Origin and post-colonization evolution of the Chatham Islands skink (Oligosoma nigriplantare nigriplantare)

Island ecosystems provide an opportunity to examine a range of evolutionary and ecological processes. The Chatham Islands are an isolated archipelago situated approximately 800 km east of New Zealand. Geological evidence indicates that the Chatham Islands re-emerged within the last 1-4 million years, following a prolonged period of marine inundation, and therefore the resident flora and fauna is the result of long-distance overwater dispersal. We examine the origin and post-colonization evolution of the Chatham Islands skink, Oligosoma nigriplantare nigriplantare, the sole reptile species occurring on the archipelago. We sampled O. n. nigriplantare from across nine islands within the Chatham Islands group, and representative samples from across the range of its closest relative, the New Zealand mainland common skink (Oligosoma nigriplantare polychroma). Our mitochondrial sequence data indicate that O. n. nigriplantare diverged from O. n. polychroma 5.86-7.29 million years ago. This pre-dates the emergence date for the Chatham Islands, but indicates that O. n. nigriplantare colonized the Chatham Islands via overwater dispersal on a single occasion. Despite the substantial morphological variability evident in O. n. nigriplantare, only relatively shallow genetic divergences (maximum divergence approximately 2%) were found across the Chatham Islands. Our analyses (haplotypic diversity, Phi(ST), analysis of molecular variance, and nested clade phylogeographical analysis) indicated restricted gene flow in O. n. nigriplantare resulting in strong differentiation between islands. However, the restrictions to gene flow might have only arisen recently as there was also a significant pattern of isolation by distance, possibly from when the Chatham Islands were a single landmass during Pleistocene glacial maxima when sea levels were lower. The level of genetic and morphological divergence between O. n. nigriplantare and O. n. polychroma might warrant their recognition as distinct species.     

The ubiquitous mountain hare mitochondria: multiple introgressive hybridization in hares, genus Lepus

Climatic oscillations during the glaciations forced dramatic changes in species distributions, such that some presently temperate regions were alternately occupied by temperate and arctic species. These species could have met and hybridized during climatic transitions. This phenomenon happened for three hare species present in Iberia (Lepus granatensis, Lepus europaeus and Lepus castroviejoi), which display high frequencies of mitochondrial DNA (mtDNA) from Lepus timidus, an arctic/boreal species presently extinct in Iberia. Here, we extend our previous geographical survey to determine whether the distribution of this mtDNA lineage extends beyond the northern half of the Iberian Peninsula, where it is found at high frequencies. We also review the taxonomy, distribution and molecular phylogeny of the genus Lepus. The phylogenetic inference reveals the presence of L. timidus-like mtDNA in several other hare species in Asia and North America, suggesting that the mitochondrial introgression observed in Iberia might be generalized. Comparison with the available nuclear gene phylogenies suggests that introgression could have happened repeatedly, possibly during different climatic transitions. We discuss demographic and adaptive scenarios that could account for the repetition in time and space of this spectacular phenomenon and suggest ways to improve our understanding of its determinants and consequences. Such high levels of introgressive hybridization should discourage attempts to revise hare taxonomy based solely on mtDNA.     

The role of vicariance vs. dispersal in shaping genetic patterns in ocellated lizard species in the western Mediterranean

The schism between North Africa and Southern Europe caused by the opening of the Strait of Gibraltar and the consequent refilling of the Mediterranean basin at the end of Messinian salinity crisis (MSC), 5.33 million years ago, has been advocated as the main event shaping biogeographical patterns in the western Mediterranean as exemplified by the distribution of species and subspecies and genetic variation within the ocellated lizard group. To reassess the role of the MSC, partial sequences of three mitochondrial DNA genes (cytochrome b , 12S and 16S ribosomal RNA) and two nuclear genes (β-fibrinogen and C-mos) from species of the ocellated lizard group were analysed. Three alternative hypotheses were tested: that divergence was initiated (i) by post-MSC vicariance as the basin filled, (ii) when separate populations established either side of the strait by pre-MSC overseas dispersal, and (iii) by post-MSC overseas dispersal. The pattern and level of divergence detected clearly refute the post-MSC vicariance hypothesis, and support a model of divergence initiated by earlier overseas dispersal. Indeed, our best estimate is that the basal Euro-African divergence predates the MSC event by several million years. The estimated divergence times among the populations in former Miocene Mediterranean islands, the current Betic and Rifian mountains, from adjacent mainland populations suggest overseas dispersal for the former and overland dispersal, or perhaps vicariance, for the latter. These results suggest that the MSC may have played a much less important role in shaping the current western Mediterranean biogeographical patterns than might have been anticipated from the dramatic nature of the episode.     

