Organization of the Mitochondrial Genome of Antarctic Krill <Emphasis Type="Italic">Euphausia superba</Emphasis> (Crustacea: Malacostraca)

We determined the nearly complete DNA sequence of the mitochondrial genome of Antarctic krill Euphausia superba (Crustacea: Malacostraca), one of the most ecologically and commercially important zooplankters in Antarctic waters. All of the genome sequences were purified by gene amplification using long polymerase chain reaction (PCR), and the products were subsequently used as templates for either direct sequencing using a primer-walking strategy or nested PCR with crustacea-versatile primers. Although we were unable to determine a portion of the genome owing to technical difficulties, the sequenced position, 14,606 bp long, contained all of the 13 protein-coding genes, 19 of the 22 transfer RNA genes, and the large subunit as well as a portion of the small subunit ribosomal RNA genes. Gene rearrangement was observed for 3 transfer RNA genes (tRNA^Cys, tRNA^Tyr, and tRNA^Trp) and the 2 leucine tRNA genes.     

The mitochondrial genome of <Emphasis Type="Italic">Euphausia superba</Emphasis> (Prydz Bay) (Crustacea: Malacostraca: Euphausiacea) reveals a novel gene arrangement and potential molecular markers

Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. In this paper, we described the gene organization, gene rearrangement and codon usage in the mitochondrial genome of Euphausia superba Dana 1852 (sampling from Prydz Bay, PB). The mitochondrial genome of E. superba is more than 15,498 bp in length (partial non-coding region was not determined). Translocation of four tRNAs (trnL ₁ , trnL ₂ , trnW and trnI) and duplication of one tRNA (trnN) were founded in the mitochondrial genome of E. superba when comparing its genome with the pancrustacean ground pattern. To investigate the phylogenetic relationship within Malacostraca, phylogenetic trees based on currently available malacostracan mitochondrial genomes were built with the maximum likelihood and the Bayesian models. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, and Brachyura, which is consistent with previous research. However, the taxonomic position of Euphausiacea within Malacostraca is unstable. From comparing the mitochondrial genome between E. superba (PB) and E. superba (sampling from Weddell Sea, WS), we found that nad2 gene contains maximal variation with 61 segregating sites, following by nad5 gene which has 12 segregating sites. Thus, nad2 and nad5 genes may be used as potential molecular markers to study the inherit diversity among different E. superba groups, which would be helpful to the exploitation and management of E. superba resources.     

Genetic variation and population structure of krill (Euphausia superba) in the Atlantic sector of Antarctic waters and off the Antarctic peninsula

Summary Samples of Antarctic krill Euphausia superba from 16 locations in the Weddell Sea, Scotia Sea and on the west coast of the Antarctic Peninsula were analysed for protein variation using enzyme electrophoresis techniques. Analysis of allele distributions indicate that samples from all locations are part of a single breeding population of krill. Significant departures from random mating expectations were observed in the distribution of electrophoretic phenotypes of the enzymes esterase and glucose phosphate isomerase. Possible explorations of these results are advanced, but they do not materially affect conclusions concerning population structure. The spatial and temporal distribution of electrophoretically detected genetic variation in Atlantic and Pacific sector krill stocks is discussed by comparing the results of this study with those of previous authors working with E. superba.     

Genetic variation and population structure of krill (Euphausia superba dana) from the Prydz Bay region of Antarctic waters

Summary Samples of Antarctic krill E. superba from six locations near Prydz Bay were analysed electrophoretically to detect genetically-based protein variation. Analyses of allele distributions at four polymorphic loci indicate no evidence of significant heterogeneity, a result consistent with the hypothesis that all samples were derived from a single breeding population of krill. The results of this study agree closely with genetic data from other studies on krill in the Atlantic sector of the Southern Ocean, suggesting that krill stocks over at least 6000 km of Antarctic waters are derived from a single interbreeding population.     

Sequence analysis of ribosomal and mitochondrial genes of the giant liver fluke Fascioloides magna (Trematoda: Fasciolidae): intraspecific variation and differentiation from Fasciola hepatica

Complete sequences of ribosomal and mitochondrial genes of the giant liver fluke Fascioloides magna are presented. In particular, small subunit (18S) and internal transcribed spacers (ITS1 and ITS2) of the ribosomal gene (rDNA), as well as cytochrome c oxidase subunit I (cox1) and nicotinamide dehydrogenase subunit I (nad1) of the mitochondrial DNA (mtDNA), were analyzed. The 18S and ITS sequences were compared with previously published sequences of the liver fluke Fasciola hepatica. Fixed interspecific genetic differences were determined that allow molecular differentiation of F. magna and F. hepatica using either the PCR-RFLP method or PCR amplification of species-specific DNA regions. Additionally, intraspecific sequence polymorphism of the complete cox1 and nad1 mitochondrial genes in geographically distinct F. magna populations was determined. Based on the sequence divergences, short (< 500 bp) variable regions suitable for broader biogeographical studies of giant liver fluke were designed.     

