Science.gov

Sample records for allelic diversity ranged

  1. Patterns of selection and allele diversity of class I and class II major histocompatibility loci across the species range of sockeye salmon (Oncorhynchus nerka).

    PubMed

    McClelland, Erin K; Ming, Tobi J; Tabata, Amy; Kaukinen, Karia H; Beacham, Terry D; Withler, Ruth E; Miller, Kristina M

    2013-09-01

    The major histocompatibility complex (MHC), an important component of the vertebrate immune system, provides an important suite of genes to examine the role of genetic diversity at non-neutral loci for population persistence. We contrasted patterns of diversity at the two classical MHC loci in sockeye salmon (Oncorhynchus nerka), MHC class I (UBA) and MHC class II (DAB), and neutral microsatellite loci across 70 populations spanning the species range from Washington State to Japan. There was no correlation in allelic richness or heterozygosity between MHC loci or between MHC loci and microsatellites. The two unlinked MHC loci may be responding to different selective pressures; the distribution of FST values for the two loci was uncorrelated, and evidence for both balancing and directional selection on alleles and lineages of DAB and UBA was observed in populations throughout the species range but rarely on both loci within a population. These results suggest that fluctuating selection has resulted in the divergence of MHC loci in contemporary populations. PMID:24033436

  2. Drift Rather than Selection Dominates MHC Class II Allelic Diversity Patterns at the Biogeographical Range Scale in Natterjack Toads Bufo calamita

    PubMed Central

    Zeisset, Inga; Beebee, Trevor J. C.

    2014-01-01

    Study of major histocompatibility complex (MHC) loci has gained great popularity in recent years, partly due to their function in protecting vertebrates from infections. This is of particular interest in amphibians on account of major threats many species face from emergent diseases such as chytridiomycosis. In this study we compare levels of diversity in an expressed MHC class II locus with neutral genetic diversity at microsatellite loci in natterjack toad (Bufo (Epidalea) calamita) populations across the whole of the species’ biogeographical range. Variation at both classes of loci was high in the glacial refugium areas (REF) and much lower in postglacial expansion areas (PGE), especially in range edge populations. Although there was clear evidence that the MHC locus was influenced by positive selection in the past, congruence with the neutral markers suggested that historical demographic events were the main force shaping MHC variation in the PGE area. Both neutral and adaptive genetic variation declined with distance from glacial refugia. Nevertheless, there were also some indications from differential isolation by distance and allele abundance patterns that weak effects of selection have been superimposed on the main drift effect in the PGE zone. PMID:24937211

  3. Allelic Diversity and Its Implications for the Rate of Adaptation

    PubMed Central

    Caballero, Armando; García-Dorado, Aurora

    2013-01-01

    Genetic variation is usually estimated empirically from statistics based on population gene frequencies, but alternative statistics based on allelic diversity (number of allelic types) can provide complementary information. There is a lack of knowledge, however, on the evolutionary implications attached to allelic-diversity measures, particularly in structured populations. In this article we simulated multiple scenarios of single and structured populations in which a quantitative trait subject to stabilizing selection is adapted to different fitness optima. By forcing a global change in the optima we evaluated which diversity variables are more strongly correlated with both short- and long-term adaptation to the new optima. We found that quantitative genetic variance components for the trait and gene-frequency-diversity measures are generally more strongly correlated with short-term response to selection, whereas allelic-diversity measures are more correlated with long-term and total response to selection. Thus, allelic-diversity variables are better predictors of long-term adaptation than gene-frequency variables. This observation is also extended to unlinked neutral markers as a result of the information they convey on the demographic population history. Diffusion approximations for the allelic-diversity measures in a finite island model under the infinite-allele neutral mutation model are also provided. PMID:24121776

  4. Allelic diversity and molecular characterization of puroindoline genes in five diploid species of the Aegilops genus.

    PubMed

    Cuesta, Susana; Guzmán, Carlos; Alvarez, Juan B

    2013-11-01

    Grain hardness is an important quality trait in wheat. This trait is related to the variation in, and the presence of, puroindolines (PINA and PINB). This variation can be increased by the allelic polymorphism present in the Aegilops species that are related to wheat. This study evaluated allelic Pina and Pinb gene variability in five diploid species of the Aegilops genus, along with the molecular characterization of the main allelic variants found in each species. This polymorphism resulted in 16 alleles for the Pina gene and 24 alleles for the Pinb gene, of which 10 and 17, respectively, were novel. Diverse mutations were detected in the deduced mature proteins of these alleles, which could influence the hardness characteristics of these proteins. This study shows that the diploid species of the Aegilops genus could be a good source of genetic variability for both Pina and Pinb genes, which could be used in breeding programmes to extend the range of different textures in wheat.

  5. MHC class II DR allelic diversity in bighorn sheep

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We hypothesized that decreased diversity and/or unique polymorphisms in MHC class II alleles of bighorn sheep (BHS, Ovis canadensis) are responsible for lower titer of antibodies against Mannheimia haemolytica leukotoxin, in comparison to domestic sheep (DS, Ovis aries). To test this hypothesis, DRA...

  6. Allelic variation of the β-, γ- and δ-kafirin genes in diverse Sorghum genotypes.

    PubMed

    Laidlaw, H K C; Mace, E S; Williams, S B; Sakrewski, K; Mudge, A M; Prentis, P J; Jordan, D R; Godwin, I D

    2010-11-01

    The β-, γ- and δ-kafirin genes were sequenced from 35 Sorghum genotypes to investigate the allelic diversity of seed storage proteins. A range of grain sorghums, including inbred parents from internationally diverse breeding programs and landraces, and three wild Sorghum relatives were selected to encompass an extensive array of improved and unimproved germplasm in the Eusorghum. A single locus exists for each of the expressed kafirin-encoding genes, unlike the multigenic α-kafirins. Significant diversity was found for each locus, with the cysteine-rich β-kafirin having four alleles, including the first natural null mutant reported for this prolamin subfamily. This allele contains a frame shift insertion at +206 resulting in a premature stop codon. SDS-PAGE revealed that lines with this allele do not produce β-kafirin. An analysis of flour viscosity reveals that these β-kafirin null lines have a difference in grain quality, with significantly lower viscosity observed over the entire Rapid ViscoAnalyser time course. There was less diversity at the protein level within the cysteine-rich γ-kafirin, with only two alleles in the cultivated sorghums. There were only two alleles for the δ-kafirin locus among the S. bicolor germplasm, with one allele encoding ten extra amino acids, of which five were methionine residues, with an additional methionine resulting from a nucleotide substitution. This longer allele encodes a protein with 19.1% methionine. The Asian species, S. propinquum, had distinct alleles for all three kafirin genes. We found no evidence for selection on the three kafirin genes during sorghum domestication even though the δ-kafirin locus displayed comparatively low genetic variation. This study has identified genetic diversity in all single copy seed storage protein genes, including a null mutant for β-kafirin in Sorghum.

