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1.
Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores)
Mario Fernández-Mazuecos José Luis Blanco-Pastor José M. Gómez Pablo Vargas 《Annals of botany》2013,112(9):1705-1722
Background and Aims
The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ∼30 species and subspecies with highly specialized corollas.Methods
A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species.Key Results
A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects.Conclusions
The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes. 相似文献2.
M��nica Font N��ria Garcia-Jacas Roser Vilatersana Cristina Roquet Alfonso Susanna 《Annals of botany》2009,103(6):985-997
Background and Aims
Section Acrocentron of the genus Centaurea is one of the largest sections of Centaurea with approx. 100 species. The geographic distribution, centred in the Mediterranean, makes it an excellent example for studies of the biogeographic history of this biodiversity-rich region.Methods
Plastid (trnH-psbA) and nuclear (ITS and ETS) DNA sequence analysis was used for phylogenetic reconstruction. Ancestral biogeographic patterns were inferred by dispersal-vicariance analysis (DIVA).Key Results
The resulting phylogeny has implications for the sectional classification of Acrocentron and confirms merging sect. Chamaecyanus into Acrocentron as a subsection. Previous suggestions of an eastern Mediterranean origin of the group are confirmed. The main centres of diversification established in previous studies are now strongly supported. Expansion of the group in two different radiations that followed patently diverse paths is inferred.Conclusions
Radiation followed two waves, widely separated in time scale. The oldest one, from Turkey to Greece and the northern Balkans and then to North Africa and Iberia, should be dated at the end of the Miocene in the Messinian period. It reached the Iberian Peninsula from the south, following a route that is landmarked by several relictic taxa in Sicily and North Africa. A later radiation during the Holocene interglacial periods followed, involving species from the north of the Balkan Peninsula, along a Eurasian pathway running from Central Iberia to the steppes of Kazakhstan. A generalized pattern of reticulation is also evident from the results, indicating past contacts between presently separated species. Molecular data also confirmed the extent of hybridization within Acrocentron and were successful in reconstructing the paleogeography of the section.Key words: Centaurea sect. Acrocentron, Cardueae, dispersal-vicariance, ETS, ITS, Mediterranean, phylogeny, psbA-trnH, radiation, reticulation 相似文献3.
The evolutionary patterns of the Mediterranean flora during the Quaternary have been relatively well documented based on phylogenetic and biogeographic analyses, but few studies have addressed the evolutionary traits that determined diversification and range expansion success during this period. We analysed previously published and newly generated sequences of three plastid noncoding regions (rpl32‐trnLUAG, trnS‐trnG and trnL‐trnF), the nuclear ribosomal internal transcribed spacer (ITS) and a low‐copy nuclear gene intron (AGT1) of Linaria sect. Supinae, a group of angiosperms that diversified in the Quaternary. The origin and recent colonization dynamics of closely related lineages were inferred by biogeographic reconstruction and phylogeographic analyses, while breeding system experiments coupled with ecological and morphological data were used to test association with range expansion and diversification. A combination of traits, including selfing, short lifespan and the ability to tolerate a wide variety of substrates, were key factors underlying range expansion after long‐distance dispersal throughout the Mediterranean basin. By contrast, self‐incompatibility may have promoted higher diversification rates in narrow ranges of the Iberian Peninsula. We argue that a few traits contributed to the adoption of two contrasting strategies that may have been predominant in the evolution of Mediterranean angiosperms. 相似文献
4.
Background and Aims
Salvia is the largest genus in Lamiaceae and it has recently been found to be non-monophyletic. Molecular data on Old World Salvia are largely lacking. In this study, we present data concerning Salvia in Africa. The focus is on the colonization of the continent, character evolution and the switch of pollination systems in the genus.Methods
Maximum likelihood and Bayesian inference were used for phylogenetic reconstruction. Analyses were based on two nuclear markers [internal transcribed spacer (ITS) and external transcribed spacer (ETS)] and one plastid marker (rpl32-trnL). Sequence data were generated for 41 of the 62 African taxa (66 %). Mesquite was used to reconstruct ancestral character states for distribution, life form, calyx shape, stamen type and pollination syndrome.Key Results
Salvia in Africa is non-monophyletic. Each of the five major regions in Africa, except Madagascar, was colonized at least twice, and floristic links between North African, south-west Asian and European species are strongly supported. The large radiation in Sub-Saharan Africa (23 species) can be traced back to dispersal from North Africa via East Africa to the Cape Region. Adaptation to bird pollination in southern Africa and Madagascar reflects parallel evolution.Conclusions
The phenotypic diversity in African Salvia is associated with repeated introductions to the continent. Many important evolutionary processes, such as colonization, adaptation, parallelism and character transformation, are reflected in this comparatively small group. The data presented in this study can help to understand the evolution of Salvia sensu lato and other large genera. 相似文献5.
