Arctic charr brain transcriptome strongly affected by summer seasonal growth but only subtly by feed deprivation.

BACKGROUND: The Arctic charr (Salvelinus alpinus) has a highly seasonal feeding cycle that comprises long periods of voluntary fasting and a short but intense feeding period during summer. Therefore, the charr represents an interesting species for studying appetite-regulating mechanisms in fish. RESULTS: In this study, we compared the brain transcriptomes of fed and feed deprived charr over a 4 weeks trial during their summer feeding season. Despite prominent differences in body condition between fed and feed deprived charr at the end of the trial, feed deprivation affected the brain transcriptome only slightly. In contrast, the transcriptome differed markedly over time in both fed and feed deprived charr, indicating strong shifts in basic cell metabolic processes possibly due to season, growth, temperature, or combinations thereof. The GO enrichment analysis revealed that many biological processes appeared to change in the same direction in both fed and feed deprived fish. In the feed deprived charr processes linked to oxygen transport and apoptosis were down- and up-regulated, respectively. Known genes encoding for appetite regulators did not respond to feed deprivation. Gene expression of Deiodinase 2 (DIO2), an enzyme implicated in the regulation of seasonal processes in mammals, was lower in response to season and feed deprivation. We further found a higher expression of VGF (non-acronymic) in the feed deprived than in the fed fish. This gene encodes for a neuropeptide associated with the control of energy metabolism in mammals, and has not been studied in relation to regulation of appetite and energy homeostasis in fish. CONCLUSIONS: In the Arctic charr, external and endogenous seasonal factors for example the increase in temperature and their circannual growth cycle, respectively, evoke much stronger responses in the brain than 4 weeks feed deprivation. The absence of a central hunger response in feed deprived charr give support for a strong resilience to the lack of food in this high Arctic species. DIO2 and VGF may play a role in the regulation of energy homeostasis and need to be further studied in seasonal fish.

Complete mitochondrial genome of clearhead icefish Protosalanx hyalocranius (Salmoniformes: Salangidae).

In this study, we sequenced and determined the complete mitochondrial genome of clearhead icefish (Protosalanx hyalocranius). The circular mitochondrial genome (16,693 bp) contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. All genes were encoded on the heavy strand with the exception of ND6 and eight tRNA genes.

Complete mitochondrial genome of Chinese icefish Neosalanx tangkahkeiis (Salmoniformes, Salangidae): comparison reveals Neosalanx taihuensis not a valid name.

The complete mitochondrial genome of Neosalanx tangkahkeiis was determined to be 16,550 bp in length with (A+T) content of 49.7%, and it consists of 13 protein-coding genes, 22 tRNAs, 2 ribosomal RNAs, and a control region. The gene composition and the structural arrangement of the N. tangkahkeiis complete mtDNA were identical to most of other vertebrates. The sequence comparison showed that mitogenome of N. tangkahkeiis had a 99.9% of similarity with so-called N. taihuensis, indicating they are the same species and N. taihuensis is not a valid name.

Genetic analysis of threatened Australian grayling Prototroctes maraena suggests recruitment to coastal rivers from an unstructured marine larval source population.

Population genetic variation of Australian grayling Prototroctes maraena was examined to determine whether the dispersal strategy of this amphidromous species favours retention of larvae and juveniles in close proximity to their natal river, or mixing of populations via marine dispersal. Variation in microsatellite and mitochondrial DNA markers was unstructured and differentiation was indistinguishable from zero across four coastal rivers spanning approximately one-quarter of the continental range of the species. This result indicates that the marine larval and juvenile phase probably facilitates extensive gene flow among coastal rivers and agrees with a previous analysis of otolith chemistry that suggested larvae probably move into the sea rather than remain in estuaries. It appears likely that the dispersal strategy of P. maraena would enable recolonization of rivers that experience localized extinction provided that connectivity between freshwater habitats and the sea is sufficient to permit migration and that enough source populations remain intact to support viability of the wider population.

Phylogenetic position of the enigmatic Lepidogalaxias salamandroides with comment on the orders of lower euteleostean fishes.