  7. DRD4 dopamine receptor allelic diversity in various primate species

    SciTech Connect

    Adamson, M.; Higley, D.; O`Brien, S.

    1994-09-01

    The DRD4 dopamine receptor is uniquely characterized by a 48 bp repeating segment within the coding region, located in exon III. Different DRD4 alleles are produced by the presence of additional 48 bp repeats, each of which adds 16 amino acids to the length of the 3rd intracytoplasmic loop of the receptor. The DRD4 receptor is therefore an intriguing candidate gene for behaviors which are influenced by dopamine function. In several human populations, DRD4 alleles with 2-8 and 10 repeats have previously been identified, and the 4 and 7 repeat alleles are the most abundant. We have determined DRD4 genotypes in the following nonhuman primate species: chimpanzee N=2, pygmy chimpanzee N=2, gorilla N=4, siamang N=2, Gelada baboon N=1, gibbon N=1, orangutan (Bornean and Sumatran) N=62, spider monkey N=4, owl monkey N=1, Colobus monkey N=1, Patas monkey N=1, ruffed lemur N=1, rhesus macaque N=8, and vervet monkey N=28. The degree of DRD4 polymorphism and which DRD4 alleles were present both showed considerable variation across primate species. In contrast to the human, rhesus macaque monkeys were monomorphic. The 4 and 7 repeat allels, highly abundant in the human, may not be present in certain other primates. For example, the four spider monkeys we studied showed the 7, 8 and 9 repeat length alleles and the only gibbon we analyzed was homozygous for the 9 repeat allele (thus far not observed in the human). Genotyping of other primate species and sequencing of the individual DRD4 repeat alleles in different species may help us determine the ancestral DRD4 repeat length and identify connections between DRD4 genotype and phenotype.

  8. Allelic diversity at the DLA-88 locus in Golden Retriever and Boxer breeds is limited.

    PubMed

    Ross, P; Buntzman, A S; Vincent, B G; Grover, E N; Gojanovich, G S; Collins, E J; Frelinger, J A; Hess, P R

    2012-08-01

    In the dog, previous analyses of major histocompatibility complex class I genes suggest a single polymorphic locus, dog leukocyte antigen (DLA)-88. While 51 alleles have been reported, estimates of prevalence have not been made. We hypothesized that, within a breed, DLA-88 diversity would be restricted, and one or more dominant alleles could be identified. Accordingly, we determined allele usage in 47 Golden Retrievers and 39 Boxers. In each population, 10 alleles were found; 4 were shared. Seven novel alleles were identified. DLA-88*05101 and *50801 predominated in Golden Retrievers, while most Boxers carried *03401. In these breeds, DLA-88 polymorphisms are limited and largely non-overlapping. The finding of highly prevalent alleles fulfills an important prerequisite for studying canine CD8+ T-cell responses. PMID:22571293

  9. Extensive Allelic Diversity of MHC Class I in Wild Mallard Ducks.

    PubMed

    Fleming-Canepa, Ximena; Jensen, Shawna M; Mesa, Christine M; Diaz-Satizabal, Laura; Roth, Alexa J; Parks-Dely, Julie A; Moon, Debra A; Wong, Janet P; Evseev, Danyel; Gossen, Desolie A; Tetrault, David G; Magor, Katharine E

    2016-08-01

    MHC class I is critically involved in defense against viruses, and diversity from polygeny and polymorphism contributes to the breadth of the immune response and health of the population. In this article, we examine MHC class I diversity in wild mallard ducks, the natural host and reservoir of influenza A viruses. We previously showed domestic ducks predominantly use UAA, one of five MHC class I genes, but whether biased expression is also true for wild mallards is unknown. Using RT-PCR from blood, we examined expressed MHC class I alleles from 38 wild mallards (Anas platyrhynchos) and identified 61 unique alleles, typically 1 or 2 expressed alleles in each individual. To determine whether expressed alleles correspond to UAA adjacent to TAP2 as in domestic ducks, we cloned and sequenced genomic UAA-TAP2 fragments from all mallards, which matched transcripts recovered and allowed us to assign most alleles as UAA Allelic differences are primarily located in α1 and α2 domains in the residues known to interact with peptide in mammalian MHC class I, suggesting the diversity is functional. Most UAA alleles have unique residues in the cleft predicting distinct specificity; however, six alleles have an unusual conserved cleft with two cysteine residues. Residues that influence peptide-loading properties and tapasin involvement in chicken are fixed in duck alleles and suggest tapasin independence. Biased expression of one MHC class I gene may make viral escape within an individual easy, but high diversity in the population places continual pressure on the virus in the reservoir species. PMID:27342841

  10. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection.

    PubMed

    Hofer, T; Ray, N; Wegmann, D; Excoffier, L

    2009-01-01

    Several studies have found strikingly different allele frequencies between continents. This has been mainly interpreted as being due to local adaptation. However, demographic factors can generate similar patterns. Namely, allelic surfing during a population range expansion may increase the frequency of alleles in newly colonised areas. In this study, we examined 772 STRs, 210 diallelic indels, and 2834 SNPs typed in 53 human populations worldwide under the HGDP-CEPH Diversity Panel to determine to which extent allele frequency differs among four regions (Africa, Eurasia, East Asia, and America). We find that large allele frequency differences between continents are surprisingly common, and that Africa and America show the largest number of loci with extreme frequency differences. Moreover, more STR alleles have increased rather than decreased in frequency outside Africa, as expected under allelic surfing. Finally, there is no relationship between the extent of allele frequency differences and proximity to genes, as would be expected under selection. We therefore conclude that most of the observed large allele frequency differences between continents result from demography rather than from positive selection.

