Y-chromosome-specific microsatellite variation in Australian aboriginals

The frequency distributions of 4 highly polymorphic Y-chromosome-specific microsatellites (DYS19, DYS390, DYS391, and DYS392) were determined in 79 unrelated Australian Aboriginal males from the Northern Territory. These results are compared with those observed in worldwide populations at both the locus and the haplotype level. Common alleles in Aboriginals are DYS19*15 (49%), DYS19*14 (28%), DYS390*19 (39%), DYS390*24 (20%), DYS391*10 (72%), DYS392*11 (63%), and DYS392*13 (28%). No evidence of reduced gene diversity was observed for these Y-chromosome alleles. DYS390 exhibits the most complex arrangement, displaying a bimodal distribution composed of common alleles (*22-*26), and rare short alleles (*18-*20), with an intermediate allele (*21) being absent. DYS390*20, previously reported only in Papuans and Samoans, is observed for the first time in Aboriginals. Compared with a recent study of Aboriginals, our sample exhibits considerable diversity in the haplotypes associated with the rare DYS390*19 allele, indicating that this allele is of considerable antiquity, if it arose as a single deletion event. Combining all 4 Y-chromosome-linked microsatellites produced 41 unique haplotypes, which were linked using a median-joining network. This network shows that most (78%) of our Aboriginal haplotypes fall into 2 distinct clusters, which likely represent 2 separate lineages. Seven haplotypes are shared with haplotypes found in a recent study of Aboriginals, and 7 are shared with a Spanish population. The cluster of Aboriginal haplotypes associated with the short DYS390 alleles does not share any haplotypes with the Spanish, indicating that this cluster of haplotypes is unique to Australian Aboriginals. Limited data from 4 worldwide populations used to construct haplotypes based on 3 loci (DYS19, DYS390, DYS392) show that only 4 of these haplotypes are seen in Australian Aboriginals. Shared haplotypes may be the result of admixture and/or recurrent mutation at these loci. Expanding the haplotype analysis to include biallelic markers on the Y chromosome will resolve this issue.     

Nuclear and chloroplast microsatellite diversity in Phaseolus vulgaris L. from Sardinia (Italy)

Studies of the level and the structure of the genetic diversity of local varieties of Phaseolus vulgaris are of fundamental importance, both for the management of genetic resources and to improve our understanding of the pathways of dissemination and the evolution of this species in Europe. We have here characterized 73 local bean populations from Sardinia (Italy) using seed traits and molecular markers (phaseolins, nuSSRs and cpSSRs). American landraces and commercial varieties were also included for comparison. We see that: (a) the Sardinian material is distinct from the commercial varieties considered; (b) the variation in the seed traits is high and it mostly occurs among populations (95%); (c) compared to the American sample and the commercial varieties, the Sardinian collection has a low level of diversity; (d) the majority (>95%) of the Sardinian individuals belong to the Andean gene pool; (e) the Sardinian material shows a strong genetic structure, both for cpSSRs and nuSSRs; (f) the nuSSRs and cpSSRs concur in differentiating between gene pools, but a lack of congruence between nuclear and chloroplast has been observed within gene pools; and (g) there are three putative hybrids between the Andean and Mesoamerican gene pools. Despite the relatively low level of diversity, which is probably due to a strong founder effect, the Sardinian landraces are worth being conserved and studied further because of their distinctiveness and because hybridization within and between the gene pools could generate variation that will be useful for breeding. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

New remarkable records of microfungi from Sardinia (Italy)