This study examines phylogenetic placement of the enigmatic Western Australian Lepidogalaxias, and extends previous studies by including eight new taxa to enable re-examination phylogenetic relationships of lower euteleostean fishes at the ordinal level, based on mitochondrial genomes from 39 ingroup taxa and 17 outgroups. Our results suggest that Lepidogalaxias occupies a basal position among all euteleosts, in contrast with earlier hypotheses that variously suggested a closer relationship to esocid fishes, or to the galaxiid Lovettia. In addition our evidence shows that Osmeriformes should be restricted Retropinnidae, Osmeridae, Plecoglossidae and Salangidae. This reduced Osmeriformes is supported in our results as the sister group of Stomiiformes. Galaxiidae, which is often closely linked to Osmeriformes, emerges as sister group of a combined Osmeriformes, Stomiiformes, Salmoniformes, Esociformes and Argentiformes, and we give Galaxiiformes the rank of order to include all remaining galaxioid fishes (Galaxias and allied taxa, Aplochiton and Lovettia). Our results also support a sister group relationship between Salmoniformes and Esociformes, which are together the sister group of Argentiniformes.

Retroposons of salmonoid fishes (Actinopterygii: Salmonoidei) and their evolution.

Short and long retroposons, or non-LTR retrotransposons (SINEs and LINEs, respectively) are two groups of interspersed repetitive elements amplifying in the genome via RNA and cDNA-mediated reverse transcription. In this process, SINEs entirely depend on the enzymatic machinery of autonomous LINEs. The impact of retroposons on the host genome is difficult to overestimate: their sequences account for significant portion of the eukaryotic genome, while propagation of their active copies gradually reshapes it. In this way, the retropositional activity plays a role of important evolutionary factor. More than 100 LINE and nearly 100 SINE families have been described to date from the genomes of various eukaryotes, and it is salmonoid fishes (Actinopterygii: Salmonoidei) that are particularly noticeable for the diversity of transposons they host in their genomes, including two LINE and seven SINE families. Moreover, this group of ray-finned fish represents an excellent opportunity to study such a rare evolutionary phenomenon as lateral gene transfer, due to a great variety of transposons and other sequences salmons share with a blood fluke, Schistosoma japonicum (Trematoda: Strigeiformes)--a parasitic helminth infecting various vertebrates. The aim of the present review is to structure all knowledge accumulated about salmonoid retroposons by now, as well as to complement it with the new data pertaining to the distribution of some SINE families.

[Mitochondrial DNA genetic differentiation of the muksun Coregonus muksun (Pallas) and related Siberian species of Coregonus (Coredonidae, Salmoniformes)].

Restriction enzyme analysis of the mitochondrial DNA (mtDNA) fragment encoding subunit 1 of the NADH dehydrogenase complex (ND-1) amplified via polymerase chain reaction (PCR) has been used to obtain data on genetic differentiation of muksun Coregonus muksun (Pallas) populations. Population polymorphism with respect to the restriction sites of 18 endonucleases has been described. It has been demonstrated that the muksun is genetically related to the pidschian C. pidschian (Gmelin), its sympatric species in Siberian waters. Analysis of the median network of mtDNA haplotypes has shown that haplotypes of muksun from various Siberian basins form a common group with haplotypes of pidschian of the Arctic Ocean basin, some frequent haplotypes been found in both forms. This raises the question as to the validity of the muksun as a species. Differences within this group of haplotypes are much smaller than those typical of species of the genus Coregonus. The possibility of a hybrid origin of the muksun from a pidschian-like ancestor and species of the cisco-peled (C. sardinella-C. peled) complex is discussed.

[Mitochondrial DNA variation in Pacific capelin (Mallotus villosus catervarius) from the Sea of Okhotsk, inferred from PCR-RFLP analysis].

Four population samples of Pacific capelin Mallotus villosus catervarius (Pennant, 1784) from geographically distant localities in the Sea of Okhotsk, Tauy Bay and the eastern coast of the Sakhalin Island, were examined using PCR-RFLP analysis of three mitochondrial DNA regions (A8/A6/COIII/ND3, ND3/ND4L/ND4, and ND5/ND6). The nucleotide divergence of mtDNA sequences among the samples, as well as the analysis of geographic heterogeneity of the haplotype frequencies and quantitative estimation of genetic differentiation performed by means of AMOVA, showed that the samples examined belonged to one panmictic population. Genealogic analysis of the mtDNA variation structure was carried out. It was demonstrated that the high level of haplotype diversity (0.9639 +/- 0.00015) along with the low level of nucleotide diversity (0.003818 +/- 0.0000003) pointed to the exponential rate of population growth of the capelin from the Sea of Okhotsk, which rather recently in its evolutionary history faced the bottleneck effect.

The evolutionary history of sharp- and blunt-snouted lenok (Brachymystax lenok (Pallas, 1773)) and its implications for the paleo-hydrological history of Siberia.