  11. Allelic Diversity of MSP1 Gene in Plasmodium falciparum from Rural and Urban Areas of Gabon.

    PubMed

    Mawili-Mboumba, Denise Patricia; Mbondoukwe, Noé; Adande, Elvire; Bouyou-Akotet, Marielle Karine

    2015-08-01

    The present study determined and compared the genetic diversity of Plasmodium falciparum strains infecting children living in 2 areas from Gabon with different malaria endemicity. Blood samples were collected from febrile children from 2008 to 2009 in 2 health centres from rural (Oyem) and urban (Owendo) areas. Genetic diversity was determined in P. falciparum isolates by analyzing the merozoite surface protein-1 (msp1) gene polymorphism using nested-PCR. Overall, 168 children with mild falciparum malaria were included. K1, Ro33, and Mad20 alleles were found in 110 (65.5%), 94 (55.9%), and 35 (20.8%) isolates, respectively, without difference according to the site (P>0.05). Allelic families' frequencies were comparable between children less than 5 years old from the 2 sites; while among the older children the proportions of Ro33 and Mad20 alleles were 1.7 to 2.0 fold higher at Oyem. Thirty-three different alleles were detected, 16 (48.5%) were common to both sites, and 10 out of the 17 specific alleles were found at Oyem. Furthermore, multiple infection carriers were frequent at Oyem (57.7% vs 42.2% at Owendo; P=0.04) where the complexity of infection was of 1.88 (±0.95) higher compared to that found at Owendo (1.55±0.75). Extended genetic diversity of P. falciparum strains infecting Gabonese symptomatic children and high multiplicity of infections were observed in rural area. Alleles common to the 2 sites were frequent; the site-specific alleles predominated in the rural area. Such distribution of the alleles should be taken into accounts when designing MSP1 or MSP2 malaria vaccine.

  12. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping.

    PubMed

    Edzesi, Wisdom M; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes.

  13. Genetic Diversity and Elite Allele Mining for Grain Traits in Rice (Oryza sativa L.) by Association Mapping

    PubMed Central

    Edzesi, Wisdom M.; Dang, Xiaojing; Liang, Lijun; Liu, Erbao; Zaid, Imdad U.; Hong, Delin

    2016-01-01

    Mining elite alleles for grain size and weight is of importance for the improvement of cultivated rice and selection for market demand. In this study, association mapping for grain traits was performed on a selected sample of 628 rice cultivars using 262 SSRs. Grain traits were evaluated by grain length (GL), grain width (GW), grain thickness (GT), grain length to width ratio (GL/GW), and 1000-grain weight (TGW) in 2013 and 2014. Our result showed abundant phenotypic and genetic diversities found in the studied population. In total, 2953 alleles were detected with an average of 11.3 alleles per locus. The population was divided into seven subpopulations and the levels of linkage disequilibrium (LD) ranged from 34 to 84 cM. Genome-wide association mapping detected 10 marker trait association (MTAs) loci for GL, 1MTAs locus for GW, 7 MTAs loci for GT, 3 MTAs loci for GL/GW, and 1 MTAs locus for TGW. Twenty-nine, 2, 10, 5, and 3 elite alleles were found for the GL, GW, GT, GL/GW, and TGW, respectively. Optimal cross designs were predicted for improving the target traits. The accessions containing elite alleles for grain traits mined in this study could be used for breeding rice cultivars and cloning the candidate genes. PMID:27375646

  14. OptiMAS: A Decision Support Tool for Marker-Assisted Assembly of Diverse Alleles

    PubMed Central

    Valente, Fabio; Gauthier, Franck; Bardol, Nicolas; Blanc, Guylaine; Joets, Johann; Charcosset, Alain

    2013-01-01

    Current advances in plant genotyping lead to major progress in the knowledge of genetic architecture of traits of interest. It is increasingly important to develop decision support tools to help breeders and geneticists to conduct marker-assisted selection methods to assemble favorable alleles that are discovered. Algorithms have been implemented, within an interactive graphical interface, to 1) trace parental alleles throughout generations, 2) propose strategies to select the best plants based on estimated molecular scores, and 3) efficiently intermate them depending on the expected value of their progenies. With the possibility to consider a multi-allelic context, OptiMAS opens new prospects to assemble favorable alleles issued from diverse parents and further accelerate genetic gain. PMID:23576670

  15. OptiMAS: a decision support tool for marker-assisted assembly of diverse alleles.

    PubMed

    Valente, Fabio; Gauthier, Franck; Bardol, Nicolas; Blanc, Guylaine; Joets, Johann; Charcosset, Alain; Moreau, Laurence

    2013-01-01

    Current advances in plant genotyping lead to major progress in the knowledge of genetic architecture of traits of interest. It is increasingly important to develop decision support tools to help breeders and geneticists to conduct marker-assisted selection methods to assemble favorable alleles that are discovered. Algorithms have been implemented, within an interactive graphical interface, to 1) trace parental alleles throughout generations, 2) propose strategies to select the best plants based on estimated molecular scores, and 3) efficiently intermate them depending on the expected value of their progenies. With the possibility to consider a multi-allelic context, OptiMAS opens new prospects to assemble favorable alleles issued from diverse parents and further accelerate genetic gain.

  16. Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep.

    PubMed

    Jones, Bryony L; Raga, Tamiru O; Liebert, Anke; Zmarz, Pawel; Bekele, Endashaw; Danielsen, E Thomas; Olsen, Anders Krüger; Bradman, Neil; Troelsen, Jesper T; Swallow, Dallas M

    2013-09-01

    The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(∗)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(∗)G, rs41525747; -13915(∗)G, rs41380347; -14010(∗)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(∗)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep. PMID:23993196

  17. Diversity of lactase persistence alleles in Ethiopia: signature of a soft selective sweep.

    PubMed

    Jones, Bryony L; Raga, Tamiru O; Liebert, Anke; Zmarz, Pawel; Bekele, Endashaw; Danielsen, E Thomas; Olsen, Anders Krüger; Bradman, Neil; Troelsen, Jesper T; Swallow, Dallas M

    2013-09-01

    The persistent expression of lactase into adulthood in humans is a recent genetic adaptation that allows the consumption of milk from other mammals after weaning. In Europe, a single allele (-13910(∗)T, rs4988235) in an upstream region that acts as an enhancer to the expression of the lactase gene LCT is responsible for lactase persistence and appears to have been under strong directional selection in the last 5,000 years, evidenced by the widespread occurrence of this allele on an extended haplotype. In Africa and the Middle East, the situation is more complicated and at least three other alleles (-13907(∗)G, rs41525747; -13915(∗)G, rs41380347; -14010(∗)C, rs145946881) in the same LCT enhancer region can cause continued lactase expression. Here we examine the LCT enhancer sequence in a large lactose-tolerance-tested Ethiopian cohort of more than 350 individuals. We show that a further SNP, -14009T>G (ss 820486563), is significantly associated with lactose-digester status, and in vitro functional tests confirm that the -14009(∗)G allele also increases expression of an LCT promoter construct. The derived alleles in the LCT enhancer region are spread through several ethnic groups, and we report a greater genetic diversity in lactose digesters than in nondigesters. By examining flanking markers to control for the effects of mutation and demography, we further describe, from empirical evidence, the signature of a soft selective sweep.