UTILITY OF THE MITOCHONDRIAL nad4L GENE FOR ALGAL AND PROTISTAN PHYLOGENETIC ANALYSIS1

Mitochondrial gene sequences, in contrast to their plastid counterparts, have been rarely exploited for use in determining algal phylogenetic relationships. Their utilization would prove advantageous particularly for the assessment of evolutionary relationships among protistan lineages that include photo synthetic species and their colorless heterotrophic dependents that contain only a reduced plastid genome as well as ancestral nonphotosynthetic relatives. Recent studies that have examined mitochondrial protein (coxl, cox2, cob, and nad5) rather than ribosomal RNA genes confirm that these algal sequences are sufficiently conserved to be used routinely in algal systematics. In this investigation, we sequenced the mitochondrial nad4L gene, encoding a small (ca. 99-amino acid) polypeptide subunit of the NADH dehydrogenase complex, from two chromophytic algae and an oomycete to determine its suitability for use in determining algal and protistan evolutionary relationships. Our analysis demonstrated that nad4L could clearly resolve these three organisms as a distinct clade, the stramenopiles, to the exclusion of terrestrial plants/chlorophytes and eufungi. However, the position of deeply rooted species within the stramenopiles proved tenuous and would best be examined in conjunction with the analysis of longer mitochondrial protein gene sequences.     

The complete mitochondrial genome of Tuta absoluta (Lepidoptera: Gelechiidae) and genetic variation in two newly invaded populations in China

Tuta absoluta (Meyrick) (Lepidoptera: Gelechiidae) is a devastating invasive pest worldwide, causing severe damage to tomatoes. Recently, it has been recorded in the northwestern and southwestern parts of China. Here, the mitogenomes and genetic variation of two newly invaded T. absoluta populations in Xinjiang and Yunnan, were determined. The results showed that the complete mitogenome size of T. absoluta is 15298 bp for the individual from Xinjiang and 15296 bp for the individual from Yunnan, which were both longer than the reported mitogenome from Spain (15290 bp). The mitogenome sequences of individuals collected from three locations showed high levels of sequence similarity, except for 8 polymorphic sites, which were in genes cox2 (1 site), cox3 (2 sites), cob (1 site), atp6 (1 site), nad1 (2 sites) and nad5 (1 site). Tuta absoluta mitogenomes share many features with other 6 Gelechiidae mitogenomes, except for several differences in the start and stop codons of protein-coding genes and the length of intergenic spacers. Seven partial mitochondrial genes (cox1, cox2, cox3, atp6, cob, nad1, and nad5) were used for genetic variation analysis, and significant population differentiation was found between the two populations based on cox2, atp6, nad1, and nad5. The complete mitogenomes and sensitive mitochondrial gene markers reported here provide useful data for further population genetics study of this pest.     

The mitochondrial genome of the thermal dimorphic fungus Penicillium marneffei is more closely related to those of molds than yeasts

We report the complete sequence of the mitochondrial genome of Penicillium marneffei, the first complete mitochondrial DNA sequence of a thermal dimorphic fungus. This 35 kb mitochondrial genome contains the genes encoding ATP synthase subunits 6, 8, and 9 (atp6, atp8, and atp9), cytochrome oxidase subunits I, II, and III (cox1, cox2, and cox3), apocytochrome b (cob), reduced nicotinamide adenine dinucleotide ubiquinone oxireductase subunits (nad1, nad2, nad3, nad4, nad4L, nad5, and nad6), ribosomal protein of the small ribosomal subunit (rps), 28 tRNAs, and small and large ribosomal RNAs. Analysis of gene contents, gene orders, and gene sequences revealed that the mitochondrial genome of P. marneffei is more closely related to those of molds than yeasts.     

The Mitochondrial Genome of Chlorogonium elongatum Inferred from the Complete Sequence

The 22,704-bp circular mitochondrial DNA (mtDNA) of the chlamydomonad alga Chlorogonium elongatum was completely cloned and sequenced. The genome encodes seven proteins of the respiratory electron transport chain, subunit 1 of the cytochrome oxidase complex (cox1), apocytochrome b (cob), five subunits of the NADH dehydrogenase complex (nad1, nad2, nad4, nad5, and nad6), a set of three tRNAs (Q, W, M), and the large (LSU)- and small (SSU)-subunit ribosomal RNAs. Six group-I introns were found, two each in the cox1, cob, and nad5 genes. In each intron an open reading frame (ORF) related to maturases or endonucleases was identified. Both the LSU and the SSU rRNA genes are split into fragments intermingled with each other and with other genes. Although the average A + T content is 62.2%, GC-rich clusters were detected in intergenic regions, in variable domains of the rRNA genes, and in introns and intron-encoded ORFs. A comparison of the genome maps reveals that C. elongatum and Chlamydomonas eugametos mtDNAs are more closely related to one another than either is to Chlamydomonas reinhardtii mtDNA. Received: 3 November 1997 / Accepted: 12 January 1998     