Amparo M. Martínez Luis T. Gama Javier Ca?ón Catarina Ginja Juan V. Delgado Susana Dunner Vincenzo Landi Inmaculada Martín-Burriel M. Cecilia T. Penedo Clementina Rodellar Jose Luis Vega-Pla Atzel Acosta Luz A. álvarez Esperanza Camacho Oscar Cortés Jose R. Marques Roberto Martínez Ruben D. Martínez Lilia Melucci Guillermo Martínez-Velázquez Jaime E. Mu?oz Alicia Postiglioni Jorge Quiroz Philip Sponenberg Odalys Uffo Axel Villalobos Delsito Zambrano Pilar Zaragoza 《PloS one》2012,7(11)
Background
American Creole cattle presumably descend from animals imported from the Iberian Peninsula during the period of colonization and settlement, through different migration routes, and may have also suffered the influence of cattle directly imported from Africa. The introduction of European cattle, which began in the 18th century, and later of Zebu from India, has threatened the survival of Creole populations, some of which have nearly disappeared or were admixed with exotic breeds. Assessment of the genetic status of Creole cattle is essential for the establishment of conservation programs of these historical resources.Methodology/Principal Findings
We sampled 27 Creole populations, 39 Iberian, 9 European and 6 Zebu breeds. We used microsatellite markers to assess the origins of Creole cattle, and to investigate the influence of different breeds on their genetic make-up. The major ancestral contributions are from breeds of southern Spain and Portugal, in agreement with the historical ports of departure of ships sailing towards the Western Hemisphere. This Iberian contribution to Creoles may also include some African influence, given the influential role that African cattle have had in the development of Iberian breeds, but the possibility of a direct influence on Creoles of African cattle imported to America can not be discarded. In addition to the Iberian influence, the admixture with other European breeds was minor. The Creoles from tropical areas, especially those from the Caribbean, show clear signs of admixture with Zebu.Conclusions/Significance
Nearly five centuries since cattle were first brought to the Americas, Creoles still show a strong and predominant signature of their Iberian ancestors. Creole breeds differ widely from each other, both in genetic structure and influences from other breeds. Efforts are needed to avoid their extinction or further genetic erosion, which would compromise centuries of selective adaptation to a wide range of environmental conditions. 相似文献6.
Klara Stefflova Matthew C. Dulik Athma A. Pai Amy H. Walker Charnita M. Zeigler-Johnson Serigne M. Gueye Theodore G. Schurr Timothy R. Rebbeck 《PloS one》2009,4(11)
Background
Population history can be reflected in group genetic ancestry, where genomic variation captured by the mitochondrial DNA (mtDNA) and non-recombining portion of the Y chromosome (NRY) can separate female- and male-specific admixture processes. Genetic ancestry may influence genetic association studies due to differences in individual admixture within recently admixed populations like African Americans.Principal Findings
We evaluated the genetic ancestry of Senegalese as well as European Americans and African Americans from Philadelphia. Senegalese mtDNA consisted of ∼12% U haplotypes (U6 and U5b1b haplotypes, common in North Africa) while the NRY haplotypes belonged solely to haplogroup E. In Philadelphia, we observed varying degrees of admixture. While African Americans have 9–10% mtDNAs and ∼31% NRYs of European origin, these results are not mirrored in the mtDNA/NRY pools of European Americans: they have less than 7% mtDNAs and less than 2% NRYs from non-European sources. Additionally, there is <2% Native American contribution to Philadelphian African American ancestry and the admixture from combined mtDNA/NRY estimates is consistent with the admixture derived from autosomal genetic data. To further dissect these estimates, we have analyzed our samples in the context of different demographic groups in the Americas.Conclusions
We found that sex-biased admixture in African-derived populations is present throughout the Americas, with continual influence of European males, while Native American females contribute mainly to populations of the Caribbean and South America. The high non-European female contribution to the pool of European-derived populations is consistently characteristic of Iberian colonization. These data suggest that genomic data correlate well with historical records of colonization in the Americas. 相似文献7.