Bird mitochondrial gene order: insight from 3 warbler mitochondrial genomes

Two main gene orders exist in birds: the ancestral gene order and the remnant control region (CR) 2 gene order. These gene orders differ by the presence of 1 or 2 copies of the CR, respectively. Among songbirds, Oscines were thought to follow the ancestral gene order, with the exception of the lyrebird and Phylloscopus warblers. Here, we determined the complete mitochondrial genome sequence of 3 non-Phylloscopus warblers species and found that the blackcap (Sylvia atricapilla) and the reed warbler (Acrocephalus scirpaceus) have 2 almost identical copies of the CR, whereas the eastern orphean warbler (Sylvia crassirostris) follows the remnant CR 2 gene order. Our results contradict previous studies suggesting that Acrocephalus and most sylvioid warblers exhibit the ancestral gene order. We were able to trace this contradiction to a misidentification of gene order from polymerase chain reaction length determination. We thus suggest that passerine gene order evolution needs to be revised.     

The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites

The mtDNA of Cycas taitungensis is a circular molecule of 414,903 bp, making it 2- to 6-fold larger than the known mtDNAs of charophytes and bryophytes, but similar to the average of 7 elucidated angiosperm mtDNAs. It is characterized by abundant RNA editing sites (1,084), more than twice the number found in the angiosperm mtDNAs. The A + T content of Cycas mtDNA is 53.1%, the lowest among known land plants. About 5% of the Cycas mtDNA is composed of a novel family of mobile elements, which we designated as "Bpu sequences." They share a consensus sequence of 36 bp with 2 terminal direct repeats (AAGG) and a recognition site for the Bpu 10I restriction endonuclease (CCTGAAGC). Comparison of the Cycas mtDNA with other plant mtDNAs revealed many new insights into the biology and evolution of land plant mtDNAs. For example, the noncoding sequences in mtDNAs have drastically expanded as land plants have evolved, with abrupt increases appearing in the bryophytes, and then in the seed plants. As a result, the genomic organizations of seed plant mtDNAs are much less compact than in other plants. Also, the Cycas mtDNA appears to have been exempted from the frequent gene loss observed in angiosperm mtDNAs. Similar to the angiosperms, the 3 Cycas genes nad1, nad2, and nad5 are disrupted by 5 group II intron squences, which have brought the genes into trans-splicing arrangements. The evolutionary origin and invasion/duplication mechanism of the Bpu sequences in Cycas mtDNA are hypothesized and discussed.     

Application of mitochondrial control region in population genetic studies of the shrimp Penaeus

This study reports a primer set for amplifying a partial fragment of about 610 bp in the fast mutating mitochondrial control region in shrimps of the genus Penaeus (Decapoda: Penaeidae). The utility of this amplified fragment for studying population differentiation and structuring, compared with more conservative mitochondrial genes (16S rRNA and COI), was explored in P. merguiensis populations over a vast geographical range based on sequence and RFLP analyses. The results indicate that the mitochondrial control region provides more informative sites and reveals more haplotypes, making it most useful for evaluating genetic variations within and between populations of Penaeus species.     

Effect of the lipophilic/hydrophilic character of cationic triarylmethane dyes on their selective phototoxicity toward tumor cells