  18. Facultative cheating supports the coexistence of diverse quorum-sensing alleles

    PubMed Central

    Pollak, Shaul; Omer-Bendori, Shira; Even-Tov, Eran; Lipsman, Valeria; Bareia, Tasneem; Ben-Zion, Ishay; Eldar, Avigdor

    2016-01-01

    Bacterial quorum sensing enables bacteria to cooperate in a density-dependent manner via the group-wide secretion and detection of specific autoinducer molecules. Many bacterial species show high intraspecific diversity of autoinducer–receptor alleles, called pherotypes. The autoinducer produced by one pherotype activates its coencoded receptor, but not the receptor of another pherotype. It is unclear what selection forces drive the maintenance of pherotype diversity. Here, we use the ComQXPA system of Bacillus subtilis as a model system, to show that pherotype diversity can be maintained by facultative cheating—a minority pherotype exploits the majority, but resumes cooperation when its frequency increases. We find that the maintenance of multiple pherotypes by facultative cheating can persist under kin-selection conditions that select against “obligate cheaters” quorum-sensing response null mutants. Our results therefore support a role for facultative cheating and kin selection in the evolution of quorum-sensing diversity. PMID:26787913

  19. Facultative cheating supports the coexistence of diverse quorum-sensing alleles.

    PubMed

    Pollak, Shaul; Omer-Bendori, Shira; Even-Tov, Eran; Lipsman, Valeria; Bareia, Tasneem; Ben-Zion, Ishay; Eldar, Avigdor

    2016-02-23

    Bacterial quorum sensing enables bacteria to cooperate in a density-dependent manner via the group-wide secretion and detection of specific autoinducer molecules. Many bacterial species show high intraspecific diversity of autoinducer-receptor alleles, called pherotypes. The autoinducer produced by one pherotype activates its coencoded receptor, but not the receptor of another pherotype. It is unclear what selection forces drive the maintenance of pherotype diversity. Here, we use the ComQXPA system of Bacillus subtilis as a model system, to show that pherotype diversity can be maintained by facultative cheating--a minority pherotype exploits the majority, but resumes cooperation when its frequency increases. We find that the maintenance of multiple pherotypes by facultative cheating can persist under kin-selection conditions that select against "obligate cheaters" quorum-sensing response null mutants. Our results therefore support a role for facultative cheating and kin selection in the evolution of quorum-sensing diversity.

  20. Facultative cheating supports the coexistence of diverse quorum-sensing alleles.

    PubMed

    Pollak, Shaul; Omer-Bendori, Shira; Even-Tov, Eran; Lipsman, Valeria; Bareia, Tasneem; Ben-Zion, Ishay; Eldar, Avigdor

    2016-02-23

    Bacterial quorum sensing enables bacteria to cooperate in a density-dependent manner via the group-wide secretion and detection of specific autoinducer molecules. Many bacterial species show high intraspecific diversity of autoinducer-receptor alleles, called pherotypes. The autoinducer produced by one pherotype activates its coencoded receptor, but not the receptor of another pherotype. It is unclear what selection forces drive the maintenance of pherotype diversity. Here, we use the ComQXPA system of Bacillus subtilis as a model system, to show that pherotype diversity can be maintained by facultative cheating--a minority pherotype exploits the majority, but resumes cooperation when its frequency increases. We find that the maintenance of multiple pherotypes by facultative cheating can persist under kin-selection conditions that select against "obligate cheaters" quorum-sensing response null mutants. Our results therefore support a role for facultative cheating and kin selection in the evolution of quorum-sensing diversity. PMID:26787913

  1. High levels of MHC class II allelic diversity in lake trout from Lake Superior

    USGS Publications Warehouse

    Dorschner, M.O.; Duris, T.; Bronte, C.R.; Burnham-Curtis, M. K.; Phillips, R.B.

    2000-01-01

    Sequence variation in a 216 bp portion of the major histocompatibility complex (MHC) II B1 domain was examined in 74 individual lake trout (Salvelinus namaycush) from different locations in Lake Superior. Forty-three alleles were obtained which encoded 71-72 amino acids of the mature protein. These sequences were compared with previous data obtained from five Pacific salmon species and Atlantic salmon using the same primers. Although all of the lake trout alleles clustered together in the neighbor-joining analysis of amino acid sequences, one amino acid allelic lineage was shared with Atlantic salmon (Salmo salar), a species in another genus which probably diverged from Salvelinus more than 10-20 million years ago. As shown previously in other salmonids, the level of nonsynonymous nucleotide substitution (d(N)) exceeded the level of synonymous substitution (d(S)). The level of nucleotide diversity at the MHC class II B1 locus was considerably higher in lake trout than in the Pacific salmon (genus Oncorhynchus). These results are consistent with the hypothesis that lake trout colonized Lake Superior from more than one refuge following the Wisconsin glaciation. Recent population bottlenecks may have reduced nucleotide diversity in Pacific salmon populations.

  2. Seven novel HLA alleles reflect different mechanisms involved in the evolution of HLA diversity: description of the new alleles and review of the literature.

    PubMed

    Adamek, Martina; Klages, Cornelia; Bauer, Manuela; Kudlek, Evelina; Drechsler, Alina; Leuser, Birte; Scherer, Sabine; Opelz, Gerhard; Tran, Thuong Hien

    2015-01-01

    The human leukocyte antigen (HLA) loci are among the most polymorphic genes in the human genome. The diversity of these genes is thought to be generated by different mechanisms including point mutation, gene conversion and crossing-over. During routine HLA typing, we discovered seven novel HLA alleles which were probably generated by different evolutionary mechanisms. HLA-B*41:21, HLA-DQB1*02:10 and HLA-DQA1*01:12 likely emerged from the common alleles of their groups by point mutations, all of which caused non-synonymous amino acid substitutions. In contrast, a deletion of one nucleotide leading to a frame shift with subsequent generation of a stop codon is responsible for the appearance of a null allele, HLA-A*01:123N. Whereas HLA-B*35:231 and HLA-B*53:31 were probably products of intralocus gene conversion between HLA-B alleles, HLA-C*07:294 presumably evolved by interlocus gene conversion between an HLA-C and an HLA-B allele. Our analysis of these novel alleles illustrates the different mechanisms which may have contributed to the evolution of HLA polymorphism.

