Peopling of the Azores Islands (Portugal): data from the Y chromosome

Nine Atlantic islands with approximately five and a half centuries of demographic history constitute the Portuguese archipelago of the Azores. Despite the recent peopling history of these islands, written records regarding the specific origin and relative proportions of the first settlers are scarce and incomplete. To gain insights into the history of the peopling of the Azores and to evaluate to what extent population imports described in historical sources left their marks on the genetic constitution of the present-day populations, we analyzed 11 Y-chromosome biallelic markers in a sample of 145 unrelated individuals of Azorean ancestry. The main results of this study indicate that the genetic profile of the Azorean male population shows high affinities with that of mainland Portugal, in accordance with the general knowledge, derived from historical sources, that the Portuguese were the major contributors to the Azorean founding population. Nevertheless, genetic traces of settlers from other origins also mentioned in historical records can still be found in the present-day population. Thus typically sub-Saharan male lineages were detected in the archipelago, in contrast to what has been described for mainland Portugal. Furthermore, compared to what has been described for the mainland Portugal population, our data support a stronger influence of people of Jewish origin, as detected by an increased frequency of lineages belonging to haplogroup J.     

Baseline Levels of Metals in Volcanic Soils of the Azores (Portugal)

Data on metal concentrations present in the soils of the Azores (Portugal) are scarce. The goal of this study was to measure the current levels of several metals in the top horizon of soils of two areas, distinguishable by their volcanic activity and physical characteristics, in order to establish some baseline concentrations of these elements. Soil samples were taken in similar ways from five sites in a volcanically active area and another five sites in an area without volcanic activity. Particle-size fractions, % organic matter, moisture content, pH, and major and trace elements compositions were measured. In general, the concentrations of trace metals in the soils from Santa Maria (inactive volcanism) were higher than those from Furnas (active volcanism), with the exception of Zn. The soils from Furnas, which have slightly lower pH and less % clay-silt than Santa Maria, will probably make such trace metals as Zn become more readily bioaccessible, and therefore pose a larger threat to living organisms inhabiting these soils.     

Understanding differences between phylogenetic and pedigree-derived mtDNA mutation rate: a model using families from the Azores Islands (Portugal)

We analyzed the control region of the mitochondrial DNA (mtDNA)from maternally related individuals originating from the AzoresIslands (Portugal) in order to estimate the mutation rate ofmtDNA and to gain insights into the process by which a new mutationarises and segregates into heteroplasmy. Length and/or pointheteroplasmies were found at least in one individual of 72%of the studied families. Eleven new point substitutions werefound, all of them in heteroplasmy, from which five appear tobe somatic mutations and six can be considered germinal, evidencingthe high frequency of somatic mutations in mtDNA in healthyyoung individuals. Different values of the mutation rate accordingto different assumptions were estimated. When considering allthe germinal mutations, the value of the mutation rate obtainedis one of the highest reported so far in family studies. However,when corrected for gender (assuming that the mutations presentin men have the same evolutionary weight of somatic mutationsbecause they will inevitably be lost) and for the probabilityof intraindividual fixation, the value for the mutation rateobtained for HVRI and HVRII (0.2415 mutations/site/Myr) wasin the upper end of the values provided by phylogenetic estimations.These results indicate that the discrepancy, that has been reportedpreviously, between the human mtDNA mutation rates observedalong evolutionary timescales and the estimations obtained usingfamily pedigrees can be minimized when corrections for genderproportions in newborn individuals and for the probability ofintraindividual fixation are introduced. The analyses performedsupport the hypothesis that (1) in a constant, tight bottleneckgenetic drift alone can explain different patterns of heteroplasmysegregation and (2) in neutral conditions, the destiny of anew mutation is strictly related to the initial proportion ofthe new variant. Another important point arising from the dataobtained is that, even in the absence of a paternal contributionof mtDNA, recombination may occur between mtDNA molecules presentin an individual, which is only observable if it occurs betweenmtDNA types that differ at two or more positions.     

