Cryptic diversity and unexpected evolutionary patterns in the meadow lizard,Darevskia praticola (Eversmann, 1834)

Darevskia praticola differs from the other species of the genus in having a large but disjunct distribution, covering the Balkan and the Caucasus regions. Furthermore, most Darevskia species occupy saxicolous habitats, whereas D. praticola inhabits meadows and forest environments. Here we determine the phylogeographic and phylogenetic relationships of Darevskia praticola sensu lato and evaluate the current, morphology-based taxonomy. We sequenced two mtDNA genes (Cyt-b and ND4) and two nuclear loci (MC1R and RELN) for samples collected across the species range. Because our sequences amplified with the Cyt-b primers appear to represent a nuclear pseudogene we excluded this marker from the final analysis. Our results support monophyly of D. praticola and show its division into three clades. The first divergence, dated to the Late Pliocene, is between the Balkans and the Caucasus. The Caucasus lineage is further subdivided in a western Greater Caucasus and a Transcaucasia clade, likely due to subsequent differentiation during the Pleistocene. Our findings do not support the current taxonomic arrangement within D. praticola. The main geographic divergence likely happened due to a vicariance event associated with Plio-Pleistocene climatic and vegetation oscillations.     

Evidence for male-biased effective sex ratio and recent step-by-step colonization in the bivalve Pinctada mazatlanica

This paper presents a comparison of the geographical distribution of genetic variability at mitochondrial and nuclear loci among pearl oyster populations from the tropical American Pacific coast (Pinctada mazatlanica). Surprisingly, both mitochondrial and nuclear gene variability decreased regularly from north to south of the studied area, which, altogether with a significant correlation between genetic and geographical distances for mtDNA, suggests a recent colonization or re-colonization of the southern areas. However, the loss of diversity between north and south was much more important for mitochondrial than for nuclear DNA, and this did not translate into measurable fixation index at nuclear loci (theta = 0.03, n.s.), contrary to the mitochondrial data (theta = 0.18*). Smaller effective size of mtDNA accentuated by a strong male-biased effective sex ratio and step-by-step colonization from northern areas can explain this discrepancy among natural populations of this protandric species.     

Increase in CpG DNA-induced inflammatory responses by DNA oxidation in macrophages and mice

Unmethylated CpG dinucleotide (CpG motif) is involved in the exacerbation of DNA-associated autoimmune diseases. We investigated the effect of DNA containing 8-hydroxydeoxyguanosine (oxo-dG), a representative DNA biomarker for oxidative stress in the diseases, on CpG motif-dependent inflammatory responses. ODN1668 and ODN1720 were selected as CpG-DNA and non-CpG DNA, respectively. Deoxyguanosine in the CpG motif (G9) or outside the motif (G15) of ODN1668 was substituted with oxo-dG to obtain oxo(G9)-1668 and oxo(G15)-1668, respectively. Oxo(G15)-1668 induced a significantly higher amount of tumor necrosis factor (TNF)-α from RAW264.7 macrophage-like cells than ODN1668, whereas oxo(G9)-1668, oxo(G8)-1720, or oxo(G15)-1720 hardly did. CpG DNA-induced TNF-α production was significantly increased by addition of oxo(G8)-1720 or oxo(G15)-1720, but not of ODN1720. This oxo-dG-containing DNA-induced increase in TNF-α production was also observed in primary cultured macrophages isolated from wild-type mice, but not observed in those from Toll-like receptor (TLR)-9 knockout mice. In addition, TNF-α production by ligands for TLR3, TLR4, or TLR7 was not affected by oxo-dG-containing DNA. Then, the footpad swelling induced by subcutaneous injection of ODN1668 into mice was increased by coinjection with oxo(G8)-1720, but not with ODN1720. These results indicate that oxo-dG-containing DNA increases the CpG motif-dependent inflammatory responses, which would exacerbate DNA-related autoimmune diseases.     