  3. Linear allele-specific long-range amplification: a novel method of long-range molecular haplotyping.

    PubMed

    Wu, Wei-Ming; Tsai, Hsiang-Ju; Pang, Jong-Hwei S; Wang, Tzu-Hao; Wang, Hsin-Shih; Hong, Hong-Shang; Lee, Yun-Shien

    2005-10-01

    Haplotypes have been repeatedly shown to be more powerful than collections of single-locus markers in gene-mapping studies. Various haplotyping methods including statistical estimation are employed but molecular haplotyping, the acquisition of information directly on physical DNA sequences, has been in demand for its accuracy and independence from family pedigrees. We investigated the allelic specificity of long-range PCR, which was successful for long-range haplotyping in recent reports, and found problems of initial mispriming and crossover amplification significantly confounded its application. Based on these observations, we designed a novel method based on linear amplification of a hemizygous DNA segment with a single phosphorothioate-modified oligonucleotide. Our results revealed, with a single nucleotide polymorphism as the discriminative marker, downstream haplotypes of 14-15 kb DNA segment could be confidently scored. With two rounds of the method and five single nucleotide polymorphisms, molecular haplotypes of 29.3 kb spanning the HCR and CDSN genes, two genes associated with the susceptibility of psoriasis, of 11 members, belonging to a CEPH family, were revealed. Clear Mendelian segregation of 35 highly heterozygous SNPs confirmed the accuracy of the method. Problems of low specificity associated with long-range PCR were not observed. The simplicity, along with long-sequence accessibility and feasibility of a single nucleotide difference as the discriminative marker indicated our method holds promise for future gene-mapping studies.

  4. Cheetah paradigm revisited: MHC diversity in the world's largest free-ranging population.

    PubMed

    Castro-Prieto, Aines; Wachter, Bettina; Sommer, Simone

    2011-04-01

    For more than two decades, the cheetah (Acinonyx jubatus) has been considered a paradigm of disease vulnerability associated with low genetic diversity, particularly at the immune genes of the major histocompatibility complex (MHC). Cheetahs have been used as a classic example in numerous conservation genetics textbooks as well as in many related scientific publications. However, earlier studies used methods with low resolution to quantify MHC diversity and/or small sample sizes. Furthermore, high disease susceptibility was reported only for captive cheetahs, whereas free-ranging cheetahs show no signs of infectious diseases and a good general health status. We examined whether the diversity at MHC class I and class II-DRB loci in 149 Namibian cheetahs was higher than previously reported using single-strand conformation polymorphism analysis, cloning, and sequencing. MHC genes were examined at the genomic and transcriptomic levels. We detected ten MHC class I and four class II-DRB alleles, of which nine MHC class I and all class II-DRB alleles were expressed. Phylogenetic analyses and individual genotypes suggested that the alleles belong to four MHC class I and three class II-DRB putative loci. Evidence of positive selection was detected in both MHC loci. Our study indicated that the low number of MHC class I alleles previously observed in cheetahs was due to a smaller sample size examined. On the other hand, the low number of MHC class II-DRB alleles previously observed in cheetahs was further confirmed. Compared with other mammalian species including felids, cheetahs showed low levels of MHC diversity, but this does not seem to influence the immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease vulnerability.

  5. Allelic diversity at class II DRB1 and DQB loci of the pig MHC (SLA).

    PubMed

    Kanai, T H; Tanioka, Y; Tanigawa, M; Matsumoto, Y; Ueda, S; Onodera, T; Matsumoto, Y

    1999-12-01

    The loci encoding the beta chain of the pig major histocompatibility complex (MHC) class II antigens, SLA-DR and -DQ, have been known to exhibit a remarkable degree of allelic polymorphism. Here, to understand the generation of SLA class II polymorphism, 25 SLA-DRB1 and 24 SLA-DQB genes including newly identified 12 SLA-DRB1 and 7 SLA-DQB genes obtained from miniature pigs were analyzed based on the nucleotide and deduced amino acid sequences. Most of the allelic diversity was attributed to the variable sequences which encode a beta1 domain consisting of a beta-pleated sheet followed by an a helix. In the beta1 domain coding region, there were four GC-rich sequences, which have been considered to involve the intra-exon sequence exchange also in other gene evolutions. The first and second GC-rich sequences were alpha-like sequences, which have been shown to be a putative recombination signal, and were stably conserved among SLA-DRB1 and DQB genes. These alpha-like sequences identified in SLA-DRB1 and SLA-DQB were found to encode the first turning point of the beta-pleated sheet and the boundary between the beta-pleated sheet and the alpha helix. Analysis of clustered sequence variation also suggested intra-exon gene conversions in which the alpha-like sequences act as putative breakpoints. In addition to point mutations and selection mechanism, intra-exon gene conversions must be an important mechanism in the generation of allelic polymorphism at the SLA-DRB1 and SLA-DQB.

  6. Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure.

    PubMed Central

    Go, M F; Kapur, V; Graham, D Y; Musser, J M

    1996-01-01

    Genetic diversity and relationships in 74 Helicobacter pylori isolates recovered from patients assigned to distinct clinical categories were estimated by examination of allelic variation in six genes encoding metabolic housekeeping enzymes by multilocus enzyme electrophoresis. Seventy-three distinct allele profiles, representing multilocus chromosomal genotypes, were identified. All six loci were highly polymorphic, with an average of 11.2 alleles per locus. The mean genetic diversity in the sample was 0.735, a value that exceeds the level of diversity recorded in virtually all bacterial species studied by multilocus enzyme electrophoresis. A high frequency of occurrence of null alleles (lack of enzyme activity) was identified and warrants further investigation at the molecular level. Lack of linkage disequilibrium (nonrandom association (of alleles over loci) indicates that horizontal transfer and recombination of metabolic enzyme genes have contributed to the generation of chromosomal diversity in H. pylori. In this sample of isolates, there was no statistically significant association of multilocus enzyme electrophoretic types or cluster of related chromosomal types and disease category. PMID:8682800

  7. Evolution of Functionally Diverse Alleles Associated with PTC Bitter Taste Sensitivity in Africa

    PubMed Central

    Campbell, Michael C.; Ranciaro, Alessia; Froment, Alain; Hirbo, Jibril; Omar, Sabah; Bodo, Jean-Marie; Nyambo, Thomas; Lema, Godfrey; Zinshteyn, Daniel; Drayna, Dennis; Breslin, Paul A. S.; Tishkoff, Sarah A.