The colonization history of Juniperus brevifolia (Cupressaceae) in the Azores Islands

Background

A central aim of island biogeography is to understand the colonization history of insular species using current distributions, fossil records and genetic diversity. Here, we analyze five plastid DNA regions of the endangered Juniperus brevifolia, which is endemic to the Azores archipelago.

Methodology/Principal Findings

The phylogeny of the section Juniperus and the phylogeographic analyses of J. brevifolia based on the coalescence theory of allele (plastid) diversity suggest that: (1) a single introduction event likely occurred from Europe; (2) genetic diversification and inter-island dispersal postdated the emergence of the oldest island (Santa Maria, 8.12 Ma); (3) the genetic differentiation found in populations on the islands with higher age and smaller distance to the continent is significantly higher than that on the younger, more remote ones; (4) the high number of haplotypes observed (16), and the widespread distribution of the most frequent and ancestral ones across the archipelago, are indicating early diversification, demographic expansion, and recurrent dispersal. In contrast, restriction of six of the seven derived haplotypes to single islands is construed as reflecting significant isolation time prior to colonization.

Conclusions/Significance

Our phylogeographic reconstruction points to the sequence of island emergence as the key factor to explain the distribution of plastid DNA variation. The reproductive traits of this juniper species (anemophily, ornithochory, multi-seeded cones), together with its broad ecological range, appear to be largely responsible for recurrent inter-island colonization of ancestral haplotypes. In contrast, certain delay in colonization of new haplotypes may reflect intraspecific habitat competition on islands where this juniper was already present.     

Algae-based biotopes of the Azores (Portugal): spatial and seasonal variation

The increasing importance of coastal management created the need for a systematic classification and characterization of marine communities. Accurate quantitative methodologies for rocky shore algae-based biotope definition, were developed and tested on the Islands of São Miguel and Santa Maria (Azores). Shores of both islands were surveyed, covering all rocky substrate types. Biotopes were defined by assessing the associated habitat and species characteristics, using ANOSIM and SIMPER analysis, respectively. A total of ten biotopes were identified. Generally both islands’ biotopes are characterized by the same taxa/ecological categories, in summer and in winter. However, association between these taxa/ecological categories and the shore height at which they occur differs geographically and temporally. There is a generalized gradual succession of taxa/ecological categories from upper intertidal down to deepest subtidal, although geographical differences occur. Diversity is highest at the land–water interface and decreases towards both extremes (upper intertidal and deepest subtidal level). The strongest evidence of seasonal variation occurs at the upper intertidal. The methodology used proves to be effective in broad scale shoreline assessment of biological communities in warm-temperate coastal marine environments, and thus suitable for the purpose it was developed for. As a consequence it should be applied to the remaining islands of the Azorean archipelago as well as to other macaronesian islands, e.g. Madeira and the Canaries.     

Physiological responses of Pterocladia and Gelidium (Gelidiales,Rhodophyta) from the Azores,Portugal

Manometric studies were conducted on Pterocladia capillacea, Gelidium latifolium and Gelidium spinulosum from the Azores, Portugal to determine optimal values of temperature, light and salinity for growth. Physiological responses were considered in relation to vertical distribution patterns of these species commonly observed throughout the Azores. Optimal parameters for the growth of Pterocladia capillacea, Gelidium latifolium and G. spinulosum were 17 to 25 °C, a photon flux density between 200 and 300 µmol m^–2 s^–1 and salinities of 25 to 35.     

A new species of Ingolfiellidae (Peracarida, Amphipoda, Crustacea) from the Azores, Portugal

A new species of Ingolfiellid Amphipod Ingolfiella azorensis n. sp. is described from samples collected in a benthic survey off the Azores archipelago, Portugal. The new species is characterized by the lack of ocular lobes, a four-toothed dactylus on the first and second gnathopods, and having dissimilar claws on the third to seventh pereiopods. Individuals were obtained from shallow subtidal samples of sand. The new findings bring the number of Ingolfiellidae from Macaronesia up to six, equalling almost 20 % of the world’s known species, suggesting this area as a potential evolutionary centre for Ingolfiellidae.     