Divergent ecological histories of two sister Antarctic krill species led to contrasted patterns of genetic diversity in their heat‐shock protein (hsp70) arsenal

The Arctic and the Antarctic Peninsula are currently experiencing some of the most rapid rates of ocean warming on the planet. This raises the question of how the initial adaptation to extreme cold temperatures was put in place and whether or not directional selection has led to the loss of genetic variation at key adaptive systems, and thus polar species’ (re)adaptability to higher temperatures. In the Southern Ocean, krill represents the most abundant fauna and is a critical member at the base of the Antarctic food web. To better understand the role of selection in shaping current patterns of polymorphisms, we examined genetic diversity of the cox‐1 and hsp70 genes by comparing two closely related species of Euphausiid that differ in ecology. Results on mtcox‐1 agreed with previous studies, indicating high and similar effective population sizes. However, a coalescent‐based approach on hsp70 genes highlighted the role of positive selection and past demographic changes in their recent evolution. Firstly, some form of balancing selection was acting on the inducible isoform C, which reflected the maintenance of an ancestral adaptive polymorphism in both species. Secondly, E. crystallorophias seems to have lost most of its hsp70 diversity because of a population crash and/or directional selection to cold. Nonsynonymous diversities were always greater in E. superba, suggesting that it might have evolved under more heterogeneous conditions. This can be linked to species’ ecology with E. superba living in more variable pelagic conditions, while E. crystallorophias is strictly associated with continental shelves and sea ice.     

Genetic homogeneity of krill (Euphausia superba Dana) in the Southern Ocean

Summary Development of a comprehensive picture of the genetic population structure of the Antarctic krill (Euphausia superba) has been hampered by a lack of genetic data from two major areas of the species' distribution, the Bellingshausen Sea and the Ross Sea. Evidence from earlier studies of a discrete Bellingshausen Sea population was based on anomalous allele frequencies in two sample sets that were collected near the west coast of the Antarctic Peninsula rather than in the Bellingshausen Sea proper. In this paper we describe the first biochemical genetic data obtained on krill from the central Bellingshausen Sea and from the Ross Sea. Analyses of eight polymorphic loci in samples from these two areas have failed to provide any evidence of population structuring within the Pacific sector of the Southern Ocean, and have indicated that Pacific sector krill cannot be genetically discriminated from Atlantic sector krill or Indian Ocean sector krill. These findings further support the hypothesis of a single circumpolar breeding population of Antarctic krill.     

Krill maintenance and experimentation at the australian antarctic division

Live Antarctic krill, Euphausia superba, have been maintained for experimental purposes at the Australian Antarctic Division since 1981. This population has been replenished on an annual basis with animals taken from the wild. Techniques used to capture and maintain live krill are discussed here, with particular reference given to the development of systems for their maintenance. Details are also provided for specific experimental systems that have been used to conduct research into the behaviour and physiology of krill both at-sea and in shore-based laboratories.     

Food and feeding ecology of emperor penguins in the eastern Weddell Sea

Summary The diet of the emperor penguin Aptenodytes forsteri in the eastern Weddell Sea, Antarctica was studied during October and November 1986 by stomach content analysis. Emperor penguins fed mainly on Antarctic krill Euphausia superba, Antarctic silverfish Pleuragramma antarcticum and squid Psychroteuthis glacialis. Benthic prey was not found. The prey composition suggests two different feeding strategies, shallow dives exploring the rugged underside of sea ice where krill is taken, and deep dives when mesopelagic fish and squid are consumed. Chicks were fed on average every 1.44 days.     

Feeding ecology of Antarctic fur seals at Cape Shirreff,South Shetlands,Antarctica

This study examined the diet of Antarctic fur seals, Arctocephalus gazella, from an active breeding colony at Cape Shirreff (62°28S, 60°48W), Livingston Island, South Shetland Archipelago, Antarctica. It analysed faecal samples from five consecutive years (1997–2001) and length distribution of krill taken by trawl nets in the vicinity of Livingston Island. Antarctic krill, Euphausia superba, was the most frequent prey item, followed by several myctophid species (Gymnoscopelus nicholsi, Electrona antarctica and Electrona carlsbergi), squid and penguin remains. From 1998 to 2001, a modal progression in krill size was evident, suggesting that A. gazella was depending on a strong krill cohort, at least over the study period. Analysis of size distribution and size selectivity of krill preyed upon by fur seals suggests a preference for larger krill (>34 mm), despite the broader size range of preys items available.     