    2012-01-01

    indicate that novel rare mutations contribute to the phenotypic variance of PTC sensitivity, illustrating the influence of rare variation on a common trait, as well as the relatively recent evolution of functionally diverse alleles at this locus. PMID:22130969

  8. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly.

    PubMed

    Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

    2013-11-01

    Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations.

  9. Rapid range expansion increases genetic differentiation while causing limited reduction in genetic diversity in a damselfly

    PubMed Central

    Swaegers, J; Mergeay, J; Therry, L; Larmuseau, M H D; Bonte, D; Stoks, R

    2013-01-01

    Many ectothermic species are currently expanding their geographic range due to global warming. This can modify the population genetic diversity and structure of these species because of genetic drift during the colonization of new areas. Although the genetic signatures of historical range expansions have been investigated in an array of species, the genetic consequences of natural, contemporary range expansions have received little attention, with the only studies available focusing on range expansions along a narrow front. We investigate the genetic consequences of a natural range expansion in the Mediterranean damselfly Coenagrion scitulum, which is currently rapidly expanding along a broad front in different directions. We assessed genetic diversity and genetic structure using 12 microsatellite markers in five centrally located populations and five recently established populations at the edge of the geographic distribution. Our results suggest that, although a marginal significant decrease in the allelic richness was found in the edge populations, genetic diversity has been preserved during the range expansion of this species. Nevertheless, edge populations were genetically more differentiated compared with core populations, suggesting genetic drift during the range expansion. The smaller effective population sizes of the edge populations compared with central populations also suggest a contribution of genetic drift after colonization. We argue and document that range expansion along multiple axes of a broad expansion front generates little reduction in genetic diversity, yet stronger differentiation of the edge populations. PMID:23820582

  10. Length of FMR1 repeat alleles within the normal range does not substantially affect the risk of early menopause

    PubMed Central

    Ruth, Katherine S.; Bennett, Claire E.; Schoemaker, Minouk J.; Weedon, Michael N.; Swerdlow, Anthony J.; Murray, Anna

    2016-01-01

    STUDY QUESTION Is the length of FMR1 repeat alleles within the normal range associated with the risk of early menopause? SUMMARY ANSWER The length of repeat alleles within the normal range does not substantially affect risk of early menopause. WHAT IS KNOWN ALREADY There is a strong, well-established relationship between length of premutation FMR1 alleles and age at menopause, suggesting that this relationship could continue into the normal range. Within the normal range, there is conflicting evidence; differences in ovarian reserve have been identified with FMR1 repeat allele length, but a recent population-based study did not find any association with age at menopause as a quantitative trait. STUDY DESIGN, SIZE, DURATION We analysed cross-sectional baseline survey data collected at recruitment from 2004 to 2010 from a population-based, prospective epidemiological cohort study of >110 000 women to investigate whether repeat allele length was associated with early menopause. PARTICIPANTS/MATERIALS, SETTING, METHOD We included 4333 women from the Breakthrough Generations Study (BGS), of whom 2118 were early menopause cases (menopause under 46 years) and 2215 were controls. We analysed the relationship between length of FMR1 alleles and early menopause using logistic regression with allele length as continuous and categorical variables. We also conducted analyses with the outcome age at menopause as a quantitative trait as well as appropriate sensitivity and exploratory analyses. MAIN RESULTS AND THE ROLE OF CHANCE There was no association of the shorter or longer FMR1 allele or their combined genotype with the clinically relevant end point of early menopause in our main analysis. Likewise, there were no associations with age at menopause as a quantitative trait in our secondary analysis. LIMITATIONS, REASONS FOR CAUTION Women with homozygous alleles in the normal range may have undetected FMR1 premutation alleles, although there was no evidence to suggest this. We

  11. Allelic Diversity and Geographical Distribution of the Gene Encoding Plasmodium falciparum Merozoite Surface Protein-3 in Thailand

    PubMed Central

    Sawaswong, Vorthon; Simpalipan, Phumin; Siripoon, Napaporn; Harnyuttanakorn, Pongchai; Pattaradilokrat, Sittiporn

    2015-01-01

    Merozoite surface proteins (MSPs) of malaria parasites play critical roles during the erythrocyte invasion and so are potential candidates for malaria vaccine development. However, because MSPs are often under strong immune selection, they can exhibit extensive genetic diversity. The gene encoding the merozoite surface protein-3 (MSP-3) of Plasmodium falciparum displays 2 allelic types, K1 and 3D7. In Thailand, the allelic frequency of the P. falciparum msp-3 gene was evaluated in a single P. falciparum population in Tak at the Thailand and Myanmar border. However, no study has yet looked at the extent of genetic diversity of the msp-3 gene in P. falciparum populations in other localities. Here, we genotyped the msp-3 alleles of 63 P. falciparum samples collected from 5 geographical populations along the borders of Thailand with 3 neighboring countries (Myanmar, Laos, and Cambodia). Our study indicated that the K1 and 3D7 alleles coexisted, but at different proportions in different Thai P. falciparum populations. K1 was more prevalent in populations at the Thailand-Myanmar and Thailand-Cambodia borders, whilst 3D7 was more prevalent at the Thailand-Laos border. Global analysis of the msp-3 allele frequencies revealed that proportions of K1 and 3D7 alleles of msp-3 also varied in different continents, suggesting the divergence of malaria parasite populations. In conclusion, the variation in the msp-3 allelic patterns of P. falciparum in Thailand provides fundamental knowledge for inferring the P. falciparum population structure and for the best design of msp-3 based malaria vaccines. PMID:25925176

  12. Allelic diversity and population structure in Oenococcus oeni as determined from sequence analysis of housekeeping genes.

