Simon Jarman

Genetic differentiation in the Antarctic coastal krill Euphausia crystallorophias.

The population genetics of the Antarctic neritic krill species Euphausia crystallorophias was examined by nucleotide sequence variation in its mitochondrial DNA. A 616 base pair region of the cytochrome c oxidase subunit I (COI) gene was screened for mutations by single-strand conformational polymorphism (SSCP) combined with restriction digestion. E. crystallorophias caught in three different regions of the Antarctic coastline were used – two samples from the Mertz Glacier Polynya and one sample each from the western side of the Antarctic Peninsula and from the Davis Sea. Significant genetic differences between krill samples were identified. However, the extent of these differences did not correlate with the degree of geographic separation between the sampling sites. This suggests that the genetic structuring may be the result of small-scale differentiation rather than differentiation between resident populations in separate parts of the Southern Ocean. The possibility that genetic differences between samples within a region are as important as differences between regions has implications for other studies of krill population genetics.

The base composition of the krill genome and its potential susceptibility to damage by UV-B

We have determined the base composition (percentage of guanine-cytosine base pairs, GC%) of total DNA from Euphausia superba to be 32% ± 0.5%. This is the lowest GC% recorded for a metazoan. Low GC% DNA has high concentrations of thymine (T) residues and consequently a greater abundance of adjacent T residues [T(n) arrays]. Ultraviolet B (280–320 nm, UV-B) radiation damages DNA primarily at (T)n arrays, so we suggest that krill DNA may be more susceptible to damage from increased levels of UV-B radiation over the Southern Ocean than the DNA of other Antarctic organisms.

Application of blocking oligonucleotides to improve signal-to-noise ratio in a PCR.

Universal or group-specific PCR primers have a tendency to predominately hybridise with the common sequences in samples with mixed templates. The result is that the rarer sequences are seldom retrieved by cloning or sequencing. The use of a blocking oligonucleotide (oligo) designed to specifically prevent amplification of dominant or unwanted DNA templates is an easy way to improve the amplification of rarer sequences. Here, we describe the different types of blocking principles and the different types of blocking oligos and give guidelines and examples of their application.

Simultaneous DNA-based diet analysis of breeding, non-breeding and chick Adélie penguins

As central place foragers, breeding penguins are restricted in foraging range by the need to return to the colony to feed chicks. Furthermore, breeding birds must balance energetic gain from self-feeding with the costs of returning to provision young. Non-breeding birds, however, are likely to be less restricted in foraging range and lack the high energy demands of provisioning, therefore may consume different prey to breeders. We used DNA dietary analysis to determine whether there was a difference in provisioning and self-feeding diet by identifying prey DNA in scat samples from breeding and chick Adélie penguins at two locations in East Antarctica. We also investigated diet differences between breeders and non-breeders at one site. Although previous work shows changing foraging behaviour between chick provisioning and self-feeding, our results suggest no significant differences in the main prey groups consumed by chicks and breeders at either site or between breeding stages. This may reflect the inability of penguins to selectively forage when provisioning, or resources were sufficient for all foraging needs. Conversely, non-breeders were found to consume different prey groups to breeders, which may reflect less restricted foraging ranges, breeders actively selecting particular prey during breeding or reduced foraging experience of non-breeders.

Variation in the Tyrosinase Gene Associated with a White Humpback Whale (Megaptera novaeangliae)

Tyrosinase-negative oculocutaneous albinism (OCA1A) is characterized by lifelong white hair and skin, a phenotype that has been described in most mammalian species worldwide. Tyrosinase is the key enzyme in melanin biosynthesis, and mutations in the tyrosinase gene result in OCA1A. We examined sequence variation at exon 1 of the tyrosinase gene in 66 humpback whale samples collected from the east coast of Australia, including an anomalously white humpback whale known as Migaloo. We identified 3 novel variants, including a cytosine deletion that results in a premature stop codon in exon 1. The deletion truncates the tyrosinase protein including the putative catalytic domains that are essential for tyrosinase enzymatic activity. Migaloo was homozygous for this deletion, suggesting that the albino phenotype is a consequence of inactive tyrosinase caused by the frameshift in the tyrosinase gene.

KrillDB: A de novo transcriptome database for the Antarctic krill (Euphausia superba)

Antarctic krill (Euphausia superba) is a key species in the Southern Ocean with an estimated biomass between 100 and 500 million tonnes. Changes in krill population viability would have catastrophic effect on the Antarctic ecosystem. One looming threat due to elevated levels of anthropogenic atmospheric carbon dioxide (CO2) is ocean acidification (lowering of sea water pH by CO2 dissolving into the oceans). The genetics of Antarctic krill has long been of scientific interest for both for the analysis of population structure and analysis of functional genetics. However, the genetic resources available for the species are relatively modest. We have developed the most advanced genetic database on Euphausia superba, KrillDB, which includes comprehensive data sets of former and present transcriptome projects. In particular, we have built a de novo transcriptome assembly using more than 360 million Illumina sequence reads generated from larval krill including individuals subjected to different CO2 levels. The database gives access to: 1) the full list of assembled genes and transcripts; 2) their level of similarity to transcripts and proteins from other species; 3) the predicted protein domains contained within each transcript; 4) their predicted GO terms; 5) the level of expression of each transcript in the different larval stages and CO2 treatments. All references to external entities (sequences, domains, GO terms) are equipped with a link to the appropriate source database. Moreover, the software implements a full-text search engine that makes it possible to submit free-form queries. KrillDB represents the first large-scale attempt at classifying and annotating the full krill transcriptome. For this reason, we believe it will constitute a cornerstone of future approaches devoted to physiological and molecular study of this key species in the Southern Ocean food web.

Genetic structure of Patagonian toothfish populations from otolith DNA

Abstract The Patagonian toothfish, Dissostichus eleginoides, is a valuable fishery species and has a discontinuous distribution across the Southern Ocean. Identification of the genetic stock structure of toothfish would allow evaluation of the suitability of the spatial scale at which fisheries management operates. Genetic subdivision seems likely given the species distribution. Population genetics studies of this species have been performed; however, they have been limited by sample size, spatial coverage and/or the type of markers investigated. As a potential solution, we developed methods for extracting toothfish DNA from otoliths that are available in large numbers from collections held at several research institutes. Genetic differentiation between the three oceanic sectors was investigated. Four mitochondrial and four nuclear markers with multiple single nucleotide polymorphisms were sequenced by high throughput sequencing for samples from six locations. Genetic differentiation was found between three sectors with nuclear markers. However, only the Pacific sector was differentiated from other sectors with mitochondrial markers. This study demonstrates the usefulness of otolith DNA as a means of increasing sample sizes for population genetics research of fish. Additionally, the combination of nuclear and mitochondrial markers may allow insight into how the observed differences in movements between male and female toothfish impact population structure.