Pino-Yanes M Corrales A Basaldúa S Hernández A Guerra L Villar J Flores C 《PloS one》2011,6(3):e18389
Background
Despite the limited genetic heterogeneity of Spanish populations, substantial evidences support that historical African influences have not affected them uniformly. Accounting for such population differences might be essential to reduce spurious results in association studies of genetic factors with disease. Using ancestry informative markers (AIMs), we aimed to measure the African influences in Spanish populations and to explore whether these might introduce statistical bias in population-based association studies.Methodology/Principal Findings
We genotyped 93 AIMs in Spanish (from the Canary Islands and the Iberian Peninsula) and Northwest Africans, and conducted population and individual-based clustering analyses along with reference data from the HapMap, HGDP-CEPH, and other sources. We found significant differences for the Northwest African influence among Spanish populations from as low as ≈5% in Spanish from the Iberian Peninsula to as much as ≈17% in Canary Islanders, whereas the sub-Saharan African influence was negligible. Strikingly, the Northwest African ancestry showed a wide inter-individual variation in Canary Islanders ranging from 0% to 96%, reflecting the violent way the Islands were conquered and colonized by the Spanish in the XV century. As a consequence, a comparison of allele frequencies between Spanish samples from the Iberian Peninsula and the Canary Islands evidenced an excess of markers with significant differences. However, the inflation of p-values for the differences was adequately controlled by correcting for genetic ancestry estimates derived from a reduced number of AIMs.Conclusions/Significance
Although the African influences estimated might be biased due to marker ascertainment, these results confirm that Northwest African genetic footprints are recognizable nowadays in the Spanish populations, particularly in Canary Islanders, and that the uneven African influences existing in these populations might increase the risk for false positives in association studies. Adjusting for population stratification assessed with a few dozen AIMs would be sufficient to control this effect. 相似文献8.
Joseph Donfack Daniel H Schneider Zheng Tan Thorsten Kurz Inna Dubchak Kelly A Frazer Carole Ober 《Respiratory research》2005,6(1):145
Background
Evolutionarily conserved sequences likely have biological function.Methods
To determine whether variation in conserved sequences in non-coding DNA contributes to risk for human disease, we studied six conserved non-coding elements in the Th2 cytokine cluster on human chromosome 5q31 in a large Hutterite pedigree and in samples of outbred European American and African American asthma cases and controls.Results
Among six conserved non-coding elements (>100 bp, >70% identity; human-mouse comparison), we identified one single nucleotide polymorphism (SNP) in each of two conserved elements and six SNPs in the flanking regions of three conserved elements. We genotyped our samples for four of these SNPs and an additional three SNPs each in the IL13 and IL4 genes. While there was only modest evidence for association with single SNPs in the Hutterite and European American samples (P < 0.05), there were highly significant associations in European Americans between asthma and haplotypes comprised of SNPs in the IL4 gene (P < 0.001), including a SNP in a conserved non-coding element. Furthermore, variation in the IL13 gene was strongly associated with total IgE (P = 0.00022) and allergic sensitization to mold allergens (P = 0.00076) in the Hutterites, and more modestly associated with sensitization to molds in the European Americans and African Americans (P < 0.01).Conclusion
These results indicate that there is overall little variation in the conserved non-coding elements on 5q31, but variation in IL4 and IL13, including possibly one SNP in a conserved element, influence asthma and atopic phenotypes in diverse populations. 相似文献9.