In June 2009 we organized a botanical student excursion to the eastern part of Sardinia, Italy. On this occasion we were able to collect and identify over 80 species of microfungi growing on higher plants. The collecting sites were spread over a large area, among them were La Caletta, Capo Comino, Monte Albo, Cala Gonone, Monte Maccione, San Teodoro, Capo Testa. The collected microfungi were parasitic or saprophytic; Basidiomycotina (Uredinales), Ascomycotina and Deuteromycotina (Hyphomycetes, Coelomycetes) were predominant. Examples are Pezicula corticola (J?rg.) NANNF. (new for Sardinia), on Pyrus communis. Puccinia chamaecyparissi TROTT. (new for Sardinia), on Santolina insularis. Sphaceloma oleae CICC. and GRANITI (new for Sardinia) and Phlyctema vagabunda DESM. (new for Sardinia), on Olea europaea and Arbutus unedo. Puccinia pseudosphaeria MONT. (new for Sardinia), on Sonchus oleraceus. Discula umbrinella (BERK. and BR.) SUTTON (new for Sardinia)(D. quercina WEST. and BARK), on Quercus coccifera. Zaghouania phillyreae PAT. (new for Sardinia), on Phillyrea angustifolia. Phymatotrichum omnivorum (DUGGAR) HENNEBERT, new on Verbascum thapsus for Sardinia. Guignardia punctoidea (COOKE) SCHROTER (new for Sardinia), on Quercus ilex. Many of the collected species are rare or unknown for the area of investigation until now. All specimens are located in the Herbarium ESS, Mycotheca Parva collection G.B. Feige and N. Ale-Agha.     

Anchusa formosa (Boraginaceae), a new species from Southern Sardinia (Italy)

ABSTRACT

A new Anchusa species was discovered in the massif of Mt. Lattias in South-Western Sardinia. This species, here described as A. formosa, shows a sharp phenotypic differentiation from the other Sardinian endemic taxa of Anchusa, especially in habit, leaf shape and size, inflorescence and calyx morphology. Ecological traits are also peculiar, the plant being restricted to siliceous debris that accumulates in small depositional areas of dry stream beds. A. formosa is likely to represent a paleogenic schizoendemism originated through isolation and genetic drift from the same genie pool of the other Corso-Sardinian endemic taxa of Anchusa. SEM analyses provide additional information on the micromorphology of the stigma and its papillar pattern, pollen grains, mericarp coat surface and trichomes. The anatomical structure of stem, root and leaf were also analysed. Due to its extreme localization and ecological specialization, A. formosa needs total protection in its natural habitat and should be added to National and International Red Lists of plants at risk of extinction.     

Remarkable desmids (Desmidiaceae, Charophyta) from Sardinia, Italy

A number of benthic microfauna samples collected in Sardinia in the 1970s, and screened for the occurrence of microalgae in the 1990s, revealed some remarkable desmid species. Most of these species could not be found in a series of samples collected in 2006. Eleven desmid taxa are discussed in detail, two of which are described as new to science; Cosmarium majaeforme sp. nov. and Xanthidium sardiniense sp. nov. The specific composition of the Sardinian desmid flora is discussed both in relation to the prevailing environmental conditions and to its geographic position close to the African continent.     

Allelic and population variation of microsatellite loci in aspen (Populus tremuloides)

To develop a robust basis for inferences about population genetics and evolution, this work assayed 192 aspens (Populus tremuloides) from 11 sites in Wisconsin, USA, for allelic and population variation at 16 microsatellite loci distributed across the Populus genome. Frequency distributions of fluorochrome-labeled alleles resolved by capillary electrophoresis were analyzed for relationships to repeat size and number. Population-level statistics were compared with those of other studies, especially in Populus. All loci were polymorphic, varying widely in the number of alleles per locus (mean = 8.25, range 2-20). Expected and observed heterozygosities were high (0.45 and 0.41, respectively), with little differentiation among populations (F(ST) = 0.006-0.045) and a moderate level of inbreeding (F(IS) = 0.09), intermediate among levels reported in studies based on isozymes. Contrary to several other reports, allele frequencies clustered tightly around the modal frequency, and the genetic diversity (measured as alleles per locus or as expected heterozygosity) was not related to either the repeat unit size or to the number of repeats.     