An integrative taxonomic revision of the Tarentola geckos (Squamata,Phyllodactylidae) of the Cape Verde Islands

Recent phylogeographical analyses using mitochondrial DNA (mtDNA) sequences indicate that the Tarentola geckos from the Cape Verde archipelago originated from a propagule that dispersed from the Canary Islands approximately 7.7 Mya and that underwent a fast evolutionary radiation. Molecular analyses carried out to date clearly show some incongruences with the current taxonomy of Tarentola from the Cape Verde Islands, with some species being paraphyletic or polyphyletic, and several independently evolving lineages needing formal taxonomic recognition. The aim of this study was to clarify the systematics of this group to unravel its taxonomy by applying an integrative approach based on information from three independent sources: mtDNA, nuclear genes, and morphology. As a result of this taxonomic revision, two novel species for the islands of S. Nicolau and Fogo are described and eight subspecies are upgraded to species level. Moreover, an identification key for the genus Tarentola from the Cape Verde archipelago is presented. This study reconciles taxonomy and phylogeny in this group, provides a better understanding of diversity patterns, new insights on evolutionary hypotheses, and supports the basic framework for the future management and conservation of this unique reptile radiation. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 328–360.     

Patterns of nuclear and mitochondrial DNA variation in Iberian populations of <Emphasis Type="Italic">Emys orbicularis</Emphasis> (Emydidae): conservation implications

The European pond turtle (Emys orbicularis) is threatened and in decline in several regions of its natural range, due to habitat loss combined with population fragmentation. In this work, we have focused our efforts on studying the genetic diversity and structure of Iberian populations with a fine-scale sampling (254 turtles in 10 populations) and a representation from North Africa and Balearic island populations. Using both nuclear and mitochondrial markers (seven microsatellites, ∼1048 bp nDNA and ∼1500 bp mtDNA) we have carried out phylogenetic and demographic analyses. Our results show low values of genetic diversity at the mitochondrial level although our microsatellite dataset revealed relatively high levels of genetic variability with a latitudinal genetic trend decreasing from southern to northern populations. A moderate degree of genetic differentiation was estimated for Iberian populations (genetic distances, F _ST values and clusters in the Bayesian analysis). The results in this study combining mtDNA and nDNA, provide the most comprehensive population genetic data for E. orbicularis in the Iberian Peninsula. Our results suggest that Iberian populations within the Iberian–Moroccan lineage should be considered as a single subspecies with five management units, and emphasize the importance of habitat management rather than population reinforcement (i.e. captive breeding and reintroduction) in this long-lived species.     

Ideal phenotypes and mismatching haplotypes – errors of mtDNA treeing in ants (Hymenoptera: Formicidae) detected by standardized morphometry

A total of 401 nest samples of Formica lugubris Zetterstedt, F. pratensis Retzius, F. aquilonia Yarrow, F. rufa Linnaeus, and F. polyctena Förster, covering the entire Palaearctic range of these species and including 2100 individual workers, was phenotypically investigated by a system of standardized morphometry, pairwise removal of allometric variance, and canonical discriminant functions. A mitochondrial DNA fragment including the cytochrome b gene was sequenced in 148 samples from basically the same range. In the more difficult F. pratensis vs. F. lugubris case, the phenotypic system correctly determined 99.6% of all nest samples, and 95.1% with p<0.05. In all other pairwise species discriminations any nest sample was correctly determined with p<0.01, and three samples with hybrids F. rufa×lugubris were identified. At four localities in the Pyrenees and the Urals, 9 samples with F. pratensis phenotypes (7 of them ideal) but F. lugubris mtDNA haplotypes could be identified, resulting in 14.5% of phenotype/haplotype mismatches. A local dominance of this mismatch combination was observed at one Pyrenean and one Ural locality. There was no indication of an F. pratensis haplotype associated with an F. lugubris phenotype. One ideal F. polyctena phenotype was associated with an F. aquilonia haplotype in a sample from the Urals, and one ideal F. aquilonia phenotype was combined with an F. lugubris haplotype in a sample from central Siberia, resulting in overall phenotype/haplotype mismatch frequencies of 12.5% and 11.1%, respectively. We conclude that all these samples cannot represent actual F₁ hybrids but are the result of hybridizations in the past followed by unidirectional purging of the nuclear genome. Whether this process of purging worked very fast or over longer periods of population history, and whether or not it was complete or incomplete, cannot be assessed from the available information. These facts of hybridizing in two thirds of the W Palaearctic wood ant species, of extreme regional hybrid frequencies (up to 26%), of unidirectional purging of nDNA associated with mismatching mtDNA haplotypes, and of occasional achievement of local dominance of these mismatch combinations, may serve as urgent warning not to perform isolated mtDNA phylogenetic studies without a geographically and locally wide sampling basis and without control by nDNA information or reliable phenotypic determination. The latter two systems definitely have superior significance when conflicts with mtDNA indications arise.     