Background
Population genetic theory holds that oceanic island populations are expected to have lower levels of genetic variation than their mainland counterparts, due to founder effect after island colonization from the continent. Cistus monspeliensis (Cistaceae) is distributed in both the Canary Islands and the Mediterranean region. Numerous phylogenetic results obtained in the last years allow performing further phylogeographic analyses in Cistus.Methodology/Principal Findings
We analyzed sequences from multiple plastid DNA regions in 47 populations of Cistus monspeliensis from the Canary Islands (21 populations) and the Mediterranean basin (26 populations). The time-calibrated phylogeny and phylogeographic analyses yielded the following results: (1) a single, ancestral haplotype is distributed across the Mediterranean, whereas 10 haplotypes in the Canary Islands; (2) four haplotype lineages are present in the Canarian Islands; (3) multiple colonization events across the archipelago are inferred; (4) the earliest split of intraspecific lineages occurred in the Early to Middle Pleistocene (<930,000 years BP).Conclusions/Significance
The contrasting pattern of cpDNA variation is best explained by genetic bottlenecks in the Mediterranean during Quaternary glaciations, while the Canarian archipelago acted as a refugium of high levels of genetic diversity. Active colonization across the Canarian islands is supported not only by the distribution of C. monspeliensis in five of the seven islands, but also by our phylogeographic reconstruction in which unrelated haplotypes are present on the same island. Widespread distribution of thermophilous habitats on every island, as those found throughout the Mediterranean, has likely been responsible for the successful colonization of C. monspeliensis, despite the absence of a long-distance dispersal mechanism. This is the first example of a plant species with higher genetic variation among oceanic island populations than among those of the continent. 相似文献10.
T. Luijkx M. J. Cramer A. Zaidi R. Rienks P. J. Senden S. Sharma F. J. van Hellemondt C. F. Buckens W. P. Mali B. K. Velthuis 《Netherlands heart journal》2012,20(10):389-395
Purpose
Left ventricular (LV) trabeculation may be more pronounced in ethnic African than in Caucasian (European) athletes, leading to possible incorrect diagnosis of left ventricular non-compaction cardiomyopathy (LVNC). This study investigates ethnic differences in LV hypertrabeculation amongst elite athletes with cardiac magnetic resonance (CMR) and electrocardiography (ECG).Methods
38 elite male football (soccer) players (mean age 23.0, range 19–34 years, 28/38 European, 10/38 African) underwent CMR and ECG. Hypertrabeculation was assessed using the ratio of non-compacted to compacted myocardium (NC/C ratio) on long-axis and short-axis segments. ECGs were systematically rated.Results
No significant differences were seen in ventricular volumes, wall mass or E/A ratio, whereas biventricular ejection fraction (EF) was significantly lower in African athletes (European/African athletes LVEF 55/50 %, p = 0.02; RVEF 51/48 %, p = 0.05). Average NC/C ratio was greater in African athletes but only significantly at mid-ventricular level (European/African athletes: apical 0.91/1.00, p = 0.65; mid-ventricular 0.89/1.45, p < 0.05; basal 0.40/0.46, p = 0.67). ECG readings demonstrated no significant group differences, and no correlation between ECG anomalies and hypertrabeculation.Conclusions
A greater degree of LV hypertrabeculation is seen in healthy African athletes, combined with biventricular EF reduction at rest. Recognition of this phenomenon is necessary to avoid misdiagnosis of LVNC. 相似文献11.
Background
The ancestry of African-descended Americans is known to be drawn from three distinct populations: African, European, and Native American. While many studies consider this continental admixture, few account for the genetically distinct sources of ancestry within Africa – the continent with the highest genetic variation. Here, we dissect the within-Africa genetic ancestry of various populations of the Americas self-identified as having primarily African ancestry using uniparentally inherited mitochondrial DNA.Methods and Principal Findings
We first confirmed that our results obtained using uniparentally-derived group admixture estimates are correlated with the average autosomal-derived individual admixture estimates (hence are relevant to genomic ancestry) by assessing continental admixture using both types of markers (mtDNA and Y-chromosome vs. ancestry informative markers). We then focused on the within-Africa maternal ancestry, mining our comprehensive database of published mtDNA variation (∼5800 individuals from 143 African populations) that helped us thoroughly dissect the African mtDNA pool. Using this well-defined African mtDNA variation, we quantified the relative contributions of maternal genetic ancestry from multiple W/WC/SW/SE (West to South East) African populations to the different pools of today''s African-descended Americans of North and South America and the Caribbean.Conclusions
Our analysis revealed that both continental admixture and within-Africa admixture may be critical to achieving an adequate understanding of the ancestry of African-descended Americans. While continental ancestry reflects gender-specific admixture processes influenced by different socio-historical practices in the Americas, the within-Africa maternal ancestry reflects the diverse colonial histories of the slave trade. We have confirmed that there is a genetic thread connecting Africa and the Americas, where each colonial system supplied their colonies in the Americas with slaves from African colonies they controlled or that were available for them at the time. This historical connection is reflected in different relative contributions from populations of W/WC/SW/SE Africa to geographically distinct Africa-derived populations of the Americas, adding to the complexity of genomic ancestry in groups ostensibly united by the same demographic label. 相似文献12.
