against control organisms, organisms exposed to low or medium toxicity diluted sediment, and chemically selective manipulations of highly toxic sediment. The expression-based classifier correctly identified organisms exposed to toxic sediment even when little mortality was observed, suggesting enhanced sensitivity of the TIE process. The ability of the expression-based end point to correctly identify toxic sediment was lost concomitantly with acute toxicity when organic contaminants were removed. Taken together, this suggests that gene expression enhances the performance of the TIE process.

Differences in the sensitivity among cryptic lineages of the Gammarus fossarum complex

Lineages that are at least superficially morphologically identical but genetically distinct are usually misclassified as a single nominal species and, hence, belong to a cryptic species complex, as for example observed for Gammarus fossarum. Since genetic differentiation between cryptic lineages of the G. fossarum complex is comparable to an interspecific level, deviations in physiological and behavioral characteristics are conceivable. The present study investigates for the first time deviations in the sensitivity between two cryptic G. fossarum lineages - namely lineage A and lineage B. Two size classes of both cryptic lineages were exposed in six independent experiments to different concentrations of the fungicide tebuconazole or the insecticide thiacloprid (each n=20) for seven days. Feeding rate on leaf discs was used as a measure of sensitivity. By combining the outcome of all bioassays in a meta-analysis, cryptic lineage A showed - with an approximate 50% more pronounced decline in feeding - a significantly higher overall sensitivity compared to lineage B (n=17). This was also obvious, when each chemical stressor was considered individually; however, data were not significant for thiacloprid. Although other reasons, like land-use of habitats around sampling sites and physiological characteristics of organisms, could not be excluded as driving factors, the results indicate that affiliation to a cryptic lineage is a potential explanatory variable for the observed deviations in sensitivity. As the present study considered only one population for each cryptic lineage, a final conclusion cannot yet be drawn. Hence, it is recommended to investigate behavioral and physiological deviations between cryptic lineages of the G. fossarum complex in further studies.

Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod

The objective of this study was to investigate whether populations inhabiting a contaminated environment are affected in terms of decreased genetic diversity due to selection of tolerant genotypes and if such effect carries a cost. Marine arctic amphipod populations (Orchomenella pinguis) were collected from sites within a contaminated fjord, as well as from sites outside the fjord on the west-coast of Greenland over three years (2006-2008). Impacts on genetic diversity, effects on resilience such as development of tolerance and cost were determined. AFLP-analysis was used to explore within and between population genetic diversity, and exposure studies were performed where the populations were subjected to known and unknown stressors to assess resilience. Populations collected at three contaminated sites all had reduced genetic diversity in 2007 compared to populations outside the fjord. This pattern was different in 2008 as all contaminated site populations increased in diversity, whereas a decrease in diversity occurred at the outer sites. However, tolerance, but even more so, cost, was related to contamination exposure in 2008, in spite of the shift in genetic diversity. We suggest that contamination rapidly induces effects that can be captured as tolerance and associated cost, whereas effects on genetic diversity can be difficult to separate from recent migration events that dilute eventual decreases in diversity due to contamination pressure. As long as impacted populations can be influenced by migration events that increase the genetic diversity and add health to an affected population, populations in contaminated areas may have enhanced probability of survival.

Genetic population structure in the Antarctic benthos: insights from the widespread amphipod, Orchomenella franklini

Currently there is very limited understanding of genetic population structure in the Antarctic benthos. We conducted one of the first studies of microsatellite variation in an Antarctic benthic invertebrate, using the ubiquitous amphipod Orchomenella franklini (Walker, 1903). Seven microsatellite loci were used to assess genetic structure on three spatial scales: sites (100 s of metres), locations (1-10 kilometres) and regions (1000 s of kilometres) sampled in East Antarctica at Casey and Davis stations. Considerable genetic diversity was revealed, which varied between the two regions and also between polluted and unpolluted sites. Genetic differentiation among all populations was highly significant (F(ST) = 0.086, R(ST) = 0.139, p<0.001) consistent with the brooding mode of development in O. franklini. Hierarchical AMOVA revealed that the majority of the genetic subdivision occurred across the largest geographical scale, with N(e)m≈1 suggesting insufficient gene flow to prevent independent evolution of the two regions, i.e., Casey and Davis are effectively isolated. Isolation by distance was detected at smaller scales and indicates that gene flow in O. franklini occurs primarily through stepping-stone dispersal. Three of the microsatellite loci showed signs of selection, providing evidence that localised adaptation may occur within the Antarctic benthos. These results provide insights into processes of speciation in Antarctic brooders, and will help inform the design of spatial management initiatives recently endorsed for the Antarctic benthos.