Testing hierarchical levels of population sub-structuring: the Azores islands (Portugal) as a case study

The Azores archipelago (Portugal) is formed by nine islands whose relative positions define them as three geographical groups: Eastern (S. Miguel and Sta. Maria), Central (Terceira, Faial, Pico, Graciosa and S. Jorge) and Western (Flores and Corvo). Using the father's surname of 187,398 individuals living on the nine Azorean Islands, a population analysis based on inter-island relationship and hierarchical organization was conducted. The relation between islands was investigated using summary statistics, analysis of molecular variance (AMOVA) as well as graphical methods. When the values of heteronymy were contrasted with values of gene diversity based on haplogroup frequencies of the Y chromosome, it was possible to verify that Graciosa and Sta. Maria appeared to have the least diverse populations, and that Flores, despite its smaller population size and geographical isolation, has considerably higher levels of diversity. As for inter-island relationships, the difficulty of directly interpreting summary statistics values was evidenced. The AMOVA revealed that only 0.77% of the variation in surnames can be attributed to among-island variation, a value that, although small, can be considered significant. Application of Malécot's model revealed that geographic distance has an important impact in the genetic structure of the archipelago. Monmonier's maximum-difference algorithm demonstrated that the most isolated island of the archipelago appears to be Graciosa, followed by the islands of the Western group and by Sta. Maria. After integrating values of summary statistics with results from AMOVA and graphical methods, a more accurate genetic profile of the Azores, highly supported by genetic data, has emerged.     

Polymorphism of the apolipoprotein E gene (APOE) in the populations of Russia and neighboring countries

Allele and genotype frequencies for the locus encoding apolipoprotein E, involved in the regulation of lipid metabolism (APOE), were evaluated in 16 populations representing 12 ethnic groups (a total of 1103 subjects) from Russia and neighboring countries. In the populations examined, the frequencies of allele ?4, which is the risk factor of Alzheimer’s disease and coronary heart disease, varied from less than 5 to more than 20%, while the variation of the major ?3 allele in these populations ranged from less than 75 to 95%. The frequencies of alleles ?3 and ?4 were 0.714 and 0.205 in Saami, 0.735 and 0.220 in Komi-Izhemts, 0.770 and 0.130 in Komi-Zyryans, 0.771 and 0.149 in Udmurts, 0.734 and 0.149 in Maris, 0.841 and 0.122 in Evenks, 0.788 and 0.163 in Buryats, 0.764 and 0.202 in Chukchi, 0.875 and 0.075 in Iranians, 0.956 and 0.044 in mountain-dwellers of the Pamirs, 0.771 and 0.094 in Ukrainians, and 0.795 and 0.091 in Belarussians, respectively. In Russians from different regions of the country, the frequencies of these alleles were 0.728 and 0.139 (Kostroma), 0.795 and 0.105 (Moscow), 0.857 and 0.092 (Rostov-on-Don), and 0.824 and 0.083 (Krasnodar), respectively. The latitudinal distribution of the APOE ?3 and ?4 allele frequencies in the populations examined was comparable to the frequency distribution pattern of these alleles in other populations of Eurasia.     

Polymorphism of the apolipoprotein E gene (APOE) in the populations of Russia and neighboring countries