Carolin Kindler Philip de Pous Salvador Carranza Menad Beddek Philippe Geniez Uwe Fritz 《Organisms Diversity & Evolution》2018,18(1):143-150
We examined phylogeographic differentiation of the red-eyed grass snake (Natrix astreptophora) using 1984 bp of mtDNA and 13 microsatellite loci from specimens collected across its distribution range in southwestern Europe and northwestern Africa. Based on phylogenetic analyses of mtDNA, European N. astreptophora constituted the sister clade to a weakly supported North African clade comprised of two deeply divergent and well-supported clades, one corresponding to Moroccan snakes and the other to snakes from Algeria and Tunisia. This tripartite differentiation was confirmed by analyses of microsatellite loci. According to a fossil-calibrated molecular clock, European and North African N. astreptophora diverged 5.44 million years ago (mya), and the two Maghrebian clades split 4.64 mya. These dates suggest that the radiation of the three clades was initiated by the environmental changes related to the Messinian Salinity Crisis and the reflooding of the Mediterranean Basin. The differentiation of N. astreptophora, with distinct clades in the Iberian Peninsula and in the western and eastern Maghreb, corresponds to a general phylogeographic paradigm and resembles the differentiation found in another co-distributed Natrix species, the viperine snake (N. maura). Despite both species being good swimmers, the Strait of Gibraltar constitutes a significant biogeographic barrier for them. The discovery that North Africa harbours two endemic lineages of N. astreptophora necessitates more conservation efforts for these imperilled snakes. 相似文献
13.
Norosoa J. Razafinarivo Romain Guyot Aaron P. Davis Emmanuel Couturon Serge Hamon Dominique Crouzillat Michel Rigoreau Christine Dubreuil-Tranchant Valerie Poncet Alexandre De Kochko Jean-Jacques Rakotomalala Perla Hamon 《Annals of botany》2013,111(2):229-248
Background and Aims
The coffee genus (Coffea) comprises 124 species, and is indigenous to the Old World Tropics. Due to its immense economic importance, Coffea has been the focus of numerous genetic diversity studies, but despite this effort it remains insufficiently studied. In this study the genetic diversity and genetic structure of Coffea across Africa and the Indian Ocean islands is investigated.Methods
Genetic data were produced using 13 polymorphic nuclear microsatellite markers (simple sequence repeats, SSRs), including seven expressed sequence tag-SSRs, and the data were analysed using model- and non-model-based methods. The study includes a total of 728 individuals from 60 species.Key Results
Across Africa and the Indian Ocean islands Coffea comprises a closely related group of species with an overall pattern of genotypes running from west to east. Genetic structure was identified in accordance with pre-determined geographical regions and phylogenetic groups. There is a good relationship between morpho-taxonomic species delimitations and genetic units. Genetic diversity in African and Indian Ocean Coffea is high in terms of number of alleles detected, and Madagascar appears to represent a place of significant diversification in terms of allelic richness and species diversity.Conclusions
Cross-species SSR transferability in African and Indian Ocean islands Coffea was very efficient. On the basis of the number of private alleles, diversification in East Africa and the Indian Ocean islands appears to be more recent than in West and West-Central Africa, although this general trend is complicated in Africa by the position of species belonging to lineages connecting the main geographical regions. The general pattern of phylogeography is not in agreement with an overall east to west (Mascarene, Madagascar, East Africa, West Africa) increase in genome size, the high proportion of shared alleles between the four regions or the high numbers of exclusive shared alleles between pairs or triplets of regions. 相似文献14.