BACKGROUND: Broad-scale phylogeographic studies of freshwater organisms provide not only an invaluable framework for understanding the evolutionary history of species, but also a genetic imprint of the paleo-hydrological dynamics stemming from climatic change. Few such studies have been carried out in Siberia, a vast region over which the extent of Pleistocene glaciation is still disputed. Brachymystax lenok is a salmonid fish distributed throughout Siberia, exhibiting two forms hypothesized to have undergone extensive range expansion, genetic exchange, and multiple speciation. A comprehensive phylogeographic investigation should clarify these hypotheses as well as provide insights on Siberia's paleo-hydrological stability. RESULTS: Molecular-sequence (mtDNA) based phylogenetic and morphological analysis of Brachymystax throughout Siberia support that sharp- and blunt-snouted lenok are independent evolutionary lineages, with the majority of their variation distributed among major river basins. Their evolutionary independence was further supported through the analysis of 11 microsatellite loci in three areas of sympatry, which revealed little to no evidence of introgression. Phylogeographic structure reflects climatic limitations, especially for blunt-snouted lenok above 56 degrees N during one or more glacial maxima. Presumed glacial refugia as well as interbasin exchange were not congruent for the two lineages, perhaps reflecting differing dispersal abilities and response to climatic change. Inferred demographic expansions were dated earlier than the Last Glacial Maximum (LGM). Evidence for repeated trans-basin exchange was especially clear between the Amur and Lena catchments. Divergence of sharp-snouted lenok in the Selenga-Baikal catchment may correspond to the isolation of Lake Baikal in the mid-Pleistocene, while older isolation events are apparent for blunt-snouted lenok in the extreme east and sharp-snouted lenok in the extreme west of their respective distributions. CONCLUSION: Sharp- and blunt-snouted lenok have apparently undergone a long, independent, and demographically dynamic evolutionary history in Siberia, supporting their recognition as two good biological species. Considering the timing and extent of expansions and trans-basin dispersal, it is doubtful that these historical dynamics could have been generated without major rearrangements in the paleo-hydrological network, stemming from the formation and melting of large-scale glacial complexes much older than the LGM.

Trans-Arctic dispersals and the evolution of a circumpolar marine fish species complex, the capelin (Mallotus villosus).

Trans-Arctic dispersals and population and range expansions during the Pleistocene enhanced opportunities for evolutionary diversification and contributed to the process of speciation within the capelin, a northern marine-fish complex exhibiting a circumpolar distribution. Capelin is composed of four highly divergent and geographically discrete mitochondrial DNA (mtDNA) clades (609 bp; cytochrome b). Two clades occur in the North Atlantic, one associated with Canadian Atlantic waters, including Hudson Bay, and the second distributed from West Greenland to the Barents Sea. Two additional clades occur in the Arctic and northeast Pacific Oceans, representing the most recent divergence within the capelin phylogenetic tree. Judged from mtDNA diversity, capelin populations comprising all clades experienced at least one demographic and spatial reduction-expansion episode during recent Pleistocene glaciations that imprinted their molecular architecture. The large contemporary populations in the northeast Pacific and Arctic Oceans exhibited significant genetic structure whereas no such structure was detected in the equally extensive North Atlantic clades. All clades are characterized by one or two prevalent mtDNA haplotypes distributed over the entire range of the clade. Assuming a Pacific ancestor for capelin, we infer that capelin dispersed on two separate occasions to the North Atlantic. A more recent event resulted in the isolation of eastern Pacific and Arctic clades, with the Arctic clade positioned for a potential third Atlantic invasion, as revealed by the presence of this clade in the Labrador Sea. The Labrador Sea is a potential contact zone for three of the four capelin clades.

Phylogenetic conservation of chromosome numbers in Actinopterygiian fishes.

The genomes of ray-finned fishes (Actinopterygii) are well known for their evolutionary dynamism as reflected by drastic alterations in DNA content often via regional and whole-genome duplications, differential patterns of gene silencing or loss, shifts in the insertion-to-deletion ratios of genomic segments, and major re-patternings of chromosomes via non-homologous recombination. In sharp contrast, chromosome numbers in somatic karyotypes have been highly conserved over vast evolutionary timescales - a histogram of available counts is strongly leptokurtic with more than 50% of surveyed species displaying either 48 or 50 chromosomes. Here we employ comparative phylogenetic analyses to examine the evolutionary history of alterations in fish chromosome numbers. The most parsimonious ancestral state for major actinopterygiian clades is 48 chromosomes. When interpreted in a phylogenetic context, chromosome numbers evidence many recent instances of polyploidization in various lineages but there is no clear indication of a singular polyploidization event that has been hypothesized to have immediately preceded the teleost radiation. After factoring out evident polyploidizations, a correlation between chromosome numbers and genome sizes across the Actinopterygii is marginally statistically significant (p = 0.012) but exceedingly weak (R (2) = 0.0096). Overall, our phylogenetic analysis indicates a mosaic evolutionary pattern in which the forces that govern labile features of fish genomes must operate largely independently of those that operate to conserve chromosome numbers.