Antarctic krill population genomics: apparent panmixia,but genome complexity and large population size muddy the water

Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA‐based analyses have focused on a limited number of markers and have covered only part of their circum‐Antarctic range. We used mitochondrial DNA and restriction site‐associated DNA sequencing (RAD‐seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD‐seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD‐seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.     

Tetrahymena australis (Protozoa,Ciliophora): A Well‐Known But “Non‐Existing” Taxon – Consideration of Its Identification,Definition and Systematic Position

A cryptic species of the Tetrahymena pyriformis complex, Tetrahymena australis, has been known for a long time but never properly diagnosed based on taxonomic methods. The species name is thus invalid according to the International Code of Zoological Nomenclature. Recently, a population isolated from a freshwater lake in Wuhan, China was investigated using live observations, silver staining methods and gene sequence data. This organism can be separated from other described species of the T. pyriformis complex by its relatively small body size, the number of somatic kineties and differences in sequences of two genes, namely the small subunit ribosomal RNA (SSU rRNA) and the mitochondrial cytochrome c oxidase subunit I (cox1). We compared the SSU rRNA gene sequences of all available Tetrahymena species to reveal the nucleotide differences within this genus. The sequence of the Wuhan population is identical to two sequences of a previously isolated strain of T. australis (ATCC #30831). Phylogenetic analyses indicate that these three sequences (X56167, M98015, KT334373) cluster with Tetrahymena shanghaiensis (EF070256) in a polytomy. However, sequence divergence of the cox1 gene between the Wuhan population and another strain of T. australis (ATCC #30271) is 1.4%, suggesting that these may represent different subspecies.     

The mitochondrial DNA of Dictyostelium discoideum: complete sequence, gene content and genome organization

We present an overview of the gene content and organization of the mitochondrial genome of Dictyostelium discoideum. The mitochondria genome consists of 55,564 bp with an A + T content of 72.6%. The identified genes include those for two ribosomal RNAs (rnl and rns), 18 tRNAs, ten subunits of the NADH dehydrogenase complex (nad1, 2, 3, 4, 4L, 5, 6, 7, 9 and 11), apocytochrome b (cytb), three subunits of the cytochrome oxidase (cox1/2 and 3), four subunits of the ATP synthase complex (atp1, 6, 8 and 9), 15 ribosomal proteins, and five other ORFs, excluding intronic ORFs. Notable features of D. discoideum mtDNA include the following. (1) All genes are encoded on the same strand of the DNA and a universal genetic code is used. (2) The cox1 gene has no termination codon and is fused to the downstream cox2 gene. The 13 genes for ribosomal proteins and four ORF genes form a cluster 15.4 kb long with several gene overlaps. (3) The number of tRNAs encoded in the genome is not sufficient to support the synthesis of mitochondrial protein. (4) In total, five group I introns reside in rnl and cox1/2, and three of those in cox1/2 contain four free-standing ORFs. We compare the genome to other sequenced mitochondrial genomes, particularly that of Acanthamoeba castellanii. Received: 5 July 1999 / Accepted: 17 January 2000     

The biology of the spiny icefish <Emphasis Type="Italic">Chaenodraco wilsoni</Emphasis> Regan, 1914

The most abundant ice fish species observed in catches off the northern tip of the Antarctic Peninsula in the last 25–30 years has been the spiny ice fish Chaenodraco wilsoni Regan 1914. C. wilsoni has been exploited on a commercial scale from the late 1970s to the end of the 1980s off Joinville–D’Urville Islands (CCAMLR Statistical Subarea 48.1) and in the Cosmonauts and Cooperation Seas and Prydz Bay in the Indian Ocean sector (CCAMLR Statistical Division 58.4.2). This paper presents new information on biological features and life history characteristics of C. wilsoni, based on research survey collections along the northern Antarctic Peninsula in 2006 and 2007 and samples taken in the commercial fishery in 1987. Length frequency compositions from the research surveys demonstrated that fish 21–34 cm long predominated in the catches. Sexual maturity is attained at 24–25 cm. Absolute fecundity and relative fecundity is low (1,000–2,500 eggs; 6–12 eggs). Oocyte diameter varied from 4.0 to 4.9 mm very close to spawning. Spawning at the tip of the Antarctic Peninsula is likely to occur in October–November. Remotely operated vehicle deployments in the northern Weddell Sea demonstrated that C. wilsoni exhibit parental nest guarding where males protect the eggs. The incubation period is likely to be 8 months long. Fish feed primarily on Antarctic krill (Euphausia superba) in the Antarctic Peninsula region and in the Cosmonauts and Cooperation Seas while fish take ice krill (Euphausia crystallorophias), Pleuragramma antarcticum and myctophids to some extent in other areas. Age determination still awaits validation. Preliminary ageing attempts suggested a maximum age of about 8–10 years.