Human population expansion and microsatellite variation

Polymorphisms at di-, tri-, and tetranucleotide microsatellite loci have been analyzed in 14 worldwide populations. A statistical index of population expansion, denoted S(k), is introduced to detect historical changes in population size using the variation at the microsatellites. The index takes the value 0 at equilibrium with constant population size and is positive or negative according to whether the population is expanding or contracting, respectively. The use of S(k) requires estimation of properties of the mutation distribution for which we use both family data of Dib et al. for dinucleotide loci and our population data on tri- and tetranucleotide loci. Statistical estimates of the expansion index, as well as their confidence intervals from bootstrap resampling, are provided. In addition, a dynamical analysis of S(k) is presented under various assumptions on population growth or decline. The studied populations are classified as having high, intermediate, or low values of S(k) and genetic variation, and we use these to interpret the data in terms of possible population dynamics. Observed values of S(k) for samples of di-, tri-, and tetranucleotide data are compatible with population expansion earlier than 60,000 years ago in Africa, Asia, and Europe if the initial population size before the expansion was on the order of 500. Larger initial population sizes force the lower bound for the time since expansion to be much earlier. We find it unlikely that bottlenecks occurred in Central African, East Asian, or European populations, and the estimated expansion times are rather similar for all of these populations. This analysis presented here suggests that modern human populations departed from Africa long before they began to expand in size. Subsequently, the major groups (the African, East Asian, and European groups) started to grow at approximately same time. Populations of South America and Oceania show almost no growth. The Mbuti population from Zaire appears to have experienced a bottleneck during its expansion.     

Miocene carbonate factories in the syn-rift Sardinia Graben Subbasins (Italy)

Summary Miocene syn-rift carbonate production areas are exposed in south-eastern Sardinia (Italy) along the eastern side of the Plio-Pleistocene Campidano Graben. Here the downfaulted margins of the Oligo-Miocene Sardinia rift-basin crop out with a complex alignment of smaller subbasins. Carbonate factories developed during the Aquitanian times in these tectonically controlled small depositional subbasins, where terrigenous input might be high due to the erosion of the uplifted pre-Neogene substrata. Terrigenous deposits generally acted as passive substratum for pioneer communities of rhodalgal-type (red algae, ostreids, bryozoans) and locally evolved into coral-dominated assemblages. Carbonate production areas occur on tilted, uplifted blocks as well as along basement margins. These have varying organic communities and facies characteristics strongly dependent on different environmental conditions. In footwall areas, devoid of (or with a very reduced) terrigenous supply, open foramol carbonate factories occur with aggradational-progradational stratigraphic geometries. The resulting pure calcareous successions are organized in sequences, bounded by tectonically driven discontinuity surfaces. In sectors close to the hinterland area, with a higher freshwater input and a consequent significant clastic input, coral-dominated assemblages grew during long periods of quiescence between flash floods. Repeated coral-rich communities developed on thick wedges of terrigenous debris. Carbonate facies composition and distribution were mainly controlled by local syn-sedimentary tectonics and eustasy as well as by climate. However, although the inception of the carbonate factories was presumably not synchronous, their growth represented the response to a relative regional sea level rise subsequent to episodes of significant clastic supply: the expression of an early syn-rift stage. During the Burdigalian (N6 zone) a hemipelagic cover uniformly sealed the neritic successions. This basin wide drowning event appears to correspond to the transgressive system tract of the TB2.1 cycle ofHaq et al. (1987) but it can also be interpreted as the expression of an evolved syn-rift stage passing to late syn-rift and quiescence stages. Beneath the hemipelagic cover in some areas, ?late Aquitanian-early Burdigalian deep erosive surfaces, terrigenous clastics and paleosoils have been recognized. These suggest a relative sea level fall and may relate to the global sea level drop at the TB1-TB2 boundary (seeHaq et al., 1987) or to diacronous uplift of different fault blocks.     

The flora of the island Piana (Sardinia,Italy)

Abstract

The author reports the results of the herborizations carried out on the island Piana (northeastern Sardinia) located between Cape Ceraso and Cape Coda Cavallo. The flora consists of 250 entities distributed in 154 genera, inclusive of 54 families. The author gives information regarding the mail features of the vegetal coverage, and points out the presence of two species: Limonistrum monopetalum (L.) Boiss. and Omithoga-lum arabicum L., which are extremely rare in the little islands.     