    PubMed

    de Las Rivas, Blanca; Marcobal, Angela; Muñoz, Rosario

    2004-12-01

    Oenococcus oeni is the organism of choice for promoting malolactic fermentation in wine. The population biology of O. oeni is poorly understood and remains unclear. For a better understanding of the mode of genetic variation within this species, we investigated by using multilocus sequence typing (MLST) with the gyrB, pgm, ddl, recP, and mleA genes the genetic diversity and genetic relationships among 18 O. oeni strains isolated in various years from wines of the United States, France, Germany, Spain, and Italy. These strains have also been characterized by ribotyping and restriction fragment length polymorphism (RFLP) analysis of the PCR-amplified 16S-23S rRNA gene intergenic spacer region (ISR). Ribotyping grouped the strains into two groups; however, the RFLP analysis of the ISRs showed no differences in the strains analyzed. In contrast, MLST in oenococci had a good discriminatory ability, and we have found a higher genetic diversity than indicated by ribotyping analysis. All sequence types were represented by a single strain, and all the strains could be distinguished from each other because they had unique combinations of alleles. Strains assumed to be identical showed the same sequence type. Phylogenetic analyses indicated a panmictic population structure in O. oeni. Sequences were analyzed for evidence of recombination by split decomposition analysis and analysis of clustered polymorphisms. All results indicated that recombination plays a major role in creating the genetic heterogeneity of O. oeni. A low standardized index of association value indicated that the O. oeni genes analyzed are close to linkage equilibrium. This study constitutes the first step in the development of an MLST method for O. oeni and the first example of the application of MLST to a nonpathogenic food production bacteria. PMID:15574919

  13. Divergent patterns of allelic diversity from similar origins: the case of oilseed rape (Brassica napus L.) in China and Australia.

    PubMed

    Chen, S; Nelson, M N; Ghamkhar, K; Fu, T; Cowling, W A

    2008-01-01

    Oilseed rape (Brassica napus) in Australia and China have similar origins, with introductions from Europe, Canada, and Japan in the mid 20th century, and there has been some interchange of germplasm between China and Australia since that time. Allelic diversity of 72 B. napus genotypes representing contemporary germplasm in Australia and China, including samples from India, Europe, and Canada, was characterized by 55 polymorphic simple sequence repeat (SSR) markers spanning the entire B. napus genome. Hierarchical clustering and two-dimensional multidimensional scaling identified a Chinese group (China-1) that was separated from "mixed group" of Australian, Chinese (China-2), European, and Canadian lines. A small group from India was distinctly separated from all other B. napus genotypes. Chinese genotypes, especially in the China-1 group, have inherited unique alleles from interspecific crossing, primarily with B. rapa, and the China-2 group has many alleles in common with Australian genotypes. The concept of "private alleles" is introduced to describe both the greater genetic diversity and the genetic distinctiveness of Chinese germplasm, compared with Australian germplasm, after 50 years of breeding from similar origins.

  14. Power Laws for Heavy-Tailed Distributions: Modeling Allele and Haplotype Diversity for the National Marrow Donor Program

    PubMed Central

    Gragert, Loren; Maiers, Martin; Chatterjee, Ansu; Albrecht, Mark

    2015-01-01

    Measures of allele and haplotype diversity, which are fundamental properties in population genetics, often follow heavy tailed distributions. These measures are of particular interest in the field of hematopoietic stem cell transplant (HSCT). Donor/Recipient suitability for HSCT is determined by Human Leukocyte Antigen (HLA) similarity. Match predictions rely upon a precise description of HLA diversity, yet classical estimates are inaccurate given the heavy-tailed nature of the distribution. This directly affects HSCT matching and diversity measures in broader fields such as species richness. We, therefore, have developed a power-law based estimator to measure allele and haplotype diversity that accommodates heavy tails using the concepts of regular variation and occupancy distributions. Application of our estimator to 6.59 million donors in the Be The Match Registry revealed that haplotypes follow a heavy tail distribution across all ethnicities: for example, 44.65% of the European American haplotypes are represented by only 1 individual. Indeed, our discovery rate of all U.S. European American haplotypes is estimated at 23.45% based upon sampling 3.97% of the population, leaving a large number of unobserved haplotypes. Population coverage, however, is much higher at 99.4% given that 90% of European Americans carry one of the 4.5% most frequent haplotypes. Alleles were found to be less diverse suggesting the current registry represents most alleles in the population. Thus, for HSCT registries, haplotype discovery will remain high with continued recruitment to a very deep level of sampling, but population coverage will not. Finally, we compared the convergence of our power-law versus classical diversity estimators such as Capture recapture, Chao, ACE and Jackknife methods. When fit to the haplotype data, our estimator displayed favorable properties in terms of convergence (with respect to sampling depth) and accuracy (with respect to diversity estimates). This

  15. Evidence that intragenic recombination contributes to allelic diversity of the S-RNase gene at the self-incompatibility (S) locus in Petunia inflata.

    PubMed

    Wang, X; Hughes, A L; Tsukamoto, T; Ando, T; Kao, T

    2001-02-01

    For Solanaceae type self-incompatibility, discrimination between self and nonself pollen by the pistil is controlled by the highly polymorphic S-RNase gene. To date, the mechanism generating the allelic diversity of this gene is largely unknown. Natural populations offer a good opportunity to address this question because they likely contain different alleles that share recent common progenitors. We identified 19 S haplotypes from a natural population of Petunia inflata in Argentina, used reverse transcriptase-polymerase chain reaction to obtain cDNAs for 15 alleles of the S-RNase gene, and sequenced all the cDNAs. Phylogenetic studies revealed that five of these alleles and two previously identified alleles form a major clade, and that the 5' region of S(19) allele was derived from an ancestor allele closely related to S(2), whereas its 3' region was derived from an ancestor allele closely related to S(8). A similar evolutionary relationship was found among S(3), S(12), and S(15) alleles. These findings suggest that intragenic recombination contributed to the generation of the allelic diversity of the S-RNase gene. Two additional findings emerged from the sequence comparisons. First, the nucleotide sequence of the S(1) allele identified in this work is completely identical to that of the previously identified S(1) allele of a different origin. Second, in the two hypervariable regions HVa and HVb, thought to be involved in determining S allele specificity, S(6) and S(9) alleles differ only by four nucleotides, all in HVb, resulting in two amino acid differences. The implications of these findings are discussed. PMID:11161057