Cytogenetic analysis of three Italian populations of Coregonus lavaretus (Pisces, Salmoniformes) with chromosomal localization of major and minor ribosomal genes, and telomeric repeats.

The European whitefish, Coregonus lavaretus, widely distributed in freshwater of northern Europe and introduced into the major lakes of northern Italy, has been restocked in central Italian lakes. In accordance with current managing practices, a reduced number of spawners contribute to reproduction within each lake and a certain degree of isolation is to be expected between populations from different lakes, resulting in the rapid fixing of chromosomal changes. A detailed survey of three populations from different lakes was carried out using classical and molecular cytogenetic techniques, to verify if specific chromosomal markers are present in the distinct populations. The comparative analysis revealed intraspecific variability of NORs and fixed differences in their number in the three populations. A co-localization of major and minor rRNA genes on one chromosome site was also observed. The original data regarding the chromosome mapping of the (TTAGGG)(n) telomeric repeat obtained in this study, demonstrated their exclusively terminal distribution, and a conspicuous inter-chromosomal variation in the number of repeats. The results are compared with data available for populations from native geographic ranges.

Chromosome study of peled (Coregonus peled, Salmoniformes).

Chromosomes of Coregonus peled were examined by Giemsa, CMA3, Ag-NOR and C-banding. The karyotype of peled had a diploid number 2n=76, arm number NF=96 and consisted of twenty meta-submeta chromosomes and 56 subtelo-acrocentric chromosomes. C-positive blocks of heterochromatin were observed on the telomeric regions of meta- and submetacentric chromosomes. Pairs no. 1 and 11 had short arms, completely heterochromatic. The NOR was observed at one acrocentric pair, no. 11. Arm length polymorphism was observed on the NOR-bearing pair.

[Homologous series by chromosome number and genome rearrangement in the phylogeny of Salmonoidei]. / Gomologicheskie riady po chislu khromosom i perestroika genoma v filogeneze lososevidnykh ryb (Salmonoidei).

Published data on chromosome numbers of Salmonoidei are summarized. The existence of homologous variation of chromosome number in different phyletic lines of this suborder is substantiated. It is suggested that the origin of homologous series is related to major genome rearrangements (simultaneous fusion of several chromosomes).

Phylogenetic placement of retropinnid fishes: data set incongruence can be reduced by using asymmetric character state transformation costs.

We used mitochondrial DNA sequences to determine the phylogenetic placement of southern smelts (Retropinnidae), a group of diadromous fishes endemic to New Zealand and Australia. Our genetic data strongly support a sister group relationship between retropinnids and northern hemisphere smelts (Osmeridae), a relationship that seems consistent with the similar appearance and life history strategies of these two groups. Our analysis indicates that Retropinnidae and Osmeridae together represent the sister group to the southern hemisphere galaxiid fishes (Galaxiidae). However, this finding conflicts with several recent osteological analyses, which supported a sister relationship for Retropinnidae and Galaxiidae, giving a monophyletic southern hemisphere assemblage (Galaxioidea). We review cases of incongruence and discuss factors that might explain significant disagreement between molecular and morphological data matrices. We suggest that repeated evolutionary simplification may have undermined the accuracy of morphological hypotheses of osmeroid relationships. Although equally weighted parsimony analysis of morphological data rejects the molecular hypothesis (Osmeridae + Retropinnidae), implementation of a range of weighting schemes suggests that incongruence is nonsignificant under asymmetric character transformation models. We propose that a simple "equal transformation cost" parsimony analysis may be biologically unrealistic, especially when reductive homoplasy is widespread; as is increasingly being accepted, complex character states are more readily lost than gained. Therefore, we recommend that morphological systematists routinely implement a range of character transformation models to assess the sensitivity of their phylogenetic reconstructions. We discuss the antitropical biogeography of osmeroid fishes in the context of vicariance and transequatorial dispersal.

Euteleost fish genomes are characterized by expansion of gene families.