Ansell SW Stenøien HK Grundmann M Russell SJ Koch MA Schneider H Vogel JC 《Annals of botany》2011,108(2):241-252
Background and Aims
Anatolia is a biologically diverse, but phylogeographically under-explored region. It is described as either a centre of origin and long-term Pleistocene refugium, or as a centre for genetic amalgamation, fed from distinct neighbouring refugia. These contrasting hypotheses are tested through a global phylogeographic analysis of the arctic–alpine herb, Arabis alpina.Methods
Herbarium and field collections were used to sample comprehensively the entire global range, with special focus on Anatolia and Levant. Sequence variation in the chloroplast DNA trnL-trnF region was examined in 483 accessions. A haplotype genealogy was constructed and phylogeographic methods, demographic analysis and divergence time estimations were used to identify the centres of diversity and to infer colonization history.Key Results
Fifty-seven haplotypes were recovered, belonging to three haplogroups with non-overlapping distributions in (1) North America/Europe/northern Africa, (2) the Caucuses/Iranian Plateau/Arabian Peninsula and (3) Ethiopia–eastern Africa. All haplogroups occur within Anatolia, and all intermediate haplotypes linking the three haplogroups are endemic to central Anatolia and Levant, where haplotypic and nucleotide diversities exceeded all other regions. The local pattern of haplotype distribution strongly resembles the global pattern, and the haplotypes began to diverge approx. 2·7 Mya, coinciding with the climate cooling of the early Middle Pleistocene.Conclusions
The phylogeographic structure of Arabis alpina is consistent with Anatolia being the cradle of origin for global genetic diversification. The highly structured landscape in combination with the Pleistocene climate fluctuations has created a network of mountain refugia and the accumulation of spatially arranged genotypes. This local Pleistocene population history has subsequently left a genetic imprint at the global scale, through four range expansions from the Anatolian diversity centre into Europe, the Near East, Arabia and Africa. Hence this study also illustrates the importance of sampling and scaling effects when translating global from local diversity patterns during phylogeographic analyses. 相似文献15.
G. Besnard A. El Bakkali H. Haouane D. Baali-Cherif A. Moukhli B. Khadari 《Annals of botany》2013,112(7):1293-1302
Background and Aims
The olive (Olea europaea subsp. europaea) was domesticated in the Mediterranean area but its wild relatives are distributed over three continents, from the Mediterranean basin to South Africa and south-western Asia. Recent studies suggested that this crop originated in the Levant while a secondary diversification occurred in most westward areas. A possible contribution of the Saharan subspecies (subsp. laperrinei) has been highlighted, but the data available were too limited to draw definite conclusions. Here, patterns of genetic differentiation in the Mediterranean and Saharan olives are analysed to test for recent admixture between these taxa.Methods
Nuclear microsatellite and plastid DNA (ptDNA) data were compiled from previous studies and completed for a sample of 470 cultivars, 390 wild Mediterranean trees and 270 Saharan olives. A network was reconstructed for the ptDNA haplotypes, while a Bayesian clustering method was applied to identify the main gene pools in the data set and then simulate and test for early generations of admixture between Mediterranean and Saharan olives.Key Results
Four lineages of ptDNA haplotypes are recognized: three from the Mediterranean basin and one from the Sahara. Only one haplotype, primarily distributed in the Sahara, is shared between laperrinei and europaea. This haplotype is detected once in ‘Dhokar’, a cultivar from the Maghreb. Nuclear microsatellites show geographic patterns of genetic differentiation in the Mediterranean olive that reflect the primary origins of cultivars in the Levant, and indicate a high genetic differentiation between europaea and laperrinei. No first-generation hybrid between europaea and laperrinei is detected, but recent, reciprocal admixture between Mediterranean and Saharan subspecies is found in a few accessions, including ‘Dhokar’.Conclusions
This study reports for the first time admixture between Mediterranean and Saharan olives. Although its contribution remains limited, Laperrine''s olive has been involved in the diversification of cultivated olives. 相似文献16.
