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One Haplotype (one + haplotype)
Selected AbstractsNeritid and thiarid gastropods from French Polynesian streams: how reproduction (sexual, parthenogenetic) and dispersal (active, passive) affect population structureFRESHWATER BIOLOGY, Issue 3 2000Marilyn J. Myers Summary 1The streams of French Polynesia contain several species of Neritidae and Thiaridae (Mollusca: Gastropoda). The neritids are dioecious and amphidromous with a freshwater adult stage and a poorly known, marine larval stage. The thiarids are parthenogenetic and viviparous, and rely on passive dispersal for colonisation of new habitats. 2Populations of the neritid Clithon spinosus and the thiarids Melanoides tuberculata and Thiara granifera were analysed using mitochondrial DNA sequences from COI to compare the population structure of the snails at three different scales: between streams (N = 9), between islands (N = 4), and between age and distance of paired islands. 3The amphidromous C. spinosus showed no evidence of genetic isolation at any of the scales tested (Fst values 0.02). Parsimony analyses resulted in two haplotype clusters separated by a three-step segment, which were not linked to geographic isolation. The larval phase of C. spinosus is most likely a long-lived planktotroph and a very effective disperser. 4Two haplotypes of M. tuberculata, separated by 16 base pairs, were found. Both haplotypes were found in snails on all islands, and individuals representing both were often collected in the same habitat. One haplotype of T. granifera was found. M. tuberculata has the characteristics of the ,general-purpose genotype' of clonal population structure and although it relies on passive dispersal, it has colonised nearly all freshwater habitats on the islands. [source] Regulatory factor X4 variant 3: A transcription factor involved in brain development and disease,JOURNAL OF NEUROSCIENCE RESEARCH, Issue 16 2007Donghui Zhang Abstract Regulatory factor X4 variant 3 (RFX4_v3) is a recently identified transcription factor specifically expressed in the brain. Gene disruption in mice demonstrated that interruption of a single allele (heterozygous, +/,) prevented formation of the subcommissural organ (SCO), resulting in congenital hydrocephalus, whereas interruption of two alleles (homozygous, ,/,) caused fatal failure of dorsal midline brain structure formation. These mutagenesis studies implicated RFX4_v3 in early brain development as well as the genesis of the SCO. Rfx4_v3 deficiency presumably causes abnormalities in brain by altering the expression levels of many genes that are crucial for brain morphogenesis, such as the signaling components in the Wnt, bone morphogenetic protein, and retinoic acid pathways. RFX4_v3 might affect these critical signaling pathways in brain development. Cx3cl1, a chemokine gene highly expressed in brain, was identified as a direct target for RFX4_v3, indicating that RFX4_v3 possesses trans -acting activity to stimulate gene expression. Rfx4_v3 is highly expressed in the suprachiasmatic nucleus and might be involved in regulating the circadian clock. One haplotype in RFX4_v3 gene is linked to a higher risk of bipolar disorder, suggesting that this protein might contribute to the pathogenesis of the disease. This Mini-Review describes our current knowledge about RFX4_v3, an important protein that appears to be involved in many aspects of brain development and disease. © 2007 Wiley-Liss, Inc. [source] INCREASED SAMPLING FOR INFERRING PHYLOGEOGRAPHIC PATTERNS IN BOSTRYCHIA RADICANS/B.JOURNAL OF PHYCOLOGY, Issue 6 2006MORITZIANA (RHODOMELACEAE, RHODOPHYTA) IN THE EASTERN USA Zuccarello and West (2003) reported on the phylogenetic diversity of algae identified as Bostrychia radicans (Montagne) Montagne and B. moritziana (Sonder ex Kützing) J. Agardh from around the world. They showed that the species complex consisted of seven distinct lineages, of which two lineages were common on the East Coast of the USA and eastern Gulf of Mexico. The distribution of haplotypes within these lineages on the East Coast of the USA showed a general north,south distribution. One haplotype of lineage 5 (B) was mostly collected in northern areas, while the other common haplotype (C) was more southerly in distribution. Samples in lineage 6 (haplotype D) were not found north of Sapelo Island, Georgia. Increased sampling from the eastern USA over 5 years later has revealed an altered pattern. Haplotype D is distributed in North Carolina and is common in some populations. Haplotype C is rare or absent in many sampled populations. Haplotype B is only observed in the northern sampled sites on both sides of the Florida