Allele and genotype frequencies for the locus encoding apolipoprotein E, involved in the regulation of lipid metabolism (APOE), were evaluated in 16 populations representing 12 ethnic groups (a total of 1103 subjects) from Russia and neighboring countries. In the populations examined, the frequencies of allele epsilon4, which is the risk factor of Alzheimer's disease and coronary heart disease, varied from less than 5 to more than 20%, while the variation of the major epsilon3 allele in these populations ranged from less than 75 to 95%. The frequencies of alleles epsilon3 and epsilon4 were 0.714 and 0.205 in Saami, 0.734 and 0.149 in Maris, 0.841 and 0.122 in Evenks, 0.788 and 0.163 in Buryats, 0.764 and 0.202 in Chukchi, 0.875 and 0.075 in Iranians, 0.956 and 0.044 in mountain-dwellers of the Pamirs, 0.771 and 0.094 in Ukrainians, and 0.795 and 0.091 in Belarussians, respectively. In Russians from different regions of the country, the frequencies of these alleles were 0.728 and 0.139 (Kostroma), 0.795 and 0.105 (Moscow), 0.857 and 0.092 (Rostov-on-Don), and 0.824 and 0.083 (Krasnodar), respectively. The latitudinal distribution of the APOE epsilon3 and epsilon4 allele frequencies in the populations examined was comparable to the frequency distribution pattern of these alleles in other populations of Eurasia.     

Mutant allele frequencies in domestic cats of Portugal and the Azores

The genetic profiles of cat populations of mainland Portugal are basically similar to those of the adjacent Atlantic littoral. The profiles of Azorean populations, while relatively homogeneous among themselves, are strikingly different from the mainland. It is tentatively concluded that some form of selective migration was the most important contributing factor in establishing the differences.     

Polymorphism of the myogens locus in some representatives of sturgeons (Acipenseridae)

This study investigates muscle proteins in Russian (Acipenser gueldensiaedtii Brandt), Siberian (Acipenser baerii Brandt), and Amur (Acipenser schrenckii Brandt) sturgeons using the method of polyacrylamide gel electrophoresis. A group of fractions, which is presumably the product of a polyallelic duplicated MY-1* locus, is recorded among the general pool of proteins. Data from densitometric analysis makes it possible to put forward a hypothesis about an eight-gene determination of this system of proteins. The highest heterogeneity and polymorphism was revealed in the Russian sturgeon. Analysis of the genotype distribution in samples of the studied species allowed us to make an assumption that the genetic structure of spawning sturgeon stocks is significantly metamorphosed under the influence of anthropogenic and natural factors.     

Isolation,sequencing, and expression analysis of a bovine apolipoprotein E (APOE) cDNA and chromosomal localization of the APOE locus

The nucleotide sequence data reported in this paper have been submitted to EMBL Data Library and have been assigned the accession number: X64839 Bos taurus mRNA for apoprotein E.     

Molecular,phytochemical and morphological characterization of the liverwort genus Radula in Portugal (mainland,Madeira, Azores)

Relationships of the eight species of the liverwort genus Radula occurring in Portugal (mainland, the Madeira and Azores archipelagos), including the Macaronesian endemics R. jonesii and R. wichurae, were evaluated based on molecular, phytochemical and morphological–anatomical data. Maximum parsimony and Bayesian analyses were performed with sequences from three plastid DNA markers (trnS _GGA-rps4 spacer, rps4 gene, trnL _UAA intron), volatile oil compounds, as well as qualitative morphological–anatomical characters. In addition, the molecular data were subjected to maximum likelihood analysis. The eight taxa, R. aquilegia, R. carringtonii, R. complanata, R. holtii, R. jonesii, R. lindenbergiana, R. nudicaulis and R. wichurae, can be clearly distinguished from each other, either by molecular data alone or by combination of characters from all three data sets. Radula aquilegia is monophyletic according to the molecular data, but shows considerable, yet undescribed intraspecific morphological and phytochemical variability. Recognition of R. complanata and R. lindenbergiana as separate species, previously based solely on the paroecious vs. dioecious sexual condition, is moderately supported by the molecular phylogenetic analyses and strongly supported by the phytochemical data. The Radula species, narrowly distributed in Macaronesia and Atlantic Europe, probably have two different origins. For Radula holtii and R. nudicaulis, connections with Radula species from the Neotropics are indicated. The other species, among them the two Macaronesian endemics, are closely related with the R. complanata/R. lindenbergiana complex, which is widely distributed in the northern hemisphere.     

