Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections.

Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing and climate change. However, there is currently no cost-effective method for implementing population scale collection genomics for krill given its genome size (48 Gbp). Here, we assessed the utility of two inexpensive methods for population genetics using historical krill samples, specifically low-coverage shotgun sequencing (i.e. 'genome-skimming') and exome capture. Two full-length transcriptomes were generated and used to identify 166 putative gene targets for exome capture bait design. A total of 20 historical krill samples were sequenced using shotgun and exome capture. Mitochondrial and nuclear ribosomal sequences were assembled from both low-coverage shotgun and off-target of exome capture data demonstrating that endogenous DNA sequences could be assembled from historical collections. Although, mitochondrial and ribosomal sequences are variable across individuals from different populations, phylogenetic analysis does not identify any population structure. We find exome capture provides approximately 4500-fold enrichment of sequencing targeted genes, suggesting this approach can generate the sequencing depth required to call identify a significant number of variants. Unlocking historical collections for genomic analyses using exome capture, will provide valuable insights into past and present biodiversity, resilience and adaptability of krill populations to climate change.

Diversification, evolution and sub-functionalization of 70kDa heat-shock proteins in two sister species of antarctic krill: differences in thermal habitats, responses and implications under climate change.

BACKGROUND: A comparative thermal tolerance study was undertaken on two sister species of Euphausiids (Antarctic krills) Euphausia superba and Euphausia crystallorophias. Both are essential components of the Southern Ocean ecosystem, but occupy distinct environmental geographical locations with slightly different temperature regimes. They therefore provide a useful model system for the investigation of adaptations to thermal tolerance. METHODOLOGY/PRINCIPAL FINDING: Initial CTmax studies showed that E. superba was slightly more thermotolerant than E. crystallorophias. Five Hsp70 mRNAs were characterized from the RNAseq data of both species and subsequent expression kinetics studies revealed notable differences in induction of each of the 5 orthologues between the two species, with E. crystallorophias reacting more rapidly than E. superba. Furthermore, analyses conducted to estimate the evolutionary rates and selection strengths acting on each gene tended to support the hypothesis that diversifying selection has contributed to the diversification of this gene family, and led to the selective relaxation on the inducible C form with its possible loss of function in the two krill species. CONCLUSIONS: The sensitivity of the epipelagic species E. crystallorophias to temperature variations and/or its adaptation to cold is enhanced when compared with its sister species, E. superba. These results indicate that ice krill could be the first of the two species to be impacted by the warming of coastal waters of the Austral ocean in the coming years due to climate change.

The mitochondrial genomes of Euphausia pacifica and Thysanoessa raschii sequenced using 454 next-generation sequencing, with a phylogenetic analysis of their position in the Malacostracan family tree.

Euphausiid krill play a critical role in coastal and oceanic food webs, linking primary producers to upper trophic levels. In addition, some species support commercial fisheries worldwide. Despite their ecological importance, the genetics of these important species remain poorly described. To improve our understanding of the genetics of these ecological links, we sequenced the mitochondrial genomes of two species of North Pacific krill, Euphausia pacifica and Thysanoessa raschii, using long-range PCR and 454 GS Junior next-generation sequencing technology. The E. pacifica mitogenome (14,692 + base pairs (bp)) encodes 13 protein-coding genes (PCGs), two ribosomal RNA (rRNA) genes, and at least 22 transfer RNA (tRNA) genes. The T. raschii mitogenome (14,240 + bp) encodes 13 PCGs, two rRNA genes, and at least 19 tRNA genes. The gene order in both species is similar to that of E. superba. Comparisons between Bering Sea and Yellow Sea E. pacifica revealed a total of 644 variable sites. The most variable protein-coding gene were atp8 (7.55 %, 12 of 159 sites variable), nad4 (6.35 %, 85 variable sites) and nad6 (6.32 %, 33 variable sites). Phylogenetic analyses to assess the phylogenetic position of the Euphausiacea, using the concatenated nucleic acid sequences of E. pacifica and T. raschii along with 46 previously published malacostracan mitogenomes, support the monophyly of the order Decapoda and indicate that the Euphausiacea share a common ancestor with the Decapoda. Future research should utilize this sequence data to explore the population genetics and molecular ecology of these species.

The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats.

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL(1), trnL(2), and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of K(a)/K(s) in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 x 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda.

[Distribution of Euphausiid and Decapod larvae in the spring plankton of the southern Barents Sea].