peninsula. This disjunct distribution agrees with geological scenarios for a strait between the western Gulf of Mexico and southern Georgia in the Miocene/Pliocene, which closed in the late Pliocene. This paper highlights the importance of increased sampling to determine phylogeographic patterns and hypotheses of dispersal scenarios in algae. [source] The phylogeography of the Placozoa suggests a taxon-rich phylum in tropical and subtropical watersMOLECULAR ECOLOGY, Issue 11 2010M. EITEL Abstract Placozoa has been a key phylum for understanding early metazoan evolution. Yet this phylum is officially monotypic and with respect to its general biology and ecology has remained widely unknown. Worldwide sampling and sequencing of the mitochondrial large ribosomal subunit (16S) reveals a cosmopolitan distribution in tropical and subtropical waters of genetically different clades. We sampled a total of 39 tropical and subtropical locations worldwide and found 23 positive sites for placozoans. The number of genetically characterized sites was thereby increased from 15 to 37. The new sampling identified the first genotypes from two new oceanographic regions, the Eastern Atlantic and the Indian Ocean. We found seven out of 11 previously known haplotypes as well as five new haplotypes. One haplotype resembles a new genetic clade, increasing the number of clades from six to seven. Some of these clades seem to be cosmopolitan whereas others appear to be endemic. The phylogeography also shows that different clades occupy different ecological niches and identifies several euryoecious haplotypes with a cosmopolitic distribution as well as some stenoecious haplotypes with an endemic distribution. Haplotypes of different clades differ substantially in their phylogeographic distribution according to latitude. The genetic data also suggest deep phylogenetic branching patterns between clades. [source] Genetic Variation and Differentiation Within a Natural Community of Five Oak Species (Quercus spp.)PLANT BIOLOGY, Issue 1 2007A. L. Curtu Abstract: Chloroplast DNA and two categories of nuclear markers - isozymes and microsatellites - were used to examine a very rich natural community of oaks (Quercus spp.) situated in west-central Romania. The community consists of five oak species: Q. robur, Q. petraea, Q. pubescens, and Q. frainetto - that are closely related -, and Q. cerris. A total of five chloroplast haplotypes was identified. Q. cerris was fixed for a single haplotype. The other four species shared the two most common haplotypes. One haplotype was confined to Q. robur and a very rare one was restricted to Q. petraea. Both types of nuclear markers revealed a larger genetic variation for Q. pubescens and Q. petraea than for Q. frainetto and Q. robur, although the differences between species are in most cases not significant. At the nuclear level, Q. cerris could be clearly separated from the other four oak species confirming the taxonomic classification. Regardless of the estimate used, the levels of polymorphism revealed by microsatellites were much higher than those based on isozymes. For the four closely related species the overall genetic differentiation was significant at both categories of nuclear markers. Several loci, such as Acp-C for isozymes, and ssrQpZAG36 and ssrQrZAG96 for microsatellites were very useful to discriminate among species. However, the level of differentiation varied markedly between pairs of species. The genetic affinities among the species may reflect different phylogenetic distances and/or different rates of recurrent gene flow at this site. [source] Genetic polymorphisms of the bovine Fatty acid binding protein 4 gene are significantly associated with marbling and carcass weight in Hanwoo (Korean Cattle)ANIMAL GENETICS, Issue 4 2010S. H. Lee Summary The objective of this study was to investigate an association between polymorphisms in the FABP4 gene and phenotypic variation for marbling and carcass weight (CWT) in a population of Hanwoo steers. We re-sequenced 4.3 kb of the FABP4 gene region in 24 Hanwoo bulls and identified 16 SNPs and 1 microsatellite polymorphism. Of these 16 SNPs, three SNPs [g.2774G>C (intron I), g.3473A>T (intron II) and g.3631G>A (exon III, creating a p.Met >Val amino acid substitution)] were genotyped in 583 steers to assess their association with carcass traits. The g.3473A allele showed a significant increasing effect on CWT (P = 0.01) and the g.3631G allele was associated with higher marbling score (P = 0.006). One haplotype of these three SNPs (CAG) was significantly associated with CWT (P = 0.02) and marbling score (P = 0.05) and could potentially be of value for marker assisted selection