Geographic variation in nrDNA and four cpDNA regions of Juniperus excelsa: Analysis of new records from Bulgaria, Cyprus and southwestern Turkey

Sequencing of nrDNA, plus four cp DNA regions: petN-psbM, trnS-trnG, trnD-trnT and trnL-trnF of newly acquired samples of J. excelsa from Bulgaria, Cyprus and Turkey showed little variation in J. excelsa (sensu stricto), except for the unusual situation in Lebanon, where J. excelsa and J. polycarpos (and likely J. p. var. turcomanica) grow near each other and may be hybridizing. The genetic composition of the eastern-most populations of J. excelsa in Turkey is unknown and deserves further study

Evidence of relictual introgression or incomplete lineage sorting in nrDNA of Juniperus excelsa and J. polycarpos in Asia Minor

DNA analysis of Juniperus excelsa from throughout its range revealed that J. polycarpos, instead of J. excelsa occupies central and eastern Turkey. Based on nrDNA (ITS) data, it appears that relictual hybridization has occurred in southeastern Turkey between J. polycarpos and J. turcomanica. Surprisingly, evidence of incomplete lineage sorting or relictual hybridization between J. polycarpos and J. seravschanica was found in central Turkey and northwest Iran

Geographic variation in nrDNA and four cpDNA regions of Juniperus excelsa: Analysis of new records from Bulgaria, Cyprus and southwestern Turkey

Sequencing of nrDNA, plus four cp DNA regions: petN-psbM, trnS-trnG, trnD-trnT and trnL-trnF of newly acquired samples of J. excelsa from Bulgaria, Cyprus and Turkey showed little variation in J. excelsa (sensu stricto), except for the unusual situation in Lebanon, where J. excelsa and J. polycarpos (and likely J. p. var. turcomanica) grow near each other and may be hybridizing. The genetic composition of the eastern-most populations of J. excelsa in Turkey is unknown and deserves further study

Morphological versus molecular markers to describe variability in Juniperus excelsa subsp. excelsa (Cupressaceae)

41 p.Background and aims: Juniperus excelsa M.-Bieb. is a major forest element in the mountains of the eastern part of Mediterranean and sub-Mediterranean regions. This study comprises the first morphological investigation covering a large part of the geographical range of J. excelsa and aims to verify the congruency between the morphological results and molecular results of a previous study. Methodology: We studied 14 populations sampled from Greece, Cyprus, Ukraine, Turkey and Lebanon, from which 11 have previously been investigated using molecular markers. Three hundred and ninety four individuals of J. excelsa were examined using nine biometric features characterising cones, seeds and shoots; and eight derived ratios. Statistical analyses were conducted in order to evaluate the intra and interpopulation morphological variability. Principal results: The level of intra-population variability observed did not show any geographic trends. The total variation mostly depended on the ratios of cone diameter/seed width and seed width/seed length. The discrimination analysis, the Ward agglomeration method and barrier analysis results showed a separation into three main clusters of the sampled populations. These results confirmed, in part, the geographic differentiation revealed by molecular markers with a lower level of differentiation and a less clear geographic pattern. The most differentiated populations using both markers corresponded to old, isolated populations in the high altitudes of Lebanon (>2000 m). Moreover a separation of the northern Turkish population from the southern Turkish populations was observed using both markers. Conclusions: Morphological variation together with genetic and biogeographic studies together make an effective good tool for detecting relict plant populations and also populations subjected to more intensive selection.The research was conducted within the statutory research programme of the Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland and supported by the Research Council of Saint-Joseph University of Beirut.Peer reviewe

Evidence of relictual introgression or incomplete lineage sorting in nrDNA of Juniperus excelsa and J. polycarpos in Asia Minor

DNA analysis of Juniperus excelsa from throughout its range revealed that J. polycarpos, instead of J. excelsa occupies central and eastern Turkey. Based on nrDNA (ITS) data, it appears that relictual hybridization has occurred in southeastern Turkey between J. polycarpos and J. turcomanica. Surprisingly, evidence of incomplete lineage sorting or relictual hybridization between J. polycarpos and J. seravschanica was found in central Turkey and northwest Iran

Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations

The Middle East was a funnel of human expansion out of Africa, a staging area for the Neolithic Agricultural Revolution, and the home to some of the earliest world empires. Post LGM expansions into the region and subsequent population movements created a striking genetic mosaic with distinct sex-based genetic differentiation. While prior studies have examined the mtDNA and Y-chromosome contrast in focal populations in the Middle East, none have undertaken a broad-spectrum survey including North and sub-Saharan Africa, Europe, and Middle Eastern populations. In this study 5,174 mtDNA and 4,658 Y-chromosome samples were investigated using PCA, MDS, mean-linkage clustering, AMOVA, and Fisher exact tests of FST's, RST's, and haplogroup frequencies. Geographic differentiation in affinities of Middle Eastern populations with Africa and Europe showed distinct contrasts between mtDNA and Y-chromosome data. Specifically, Lebanon's mtDNA shows a very strong association to Europe, while Yemen shows very strong affinity with Egypt and North and East Africa. Previous Y-chromosome results showed a Levantine coastal-inland contrast marked by J1 and J2, and a very strong North African component was evident throughout the Middle East. Neither of these patterns were observed in the mtDNA. While J2 has penetrated into Europe, the pattern of Y-chromosome diversity in Lebanon does not show the widespread affinities with Europe indicated by the mtDNA data. Lastly, while each population shows evidence of connections with expansions that now define the Middle East, Africa, and Europe, many of the populations in the Middle East show distinctive mtDNA and Y-haplogroup characteristics that indicate long standing settlement with relatively little impact from and movement into other populations

Genome-Wide Association Study in a Lebanese Cohort Confirms PHACTR1 as a Major Determinant of Coronary Artery Stenosis

The manifestation of coronary artery disease (CAD) follows a well-choreographed series of events that includes damage of arterial endothelial cells and deposition of lipids in the sub-endothelial layers. Genome-wide association studies (GWAS) of multiple populations with distinctive genetic and lifestyle backgrounds are a crucial step in understanding global CAD pathophysiology. In this study, we report a GWAS on the genetic basis of arterial stenosis as measured by cardiac catheterization in a Lebanese population. The locus of the phosphatase and actin regulator 1 gene (PHACTR1) showed association with coronary stenosis in a discovery experiment with genome wide data in 1,949 individuals (rs9349379, OR = 1.37, p = 1.57×10−5). The association was replicated in an additional 2,547 individuals (OR = 1.31, p = 8.85×10−6), leading to genome-wide significant association in a combined analysis (OR = 1.34, p = 8.02×10−10). Results from this GWAS support a central role of PHACTR1 in CAD susceptibility irrespective of lifestyle and ethnic divergences. This association provides a plausible component for understanding molecular mechanisms involved in the formation of stenosis in cardiac vessels and a potential drug target against CAD

High genetic diversity with moderate differentiation in Juniperus excelsa from Lebanon and the eastern Mediterranean region

Juniperus excelsa constitutes a precious woody species of high ecological value able to grow up to Mountain treeline around the Mediterranean. Nuclear microsatellites were used to shed light on genetic diversity and differentiation of different Mediterranean populations. This information is essential in planning conservation strategies and reforestation programs

Large Scale Association Analysis Identifies Three Susceptibility Loci for Coronary Artery Disease

Genome wide association studies (GWAS) and their replications that have associated DNA variants with myocardial infarction (MI) and/or coronary artery disease (CAD) are predominantly based on populations of European or Eastern Asian descent. Replication of the most significantly associated polymorphisms in multiple populations with distinctive genetic backgrounds and lifestyles is crucial to the understanding of the pathophysiology of a multifactorial disease like CAD. We have used our Lebanese cohort to perform a replication study of nine previously identified CAD/MI susceptibility loci (LTA, CDKN2A-CDKN2B, CELSR2-PSRC1-SORT1, CXCL12, MTHFD1L, WDR12, PCSK9, SH2B3, and SLC22A3), and 88 genes in related phenotypes. The study was conducted on 2,002 patients with detailed demographic, clinical characteristics, and cardiac catheterization results. One marker, rs6922269, in MTHFD1L was significantly protective against MI (OR = 0.68, p = 0.0035), while the variant rs4977574 in CDKN2A-CDKN2B was significantly associated with MI (OR = 1.33, p = 0.0086). Associations were detected after adjustment for family history of CAD, gender, hypertension, hyperlipidemia, diabetes, and smoking. The parallel study of 88 previously published genes in related phenotypes encompassed 20,225 markers, three quarters of which with imputed genotypes The study was based on our genome-wide genotype data set, with imputation across the whole genome to HapMap II release 22 using HapMap CEU population as a reference. Analysis was conducted on both the genotyped and imputed variants in the 88 regions covering selected genes. This approach replicated HNRNPA3P1-CXCL12 association with CAD and identified new significant associations of CDKAL1, ST6GAL1, and PTPRD with CAD. Our study provides evidence for the importance of the multifactorial aspect of CAD/MI and describes genes predisposing to their etiology