New data have been obtained on the spatial distribution of the early developmental stages of Malacostraca in the mesozooplankton of the southern Barents Sea. In spring 2007, the euphausiid stages with the highest abundance (over 80%) were eggs and nauplii. Decapod larvae were represented by zoeae of Paralithodes camtschaticus, Paguruspubescens, and Hyas araneus; their abundance was at most 1.5% of total zooplankton abundance. The larvaton groups dominant by abundance were furciliae of Euphasiacea (14.5 +/- 6.2 mg/m3) and zoeae of P. camtschaticus (32.7 +/- 15.9 mg/m3). The size structure of larval hemipopulations was similar over the studied water area. Comparison with data on the larval body length obtained in other areas of the sea leads to a conclusion on the independence of the decapod groups of Eastern and Western Murman.

An introduction to the biology of Northern krill (Meganyctiphanes norvegica Sars).

This chapter provides a background to research on Northern krill biology, starting with a description of its morphology and identifying features, and the historical path to its eventual position as a single-species genus. There is a lack of any euphausiid fossil material, so phylogenetic analysis has relied on comparative morphology and ontogeny and, more recently, genetic methods. Although details differ, the consensus of these approaches is that Meganyctiphanes is most closely related to the genus Thysanoessa. The light organs (or photophores) are well developed in Northern krill and the control of luminescence in these organs is described. A consideration of the distribution of the species shows that it principally occupies shelf and slope waters of both the western and eastern coasts of the North Atlantic, with a southern limit at the boundary with sub-tropical waters (plus parts of the Mediterranean) and a northern limit at the boundary with Arctic water masses. Recent evidence of a northward expansion of these distributional limits is considered further. There have been a variety of techniques used to sample and survey Northern krill populations for a variety of purposes, which this chapter collates and assesses in terms of their effectiveness. Northern krill play an important ecological role, both as a contributor to the carbon pump through the transport of faecal material to the deeper layers, and as a key prey item for groundfish, squid, baleen whales, and seabirds. The commercial exploitation of Northern krill has been slow to emerge since its potential was considered by Mauchline [Mauchline, J (1980). The biology of mysids and euphausiids. Adv. Mar. Biol. 18, 1-681]. However, new uses for products derived from krill are currently being found, which may lead to a new wave of exploitation.

A DNA-based method for identification of krill species and its application to analysing the diet of marine vertebrate predators.

Accurate identification of species that are consumed by vertebrate predators is necessary for understanding marine food webs. Morphological methods for identifying prey components after consumption often fail to make accurate identifications of invertebrates because prey morphology becomes damaged during capture, ingestion and digestion. Another disadvantage of morphological methods for prey identification is that they often involve sampling procedures that are disruptive for the predator, such as stomach flushing or lethal collection. We have developed a DNA-based method for identifying species of krill (Crustacea: Malacostraca), an enormously abundant group of invertebrates that are directly consumed by many groups of marine vertebrates. The DNA-based approach allows identification of krill species present in samples of vertebrate stomach contents, vomit, and, more importantly, faeces. Utilizing samples of faeces from vertebrate predators minimizes the impact of dietary studies on the subject animals. We demonstrate our method first on samples of Adelie penguin (Pygoscelis adeliae) stomach contents, where DNA-based species identification can be confirmed by prey morphology. We then apply the method to faeces of Adelie penguins and to faeces of the endangered pygmy blue whale (Balaenoptera musculus brevicauda). In each of these cases, krill species consumed by the predators could be identified from their DNA present in faeces or stomach contents.

[Euphausiids (Crustacea: Melacostraca) from the southern Mexican Caribbean Sea]. / Eufáusidos (Crustacea: Malacostraca) del centro y sur del Mar Caribe mexicano.

The composition, abundance and distribution of euphausiids from the southern part of the Mexican Caribbean Sea (August 1986) were sampled during the ARCOMM I cruise on board the R/V "Justo Sierra" of UNAM. Sampling was done using a Bongo-net (0.5 mm mesh size) performing oblique hauls from 200 m to the surface at 28 stations. Of the total euphausiid numbers, the most abundant species was Stylocheiron carinatum (49%), followed by Euphausia americana (9.8%) and E. tenera with (7.8%). The highest total density and that of the three most abundant species occurred during the night sampling, and probably was related to vertical migration patterns. The Bray-Curtis index revealed three station assemblages, related to the day-night variations of the euphausiid community. Species were distributed mainly in the oceanic area, and were absent in the neritic zones. The local fauna shows a strong affinity for the euphausiid community of the Gulf of Mexico and other areas of the Caribbean Sea. Four species are considered to be new records for the western Caribbean Sea.