The presence of additional hox clusters in the zebrafish has led to the hypothesis that there was a whole genome duplication at the origin of modern fish. To investigate the generality of this assumption, we analyzed all available actinopterygian fish gene families, and sequenced nuclear receptors from diverse teleost fish. The origin and timing of duplications was systematically determined by phylogenetic analysis. More genes are indeed found in zebrafish than in mouse. This abundance is shared by all major groups of euteleost fish, but not by eels. Phylogenetic analysis shows that it may result from frequent independent duplications, rather than from an ancestral genome duplication. We predict two zebrafish paralogs for most mouse or human genes, thus expressing a note of caution in functional comparison of fish and mammalian genomes. Redundancy appears to be the rule in fish developmental genetics. Finally, our results imply that the outcome of genome projects cannot be extrapolated easily between fish species.

Molecular evolution of transferrin: evidence for positive selection in salmonids.

Transferrins are iron-binding proteins that are involved in iron storage and resistance to bacterial disease. Previous work has shown that nonsynonymous-to-synonymous-site substitution ratios (d(n)/d(s) ratios) between transferrin genes from some salmonid species were significantly greater than 1.0, providing evidence for positive selection at the transferrin gene. The purpose of the current study was to put these earlier results in a broader evolutionary context by examining variation among 25 previously published transferrin sequences from fish, amphibians, and mammals. The results of the study show that evidence for positive selection at transferrin is limited to salmonids-d(n)/d(s) ratios estimated for nonsalmonid lineages were generally less than 1.0. Within the salmonids, approximately 13% of the transferrin codon sites are estimated to be subject to positive selection, with an estimated d(n)/d(s) ratio of approximately 7. The three- dimensional locations of some of the selected sites were inferred by comparing these sites to homologous sites in the bovine lactoferrin crystallographic structure. The selected sites generally fall on the outside of the molecule, within and near areas that are bound by transferrin-binding proteins from human pathogenic bacteria. The physical locations of sites estimated to be subject to positive selection support previous speculation that competition for iron from pathogenic bacteria could be the source of positive selection.

Across the Southern Alps by river capture? Freshwater fish phylogeography in South Island, New Zealand.

We used DNA analysis of galaxiid fish to test a hypothesis of localized headwater capture in South Island, New Zealand. The restricted western, but widespread eastern, distributions of three nonmigratory freshwater fish species suggest that part of the east-flowing Waiau River has been captured by the west-flowing Buller River. However, mitochondrial control region (Kimura 2-parameter distance = 4.1-5.4%) and microsatellite flanking sequences do not support a relationship between Waiau (N = 4 fish sequences) and western populations (N = 8) of Galaxias vulgaris. Instead, the point of capture is probably to the north-east, perhaps the Nelson lakes region. Phylogenetic analysis indicates that western populations, along with populations in the north-east (N = 18), represent a previously unidentified monophyletic Evolutionarily Significant Unit, possibly a cryptic species. We suggest a general caveat for zoogeographic conclusions based on distributional data alone.

Genetic variation, population structure and cryptic species within the black mudfish, Neochanna diversus, an endemic galaxiid from New Zealand.

To investigate the phylogenetic relationships and geographical structure among landlocked populations of the black mudfish, Neochanna diversus, mitochondrial DNA nucleotide sequence data were sampled from seven populations from the Waikato and Northland regions of New Zealand. The complete D-loop region was sequenced from 70 individuals, with 913 bp from the tRNA-pro end used in population and phylogenetic analysis. A tandem repeat array, which ranged in size up to 200 bp, was found in most populations at the 3' end of the D-loop that was not able to be aligned for analysis. Of the seven sites sampled, two from Northland exhibited significant sequence divergence from all other sites. There was also a clear distinction among remaining Northland sites and those from the Waikato. An additional 518 bp segment of the 16S region was sequenced from all sites and compared with the other New Zealand mudfish species, N. apoda, N. burrowsius and the Tasmanian mudfish Galaxias (Neochanna) cleaveri using Galaxias maculatus as an outgroup. Both D-loop and 16S sequence data provided strong evidence for a cryptic species of mudfish present in Northland. The significant genetic structure apparent in the black mudfish appears most probably to be attributed to geological conditions during the Pliocene, where peat wetlands became apparent in the Waikato while Northland consisted of disjunct 'islands'. Conservation and management of these populations must take into account the historical processes that have shaped these patterns of genetic diversity.

[Primary structure of DNA, complementary for mRNA for the Baikal omul growth hormone]. / Pervichnaia struktura DNK, komplementarnoi mRNK gormona rosta Baikal'skogo omulia.

The pregrowth hormone DNA was synthesized by polymerase chain reaction from a pituitary gland cDNA library of Baikal omul (Coregonus autumnalis Pallas). A cDNA was sequenced and found to encode a precursor protein of 210 amino acid residues, which included a putative signal peptide of 22 amino acid residues. Sequence comparison reveals close similarity of the omul growth hormone to those of other Salmoniformes species.