in Hanwoo cattle. The CAG haplotype effect for CWT was larger (11.14 ± 5.03 kg) than the largest single locus effect of g.3473A>T (5.01 ± 2.2 kg). [source] The variant red coat colour phenotype of Holstein cattle maps to BTA27ANIMAL GENETICS, Issue 1 2010D. L. Dreger Summary The variant red phenotype in Holstein cattle is indistinguishable from the traditional e/e recessive red phenotype caused by a mutation in melanocortin 1 receptor, but is inherited as a dominant trait in relation to black. Co-segregation analysis in four half-sib families segregating for variant red was conducted, excluding melanocortin 1 receptor, agouti signalling protein, attractin and melatonin receptor 1A as causative genes. However, variant red co-segregated with markers in a region of BTA27 that includes beta-defensin 103 (DEFB103). Two newly identified microsatellites and 5 SNPs 5, of DEFB103 were used for linkage mapping in four segregating families (LOD = 3.26). One haplotype was inherited in VR cattle in a 6-generation pedigree. [source] Association of Molecular Variants, Haplotypes, and Linkage Disequilibrium Within the Human Vitamin D-Binding Protein (DBP) Gene With Postmenopausal Bone Mineral Density,JOURNAL OF BONE AND MINERAL RESEARCH, Issue 9 2003Yoichi Ezura Abstract Possible contribution of vitamin D-binding protein (DBP) gene for determination of BMD was tested by characterizing 13 SNPs in 384 adult Japanese women. When the effect of a specific single SNP was tested, five SNPs (,39C>T, IVS1+827C>T, IVS1+1916C>T, IVS1-1154A>G, and IVS11+1097G>C) correlated with BMD significantly at various levels. The chromosomal dosage of one haplotype (T-C-C-G-T-C in ,39C>T, IVS1+827C>T, IVS1+1916C>T, IVS1-1154A>G, D432E, and IVS11+1097G>C) displayed significant correlation with adjusted radial BMD (r = 0.15, p = 0.008; n = 331). Multiple regression analyses revealed a most significant correlation with the combination of IVS1+827C>T and D432E (r2 = 0.029, p = 0.005). These results indicate a complex combined effect of several SNPs within the DBP gene that might underlie susceptibility to low radial BMD and osteoporosis. Introduction: Osteoporosis results from the interplay of multiple environmental and genetic determinants. The gene encoding vitamin D-binding protein (DBP), a key factor for regulating calcium homeostasis through the vitamin D endocrine system, is a probable candidate for conferring susceptibility to osteoporosis. Methods: To test a possible contribution of the DBP gene for determination of bone mineral density (BMD) of adult women, we have characterized 13 single nucleotide polymorphisms (SNPs) within the DBP gene in DNA from 384 adult Japanese women and attempted to correlate specific SNPs with BMD. Results and Conclusions: Sixteen major haplotypes accounted for 80% of the variations, indicating allelic complexity in this genomic region. Pairwise linkage disequilibrium (LD), measured by the D, and r2 statistics, demonstrated a general pattern of decline with increasing distance, but individual LD values within small genomic segments were diverse. Regression analysis for adjusted BMD revealed significant correlation with respect to five of them (,39C>T, IVS1+827C>T, IVS1+1916C>T, IVS1-1154A>G, and IVS11+1097G>C) at various levels. An intronic SNP (IVS11+1097G>C) with the highest significance of association (p = 0.006) showed significant LD with four SNPs located around the first exon (r2 values >0.18, D, > 0.5). A non-synonymous coding SNP, D432E, showed a comparable level of correlation, but it was in a moderate LD only with IVS11+1097G>C. The chromosomal dosage of one haplotype (T-C-C-G-T-C in ,39C>T, IVS1+827C>T, IVS1+1916C>T, IVS1-1154A>G, D432E and IVS11+1097G>C) estimated in each subject displayed significant correlation with adjusted radial BMD (r = 0.15, p = 0.008; n = 331). Furthermore, multiple regression analyses revealed that the most significant correlation was achieved for the combination of IVS1+827C>T and D432E (r2 = 0.029, p = 0.005). These results indicate a complex combined effect of several SNPs within the DBP gene that might underlie susceptibility to low radial BMD and osteoporosis. [source] Molecular ecology of zebra mussel invasionsMOLECULAR ECOLOGY, Issue 4 2006GEMMA E. MAY Abstract The invasion of the zebra mussel, Dreissena polymorpha, into North American waters has resulted in profound ecological disturbances and large monetary losses. This study examined the invasion history and patterns of genetic diversity among endemic and invading populations of zebra mussels using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. Patterns of haplotype frequency indicate that all invasive populations of zebra mussels from North