Steinernema ichnusae sp. n. (Nematoda: Steinernematidae) a new entomopathogenic nematode from Sardinia Island (Italy)

A new Steinernema species was isolated from three different sandy soil samples along the Platamona Beach, in the north-west coast of Sardinia Island (Italy). This new species is characterized by the following morphological characters: infective third-stage juvenile with a body length of 866 ± 61 (767-969) μm, distance from head to excretory pore of 63 ± 2.7 (59-68) μm, tail length of 81 ± 3.2 (76-89) μm, ratio E (%) 77 ± 3.4 (68-83); male tail with a mucron only in the second generation, spicule length of 66 ± 1.4 (64-67) μm and gubernaculum length of 44 ± 1.4 (43-46) μm in the first generation male; female of first generation with a slight vulval protrusion and ratio D (%) of 53 ± 4.0 (47-63). The new species differs distinctly from the related species (S. feltiae, S. kraussei, S. litorale, S. oregonense and S. cholashanense) in some morphometric values such as percentage of hyaline portion, ratios of gubernaculum/spicule length, spicule head length/width. The DNA analyses of the internal transcribed spacers and D2D3 regions show that the studied nematode isolates are a new species. Cross hybridisation tests with S. feltiae, S. kraussei, S. litorale, S. weiseri and S. oregonense showed that these species were reproductively isolated.     

G1m phenotypes in a sample population from Tirana (Albania)

This report presents the distribution of G1m phenotypes (allotypes z, a, x, f,) observed in a sample population from Tirana (Albania). The comparison between these data and those previously found in a sample group of Arbreshes (Albanians who live in South Italy where they immigrated about 4 centuries ago) showed that, at least for the tested markers, the cultural identity of Arbreshes is not reflected by a genetic isolation from Southern Italians.     

The peopling of Sardinia (Italy): history and effects

Over the last ten years the population of the Mediterranean island of Sardinia has been object of numerous studies in the fields of anthropology and population genetics. Its insularity, central position in the Mediterranean area and rich historical past have made the island a veritable laboratory for the study and understanding of those interacting evolutionary mechanisms which determine a population's genetic structure. Indeed, from work performed at different levels on genetic structure analysis there emerges an extremely complex picture of the relationships between Sardinian and other Italian and Mediterranean populations, but also of relationships within the Sardinian population itself The diversification from Mediterranean and Italian populations can be explained by Sardinia's historical and demographic past. Internal heterogeneity can be attributed, in part, to strict isolation and the accompanying high levels of endogamy and inbreeding, and in part to the endemic presence of malaria which exerted a strong selective pressure on some characteristics; determining, for example, the differentiation between the plains and the mountain areas. Finally, an influence on Sardinia's biological history not to be neglected could be attributed to the demographic events, which triggered off phenomena of genetic drift and to cultural factors.     

A new taxon in the Infundibulicybe gibba complex (Basidiomycota, Agaricales, Tricholomataceae) from Sardinia (Italy)

A new species of Infundibulicybe (viz. I. mediterranea sp. nov.) is described from Sardinia based both on morphological and molecular ITS data. The species, a close ally of I. gibba, differs from the latter in the darker tinges of the basidiomata, the stipe, which is nearly concolorous with the pileus, and smaller basidiospores. Drawings of the main micro-morphological features as well as a color photograph of fresh basidiomata in situ are provided.     

Genetics,geography, and culture: The population of S. Pietro Island (Sardinia,Italy)

An interesting aspect of the island of Sardinia (Italy) is the wide range of genetic variability within the island itself. The variability is widened by the presence of some populations of different ethnic origin who speak a language other than Sardinian. This work deals with the study of the genetic structure of the Carloforte population which inhabits the tiny island of S. Pietro 4 km off the southwest coast of Sardinia. S. Pietro was first populated in 1738 by emigrants coming from the island of Tabarka (Tunisia) who spoke an archaic form of the Ligurian dialect. Data on genetic polymorphisms in the Carloforte population are presented and discussed in relation to some Sardinian and Italian populations. Data on demographic and matrimonial structure are also presented. The genetic analyses show the Carloforte population as being clearly separated from both Sardinians and continental Italians. The isolation of Carloforte, highlighted by language diversity, endogamy, and consanguinity levels and marriage area, supports the idea of genetic diversity linked to cultural peculiarity. © 1996 Wiley-Liss, Inc.     