Two new species of Aporhynchus (Cestoda: Trypanorhyncha) from deep water lanternsharks (Squaliformes: Etmopteridae) in the Azores, Portugal

New collections of cestodes from the spiral intestines of the lanternsharks Etmopterus spinax and Etmopterus pusillus off the island of Faial, in the Azores, Atlantic Ocean, have yielded 2 new species of trypanorhynchs belonging to Aporhynchus. Both species share the distinctive lack of all elements of the rhyncheal system that are characteristic of this genus. The identity of Aporhynchus norvegicus is clarified to allow it to be distinguished from A. menezesi n. sp., which also parasitizes E. spinax. This new species differs conspicuously from its congeners in that its mature and gravid proglottids are wider than long, rather than longer than wide, and also in its lack of spinitriches on the scolex. Aporhynchus pickeringae n. sp., the new species from E. pusillus , differs from all of its congeners except A. norvegicus in that it is a relatively delicate worm with relatively fewer testes. It also possesses fewer proglottids and a wider pedunculus scolecis than does A. norvegicus. Sections through the scolex of A. menezesi n. sp. support use of the term bothriate, rather than difossate, in reference to the scolex configuration of some trypanorhynchs. A key to the 4 species of Aporhynchus is provided.     

Analysis of Leptospira isolates from mainland Portugal and the Azores islands

From 228 recent Leptospira isolates from mainland Portugal and Azorean wild mammals, 149 were characterized at the serovar level by monoclonal antibodies (MAbs), a quick serological method in epidemiological studies. In order to compare this antigenic information with that from new genetic techniques, a sample of isolates was analyzed through pulsed-field agarose gel electrophoresis (PFGE) (n=71), mapped restriction site polymorphisms (MRSPs) in PCR-amplified rRNA genes (n=45, including 13 saprophytes) and arbitrarily primed polymerase chain reaction (AP-PCR) fingerprinting (n=32). MRSP and AP-PCR lead to species identification of the studied 32 pathogenic isolates: Leptospira interrogans (n=3), Leptospira kirschneri (n=8) and Leptospira borgpetersenii (n=21). MAbs and PFGE characterized pathogenic isolates at the serovar level and resulted mainly in agreement (64%) although many discrepancies (35%) were observed.     

The APOE locus and the pharmacogenetics of lipid response

Genetic variation at the APOE locus has been associated with plasma lipoprotein concentrations in the fasting (low-density, and high-density lipoproteins and triglycerides), and in the postprandial (triglyceride-rich lipoproteins) states. Resulting from these associations, the APOE locus has been found to be a significant genetic determinant of cardiovascular disease in the general population. Beyond the traditional association studies, APOE genetic variation has been shown to play a significant role, which explains some of the individual variations in therapies aimed at normalizing plasma lipid concentrations. Thus, the APOE E4 allele has been shown in some studies to be associated with increased response to dietary intervention. Conversely, APOE E2 carriers appear to be more responsive to statin therapy. The mechanisms behind these observations, however, have not been elucidated. Moreover, several other gene:environment and gene:therapy interactions have recently been demonstrated, thus further increasing the interest in this remarkable apolipoprotein.     

内蒙古蒙古族人群DYS413基因座的多态性分布

为调查DYS413(YCA Ⅲ)基因座在内蒙古蒙古族人群中的分布情况,为其应用于法医学和人类遗传学研究提供依据,采集了120例内蒙古蒙古族男性无关个体静脉血,EDTA抗凝,用酚-氯仿法抽提DNA,PCR扩增DYS413基因座,6％非变性聚丙烯酰胺凝胶电泳,1‰硝酸银(AgNO_3)染色分型。在120例内蒙古蒙古族男性人群中共检出30个不同的单倍型,其频率介于0.0007至0.01361之间,其HD(单倍型多样性)值为0.94054。表明DYS413基因座在内蒙古蒙古族人群中分布好,对法医学和人类遗传学研究具有重要价值。