The observation that enhanced mitochondrial transmembrane potential is a prevalent tumor cell phenotype has provided the conceptual basis for the development of mitochondrial targeting as a novel therapeutic strategy for both chemo- and photochemotherapy of neoplastic diseases. Because the plasma transmembrane potential is negative on the inner side of the cell and the mitochondrial transmembrane potential is negative on the inner side of this organelle, extensively conjugated cationic molecules (dyes) displaying appropriate structural features are driven electrophoretically through these membranes and tend to accumulate inside energized mitochondria. As a result of the higher mitochondrial transmembrane potential typical of tumor cells, a number of cationic dyes preferentially accrue and are retained for longer periods in the mitochondria of these cells compared to normal cells. This differential in both drug loading and retention brings about the opportunity to attack and destroy tumor cells with a high degree of selectivity. Only a small subset of the cationic dyes known to accumulate in energized mitochondria mediate the destruction of tumor cells with a high degree of selectivity, and the lack of a reliable model to describe the structural determinants of this tumor specificity has prevented mitochondrial targeting from becoming a more reliable therapeutic strategy. We describe here a systematic study of how the molecular structure of closely related cationic triarylmethanes affects the selectivity with which these dyes mediate the photochemical destruction of tumor cells. Based on our observations of how the lipophilic/hydrophilic character of these dyes affects tumor selectivity, we propose a simple model to assist in the design of new drugs tailored specifically for imaging and selective destruction of neoplastic tissue via mitochondrial targeting.     

Complete loss of MHC genetic diversity in the Common Hamster (Cricetus cricetus) population in The Netherlands. Consequences for conservation strategies

The Common Hamster (Cricetus cricetus L.)has suffered from changes in agriculturalpractices. In some Western European countriesthe populations have become so small andscattered that they are threatened withextinction. We studied the genetic diversity ofmitochondrial and major histoincompatibilitycomplex (MHC) loci in the few animals left inthe South of the Netherlands and in threeanimals from the Alsace region in France, andcompared it to the diversity in Dutch animalsin the past (samples taken from stuffed animalsin museum collections dating back to the period1924–1956) and in a large present-daypopulation from Czech Republic. For themitochondrial cytochrome b gene, SNP mappingdemonstrated a total of nine alleles among 14Czech samples, of which one (possibly two) waspresent in the Dutch museum samples, and onlyone in the current Dutch animals. For the MHCgenes, DQA exon 2 and 3 showed no variation,while 14 different alleles were found at DRBexon 2. The Czech population contained 13different alleles in 15 animals sampled, andmost animals were heterozygous (H_o = 0.80,H_e = 0.91). Therefore, the solitary livingHamster maintains, in nature, a large diversityat this MHC locus. The Dutch museum samplescontained eight different alleles in 20 samples, and they were slightly less heterozygous (H_o = 0.60, H_e = 0.75). All but one ofthese alleles were also found in the Czechsamples. In contrast, the present Dutch andFrench animals (a total of 16 samples)contained only one of these alleles, and allanimals were genetically identical andhomozygous. We conclude that the remaininganimals have lost all diversity at this MHClocus. This is probably the result of a severebottleneck, which may have been quite severe,reducing diversity in many loci. In addition,the remaining Dutch animals are partly derivedfrom one family. These animals are now part ofa breeding program. Options for restocking thegenetic diversity are discussed.     

Conservation units based on mitochondrial and nuclear DNA variation among European bullhead populations (Cottus gobio L., 1758) from Flanders, Belgium

In this study, we aimed to delineateevolutionarily significant units (ESUs) andmanagement units (MUs) for the Europeanbullhead in Flanders (Belgium). Therefore, wedetermined the genetic interrelationshipsbetween 11 bullhead populations, using lengthvariation at 7 polymorphic microsatellite lociand sequence variation in the d-loop of themitochondrial DNA (mtDNA). Despite therelatively small geographical scale of ourstudy, the analysis of the d-loop sequencesshows that the Flemish bullhead populationscontain 3 haplotype groups, which can beassigned to 3 previously described EuropeanmtDNA clades. Because of the importantdifferences between these clades, they may bedefined as evolutionarily significant units,which should be managed separately. Analysis ofmicrosatellite data reveals very high degreesof isolation between populations, with theexception of 3 pairwise comparisons whichinvolved adjacent populations. Our data suggestthat the 3 haplotype groups probably qualify asESUs, as they show phylogeographicdifferentiation for mtDNA variants as well assignificant divergence of allele frequencies atnuclear loci. However, one of these units,limited to a single population, may be ofCentral European origin. All populations of theScheldt basin meet the criteria for MUrecognition, since significantly differentmicrosatellite allele frequencies as well asprivate alleles are found. In contrast, geneticdifferentiation among the 3 populations of theMeuse basin is very low.