An updated inventory of the non-native flora of Sardinia (Italy)

We provide an updated inventory of the non-native flora of the Italian island of Sardinia, including accepted names, family, synonyms, biological form, fruit type, introduction pathway and native origin. This inventory was performed by reviewing the available literature and conducting dedicated field surveys across the entire island. The inventory catalogues 931 non-native taxa, including 31 cryptogenic species, 901 species, 14 subspecies, 13 varieties, two forms and one cultivar. We utilised the position on the introduction–invasion continuum concept and meta-population criterion to further label each species. Based on these frameworks, the non-native flora of Sardinia can be divided into 274 casual, 169 naturalised, 19 invasive, 440 exclusively planted and 29 unobserved after 1950. There are 204 archaeophytes and 727 neophytes. The majority of the non-native species (791) were introduced to the island voluntarily, and 140 species were introduced accidentally. The present inventory identifies 72 additional non-native taxa not previously reported in the literature.     

The rodents from the Late Miocene Oreopithecus-bearing site of Fiume Santo (Sardinia,Italy)

The locality of Fiume Santo (Sardinia, Italy) represents the westernmost extension of endemic Oreopithecus-bearing faunas. Here we describe the rodent fauna recovered at this site, which only includes the murids Huerzelerimys oreopitheci and Anthracomys lorenzi, and the glirids Anthracoglis engesseri nov. sp. and Anthracoglis nov. sp. I. A. engesseri nov. sp. differs from Anthracoglis marinoi, the other species of this genus known so far, by its larger size, wider upper cheek teeth and more reduced accessory ridges, particularly in the upper cheek teeth. Anthracoglis nov. sp. I is only known by a single tooth and cannot be adequately characterized. The fauna seems to be a mixture of elements from the V-1, V-2 and V-3 local zones of the Baccinello-Cinigiano basin (Tuscany, Italy), with H. oreopitheci being characteristic from zone V-1 and Anthracoglis lorenzi from zone V-3. Nevertheless, a few remains of A. lorenzi have been also recovered from V-2 assemblages at Baccinello and A. engesseri nov. sp. is also recorded in Monte Bamboli, which is correlated to V-2 faunas. Accordingly, a correlation to V-2 zone of the Baccinello-Cinigiano basin is preferred. Finally, the structure and composition of the rodent assemblage is compared to those of the Tuscan sites. The Fiume Santo assemblage resembles the insular faunas of Tuscany by its low species richness, although it is more balanced. This may be related to slight chronological or environmental differences between the two areas or to the existence of a geographical barrier.     

Genetic variation in prehistoric Sardinia

We sampled teeth from 53 ancient Sardinian (Nuragic) individuals who lived in the Late Bronze Age and Iron Age, between 3,430 and 2,700 years ago. After eliminating the samples that, in preliminary biochemical tests, did not show a high probability to yield reproducible results, we obtained 23 sequences of the mitochondrial DNA control region, which were associated to haplogroups by comparison with a dataset of modern sequences. The Nuragic samples show a remarkably low genetic diversity, comparable to that observed in ancient Iberians, but much lower than among the Etruscans. Most of these sequences have exact matches in two modern Sardinian populations, supporting a clear genealogical continuity from the Late Bronze Age up to current times. The Nuragic populations appear to be part of a large and geographically unstructured cluster of modern European populations, thus making it difficult to infer their evolutionary relationships. However, the low levels of genetic diversity, both within and among ancient samples, as opposed to the sharp differences among modern Sardinian samples, support the hypothesis of the expansion of a small group of maternally related individuals, and of comparatively recent differentiation of the Sardinian gene pools. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Analysis of microsatellite variation in the rainbow trout (Parasalmo (Oncorhynchus) mykiss) from Kamchatka

Genetic variation of Kamchatka rainbow trout Parasalmo (O.) mykiss was examined using 10 microsatellite DNA loci, and phylogeographic comparison with other representatives of the species across the distribution range was performed. It was demonstrated that Kamchatka populations differed from other geographic groups of rainbow trout in a number of microsatellite loci. These populations also displayed distinct clustering and were characterized by lower genetic diversity. Analysis of a set of 26 different microsatellite loci (personal and literature data) demonstrated that most of the populations within the Kamchatka region were separated from one another, characterized by marked geographic differentiation, and affiliation to certain river basins. In Kamchatka rainbow trout, with high degree of probability, three geographic clusters (northwestern, southwestern, and eastern) were identified. In general, analysis of microsatellite DNA supported the data on low genetic diversity of the Kamchatka group Parasalmo (O.) mykiss, based on the variation estimates for a number of genes of nuclear and mitochondrial DNA, and allozyme loci.