America and Europe originated from the Ponto-Caspian Sea region. The distribution of haplotypes was consistent with invasive populations arising from the Black Sea drainage, but could not exclude the possibility of an origin from the Caspian Sea drainage. Similar haplotype frequencies among North American populations of D. polymorpha suggest colonization by a single founding population. There was no evidence of invasive populations arising from tectonic lakes in Turkey, while lakes in Greece and Macedonia contained only Dreissena stankovici. Populations in Turkey might be members of a sibling species complex of D. polymorpha. Ponto-Caspian derived populations of D. polymorpha (, = 0.0011) and Dreissena bugensis (one haplotype) exhibited low levels of genetic diversity at the COI gene, perhaps as a result of repeated population bottlenecks. In contrast, geographically isolated tectonic lake populations exhibited relatively high levels of genetic diversity (, = 0.0032 to 0.0134). It is possible that the fluctuating environment of the Ponto-Caspian basin facilitated the colonizing habit of invasive populations of D. polymorpha and D. bugensis. Our findings were concordant with the general trend of destructive freshwater invaders in the Great Lakes arising from the Ponto-Caspian Sea basin. [source] Genetic diversity in populations of the fungi Phaeomoniella chlamydospora and Phaeoacremonium aleophilum on grapevine in FrancePLANT PATHOLOGY, Issue 1 2002B. Borie Isolates of Phaeomoniella chlamydospora (Phc) and Phaeoacremonium aleophilum (Pha), two haploid, deuteromycetous fungi, were obtained from vines showing symptoms of esca disease in different localities in two French regions, and within a single vineyard in one of these regions. The population genetic structure was determined in both fungi using random amplified polymorphic DNA (RAPD) analysis. Populations of Phc showed similar levels of diversity at local and regional levels. The most frequent Phc haplotypes were found in every population, and the frequencies of positive alleles of markers were similar across populations. The hypothesis that recombination had occurred was rejected for the full set of samples, but not for the samples reduced to haplotypes, indicating that Phc may be a recombining species. Different features were identified in Pha populations. First, the southern population of Pha appeared more diverse than the south-western populations. Second, genetic differentiation was identified between Pha populations from southern and south-western regions for several RAPDs. Finally, in the southern population of Pha no evidence for recombination was obtained, even by reducing the sample to haplotypes. Within the single vineyard surveyed, several haplotypes of both fungi were recovered and randomly distributed. Thus different infection events appeared to have occurred on a low spatial scale. Data from this study showed that haplotypes of both fungi were distributed over long distances geographically, and that most of the vineyards surveyed were infested by more than one haplotype of Phc and Pha. [source] Genetic variability of Austropotamobius italicus in the Marches region: implications for conservationAQUATIC CONSERVATION: MARINE AND FRESHWATER ECOSYSTEMS, Issue 3 2010Rosaria Cataudella Abstract 1.Ten populations of Austropotamobius italicus from the Marches region (Central Italy), two populations from the Appennines of Calabria and Basilicata (Southern Italy) and four populations from Friuli Venezia Giulia region were sampled to elucidate the geographical pattern of genetic variability in relation to recent and historical factors. 2.A total of nine COI haplotypes belonging to three separate lineages have been characterized. Both lineage A (Northern Marches region) and C (Friuli Venezia Giulia region) were represented by one haplotype and were related to the Istria 1 peninsula and SouthAlps/Western Balkans lineages respectively. The lineage B included seven haplotypes belonging to the Appenines lineage. 3.Two hypotheses on the origin of individuals belonging to the Istrian lineage in Marches are discussed: (i) a natural colonization from the Istria peninsula refugia by migrating westwards across the bridge between the Istria peninsula and Italy, (ii) an anthropogenic origin. Based on 16S rRNA sequences, the taxonomic status of lineage B and C, defined from COI mtDNA markers, belongs to A. i. meridionalis and that of lineage A belongs to A. i. carsicus. The existence of a complex geographic structure between Marches populations (,st=0.66) of A. i. meridionalis should be further considered in conservation management. Copyright © 2010 John Wiley & Sons, Ltd. [source] | ||||||||||