Laurent Hardion Régine Verlaque Kristin Saltonstall Agathe Leriche Bruno Vila 《Annals of botany》2014,114(3):455-462
Background and Aims
The hypothesis of an ancient introduction, i.e. archaeophyte origin, is one of the most challenging questions in phylogeography. Arundo donax (Poaceae) is currently considered to be one of the worst invasive species globally, but it has also been widely utilzed by man across Eurasia for millennia. Despite a lack of phylogenetic data, recent literature has often speculated on its introduction to the Mediterranean region.Methods
This study tests the hypothesis of its ancient introduction from Asia to the Mediterranean by using plastid DNA sequencing and morphometric analysis on 127 herbarium specimens collected across sub-tropical Eurasia. In addition, a bioclimatic species distribution model calibrated on 1221 Mediterranean localities was used to identify similar ecological niches in Asia.Key Results
Despite analysis of several plastid DNA hypervariable sites and the identification of 13 haplotypes, A. donax was represented by a single haplotype from the Mediterranean to the Middle East. This haplotype is shared with invasive samples worldwide, and its nearest phylogenetic relatives are located in the Middle East. Morphometric data characterized this invasive clone by a robust morphotype distinguishable from all other Asian samples. The ecological niche modelling designated the southern Caspian Sea, southern Iran and the Indus Valley as the most suitable regions of origin in Asia for the invasive clone of A. donax.Conclusions
Using an integrative approach, an ancient dispersion of this robust, polyploid and non-fruiting clone is hypothesized from the Middle East to the west, leading to its invasion throughout the Mediterranean Basin. 相似文献17.
Totaro MC Tolusso B Napolioni V Faustini F Canestri S Mannocci A Gremese E Bosello SL Alivernini S Ferraccioli G 《PloS one》2011,6(9):e24292
Objective
The PTPN22 rs2476601 polymorphism is associated with rheumatoid arthritis (RA); nonetheless, the association is weaker or absent in some southern European populations. The aim of the study was to evaluate the association between the PTPN22 rs2476601 polymorphism and RA in Italian subjects and to compare our results with those of other European countries, carrying out a meta-analysis of European data.Methods
A total of 396 RA cases and 477 controls, all of Italic ancestry, were genotyped for PTPN22 rs2476601 polymorphism. Patients were tested for autoantibodies positivity. The meta-analysis was performed on 23 selected studies.Results
The PTPN22 T1858 allele was significantly more frequent in RA patients compared to controls (5.7% vs. 3.7%, p = 0.045). No clear relationship arose with the autoantibodies tested. The 1858T allele frequency in Italian RA patients was lower than the one described in northern European populations and similar to the frequency found in Spain, Turkey, Greece, Tunisia. A clear-cut North-South gradient arose from the analysis.Conclusions
The PTPN22 T1858 allele is associated with RA in the Italian population. A North-South gradient of the allele frequency seems to exist in Europe, with a lower prevalence of the mutation in the Mediterranean area. 相似文献18.
Bentley SD Comas I Bryant JM Walker D Smith NH Harris SR Thurston S Gagneux S Wood J Antonio M Quail MA Gehre F Adegbola RA Parkhill J de Jong BC 《PLoS neglected tropical diseases》2012,6(2):e1552
Background
M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis.Methodology/Principal Findings
In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the “modern” M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle.Conclusions/Significance
The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa. 相似文献19.
Rachel Brower-Sinning Diana Zhong Misty Good Brian Firek Robyn Baker Chhinder P. Sodhi David J. Hackam Michael J. Morowitz 《PloS one》2014,9(9)
Background
Previous studies of infant fecal samples have failed to clarify the role of gut bacteria in the pathogenesis of NEC. We sought to characterize bacterial communities within intestinal tissue resected from infants with and without NEC.Methods
26 intestinal samples were resected from 19 infants, including 16 NEC samples and 10 non-NEC samples. Bacterial 16S rRNA gene sequences were amplified and sequenced. Analysis allowed for taxonomic identification, and quantitative PCR was used to quantify the bacterial load within samples.Results
NEC samples generally contained an increased total burden of bacteria. NEC and non-NEC sample sets were both marked by high inter-individual variability and an abundance of opportunistic pathogens. There was no statistically significant distinction between the composition of NEC and non-NEC microbial communities. K-means clustering enabled us to identify several stable clusters, including clusters of NEC and midgut volvulus samples enriched with Clostridium and Bacteroides. Another cluster containing both NEC and non-NEC samples was marked by an abundance of Enterobacteriaceae and decreased diversity among NEC samples.Conclusions
The results indicate that NEC is a disease without a uniform pattern of microbial colonization, but that NEC is associated with an abundance of strict anaerobes and a decrease in community diversity. 相似文献20.
Christiane Cuny Rolf Nathaus Franziska Layer Birgit Strommenger Doris Altmann Wolfgang Witte 《PloS one》2009,4(8)