High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies

Understanding the genetic and evolutionary basis of animal morphological diversity will require comparative developmental studies that use new model organisms. This necessitates development of tools for the study of genetics and also the generation of sequence information of the organism to be studied. The development of next generation sequencing technology has enabled quick and cost effective generation of sequence information. Parhyale hawaiensis has emerged as a model organism of choice due to the development of advanced molecular tools, thus P. hawaiensis genetic information will help drive functional studies in this organism.

Here we present a transcriptome and miRNA collection generated using next generation sequencing platforms. We generated approximately 1.7 million reads from a P. hawaiensis cDNA library constructed from embryos up to the germ band stage. These reads were assembled into a dataset comprising 163,501 transcripts.

Using the combined annotation of Annot8r and pfam2go, Gene Ontology classifications was assigned to 20,597 transcripts. Annot8r was used to provide KEGG orthology to our transcript dataset. A total of 25,292 KEGG pathway assignments were defined and further confirmed with reciprocal blast against the NCBI nr protein database. This has identified many P. hawaiensis gene orthologs of key conserved signalling pathways involved in development. We also generated small RNA sequences from P. hawaiensis, identifying 55 conserved miRNAs. Sequenced small RNAs that were not annotated by stringent comparison to mirBase were used to search the Daphnia pulex for possible novel miRNAs. Using a conservative approach, we have identified 51 possible miRNA candidates conserved in the Daphnia pulex genome, which could be potential crustacean/arthropod specific miRNAs. Our study presents gene and miRNA discovery in a new model organism that does not have a sequenced genome. The data provided by our work will be valuable for the P. hawaiensis community as well as the wider evolutionary developmental biology community.

Spatial distribution of cryptic species diversity in european freshwater amphipods (Gammarus fossarum) as revealed by pyrosequencing

In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C). We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany). A clear transition is observed from type A in the east (Danube and Po drainages) to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems). Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present.

Eocene habitat shift from saline to freshwater promoted Tethyan amphipod diversification

Current theory predicts that a shift to a new habitat would increase the rate of diversification, while as lineages evolve into multiple species, intensified competition would decrease the rate of diversification. We used Holarctic amphipods of the genus Gammarus to test this hypothesis. We sequenced four genes (5,088 bp) for 289 samples representing 115 Gammarus species. A phylogenetic analysis showed that Gammarus originated from the Tethyan region with a saline ancestry in the Paleocene, and later colonized the freshwater habitat in the Middle Eocene. Ancestral range reconstruction and diversification mode analysis combined with paleogeological and paleoclimatic evidence suggested that the habitat shift from saline to freshwater led to an increased diversification rate. The saline lineage of Gammarus dispersed to both sides of the Atlantic at 55 million years ago (Ma), because of the few barriers between the Tethys and the Atlantic, and diversified throughout its evolutionary history with a constant diversification rate [0.04 species per million years (sp/My)]. The freshwater Gammarus, however, underwent a rapid diversification phase (0.11 sp/My) until the Middle Miocene, and lineages successively diversified across Eurasia via vicariance process likely driven by changes of the Tethys and landmass. In particular, the freshwater Gammarus lacustris and Gammarus balcanicus lineages had a relatively high diversification shift, corresponding to the regression of the Paratethys Sea and the continentalization of Eurasian lands during the Miocene period. Subsequently (14 Ma), the diversification rate of the freshwater Gammarus decreased to 0.05 and again to 0.01 sp/My. The genus Gammarus provides an excellent aquatic case supporting the hypothesis that ecological opportunities promote diversification.