Phylogenetics and biogeography of the broad-nosed bats, genus Platyrrhinus (Chiroptera: Phyllostomidae)

The Neotropical broad-nosed bats, genus Platyrrhinus, represent a well-defined monophyletic group of 14 recognized species. A recent study of morphological characters confirmed Platyrrhinus monophyly and species diagnosis, but offered little support to their intra-specific relationships. We conducted phylogenetic analyses of the genus, using dense taxonomic sampling in combination with four gene sequences representing both mitochondrial and nuclear DNA transmission systems. Our aim was to elucidate the phylogenetic structure among species, using the resulting 3341 bp of DNA. Maximum parsimony, maximum likelihood, and Bayesian inference analyses produced similar topologies that confirm the monophyly of the genus Platyrrhinus and strongly support many previously unrecognized groups. Paraphyly of Platyrrhinus helleri and the unclear position of P. brachycephalus in the clades were also apparent in the data. Our biogeographical analysis suggests a Brazilian Shield origin for Platyrrhinus, followed by subsequent radiations of lineages in the Amazon Basin and Andes. Secondary dispersal from Amazonian and Andean centers is responsible for the Platyrrhinus inhabiting the Guianan Shield and the Pacific lowlands and Central America, respectively.     

Genotypic and phenotypic evaluation of Rutilus spp. from Skadar, Ohrid and Prespa Lakes supports revision of endemic as well as taxonomic status of several taxa

One mtDNA gene (cytochrome b), one nuclear DNA fragment, five microsatellites and a suite of morphological characters were evaluated in samples of Rutilus spp. from Skadar, Ohrid and Prespa Lakes. Both genetic and phenotypic data supported two sympatric taxa in Lake Skadar, whereby Prespa and Ohrid Lakes revealed only a single taxon each. One of the taxa from Lake Skadar was similar to samples from Lake Prespa, whereas the second taxon was the most divergent in the data set. The estimated time to the most recent common ancestor of these two sympatric taxa in Lake Skadar was between 125 000 and 500 000 years. The data did not support existing taxonomic schemes for Rutilus in these lakes. This study poses the following working hypothesis: (1) Rutilus prespensis lives both in Lake Prespa and Lake Skadar and therefore is not endemic to Lake Prespa, (2) Rutilus ohridanus lives in Lake Ohrid only and therefore could be considered an endemic if its species status is retained and (3) a third recently described taxon (Rutilus albus) sympatric to R. prespensis lives in Lake Skadar.     

DNA在鸟类分子系统发育研究中的应用

鸟类分子系统发育研究中常用的DNA技术有DNA杂交、RFLP和DNA序列分析等。DNA杂交技术曾在鸟类中有过大规模的应用,并由此诞生了一套新的鸟类分类系统。在鸟类的RFLP分析中,用的最多的靶序列是线粒体DNA。DNA序列分析技术被认为是进行分子系统发育研究最有效、最可靠的方法。在DNA序列分析中,线粒体基因应用最广泛,但由于其自身的一些不足,近年来,不少学者把目光投向了核基因,将线粒体基因和核基因结合起来进行系统发育研究。目前在鸟类分子系统发育中,应用较多的核基因是scnDNA,其内含子可以用于中等阶元水平的系统研究,而外显子主要用于高等阶元的系统研究。除了分子标记自身的问题之外,鸟类分子系统发育研究中还存在着方法上的问题,包括分子标记的选择,样本数量以及数据处理等。今后鸟类分子系统发育研究应该更加注重方法的标准化。     

Assignment ofKluyveromyces cellobiovorus nomen nudum toCandida intermedia (Ciferri & Ashford) Langeron et Guerra

A yeast culture isolated in Japan from soil and invalidly described asKluyveromyces cellobiovorus nom. nud. DBVPG 6286 (CBS 7153) was compared for its physiological and morphological properties and by nDNA-nDNA reassociation experiments with the type strains of several species of the genusKluyveromyces as well as of variousCandida species exhibiting similar phenotypic profiles. DBVPG 6286 was found to be conspecific with the type strain ofCandida intermedia (Ciferri & Ashford) Langeron et Guerra (1938).