  16. Y chromosome STR allelic and haplotype diversity in a Rwanda population from East Central Africa.

    PubMed

    Balamurugan, Kuppareddi; Duncan, George

    2012-03-01

    We have analyzed 17 Y-chromosomal STR loci in a population sample of 69 unrelated male individuals of the Rwanda-Hutu population from East Central Africa using an AmpFlSTR® Yfiler™ PCR amplification kit. A total of 62 unique haplotypes were identified among the 69 individuals studied. The haplotype diversity was found to be 0.9970 for this population. The gene diversity ranged from 0.1130 (DYS392) to 0.7722 (DYS385). Comparison of populations in this study with twenty-five other national and global populations using Principal Co-ordinate Analysis (PCA) and phylogenetic molecular analysis using a genetic distance matrix indicates a delineation of all the African populations from other unrelated populations. The results of population pair-wise Fst p values indicate statistically significant differentiation of the Rwandan population when compared with 25 other global populations including four African populations (p=0.0000). Analysis of Molecular Variance (AMOVA) of the Rwanda population with four other African populations indicated a 93% variance within populations and 7% variance among the five populations. A data base search of the 62 haplotypes yielded only one non-African haplotype match, suggesting these haplotypes are unique to the African continent. PMID:22285642

  17. HLA-B15: a widespread and diverse family of HLA-B alleles.

    PubMed

    Hildebrand, W H; Domena, J D; Shen, S Y; Lau, M; Terasaki, P I; Bunce, M; Marsh, S G; Guttridge, M G; Bias, W B; Parham, P

    1994-04-01

    HLA-B15 embraces a multiplicity of antigenic specificities which vary in their distribution amongst human populations. To correlate B15 molecular structure with the serological picture we have sequenced alleles encoding the various subspecificities of the B15 antigen: B62, B63, B75, B76 and B77, and a number of "variants" of these antigens including the 8w66 split of B63. HLA-B63 (B*1517) and 8w66 (B*1516) heavy chains have sequence identity to B17 in the alpha 1 helix correlating with the antigenic crossreactivity of these molecules. HLA-B77(B*1513) and B75 (B*1502) heavy chains differ solely in segments determining the Bw4 and Bw6 public epitopes, consistent with the serological description of the B77 and B75 antigens. One allele encoding the B76 antigen (B*1512) appears to be the product of gene conversion between the HLA-A and -B loci and differs from B*1501 in codons 166 and 167. In contrast, a second allele encoding the B76 antigen (B*1514) differs from B*1501 by an unrelated substitution in codon 167 which confers similarily with B45, an antigen crossreactive with B76. A third allele encoding B76, B*1519, differs from B*1512 by a unique point substitution in exon 4. Three alleles encoding variant B15 and B62 antigens (B*1508, B*1511 and B*1515) differ from B*1501 by localized clusters of substitutions that probably result from interallelic conversion. The B15 sequences described in this paper, in combination with those previously determined, define a family of 22 alleles, including those encoding the B46 and B70 antigens. Within this family the patterns of allelic substitution are analogous to those of other HLA-A and -B families, in that pairwise differences almost always involve functional positions of the antigen recognition site and recombination is the major agent of diversification.

  18. Global phylogeography of the avian malaria pathogen Plasmodium relictum based on MSP1 allelic diversity

    USGS Publications Warehouse

    Hellgren, Olof; Atkinson, Carter T.; Bensch, Staffan; Albayrak, Tamer; Dimitrov, Dimitar; Ewen, John G.; Kim, Kyeong Soon; Lima, Marcos R.; Martin, Lynn; Palinauskas, Vaidas; Ricklefs, Robert; Sehgal, Ravinder N. M.; Gediminas, Valkiunas; Tsuda, Yoshio; Marzal, Alfonso

    2015-01-01

    Knowing the genetic variation that occurs in pathogen populations and how it is distributed across geographical areas is essential to understand parasite epidemiology, local patterns of virulence, and evolution of host-resistance. In addition, it is important to identify populations of pathogens that are evolutionarily independent and thus ‘free’ to adapt to hosts and environments. Here, we investigated genetic variation in the globally distributed, highly invasive avian malaria parasite Plasmodium relictum, which has several distinctive mitochondrial haplotyps (cyt b lineages, SGS1, GRW11 and GRW4). The phylogeography of P. relictum was accessed using the highly variable nuclear gene merozoite surface protein 1 (MSP1), a gene linked to the invasion biology of the parasite. We show that the lineage GRW4 is evolutionarily independent of GRW11 and SGS1 whereas GRW11 and SGS1 share MSP1 alleles and thus suggesting the presence of two distinct species (GRW4 versus SGS1 and GRW11). Further, there were significant differences in the global distribution of MSP1 alleles with differences between GRW4 alleles in the New and the Old World. For SGS1, a lineage formerly believed to have both tropical and temperate transmission, there were clear differences in MSP1 alleles transmitted in tropical Africa compared to the temperate regions of Europe and Asia. Further, we highlight the occurrence of multiple MSP1 alleles in GRW4 isolates from the Hawaiian Islands, where the parasite has contributed to declines and extinctions of endemic forest birds since it was introduced. This study stresses the importance of multiple independent loci for understanding patterns of transmission and evolutionary independence across avian malaria parasites.

  19. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

    PubMed Central

    Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D.; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S.; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C. L. L.; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K.; Parida, Swarup K.

    2015-01-01

    The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93–96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13–89%)/functional allelic diversity (18–77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54–0.68) and extended LD decay (400–500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically

  20. Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea.

    PubMed

    Kujur, Alice; Bajaj, Deepak; Upadhyaya, Hari D; Das, Shouvik; Ranjan, Rajeev; Shree, Tanima; Saxena, Maneesha S; Badoni, Saurabh; Kumar, Vinod; Tripathi, Shailesh; Gowda, C L L; Sharma, Shivali; Singh, Sube; Tyagi, Akhilesh K; Parida, Swarup K

    2015-01-01

    The genome-wide discovery and high-throughput genotyping of SNPs in chickpea natural germplasm lines is indispensable to extrapolate their natural allelic diversity, domestication, and linkage disequilibrium (LD) patterns leading to the genetic enhancement of this vital legume crop. We discovered 44,844 high-quality SNPs by sequencing of 93 diverse cultivated desi, kabuli, and wild chickpea accessions using reference genome- and de novo-based GBS (genotyping-by-sequencing) assays that were physically mapped across eight chromosomes of desi and kabuli. Of these, 22,542 SNPs were structurally annotated in different coding and non-coding sequence components of genes. Genes with 3296 non-synonymous and 269 regulatory SNPs could functionally differentiate accessions based on their contrasting agronomic traits. A high experimental validation success rate (92%) and reproducibility (100%) along with strong sensitivity (93-96%) and specificity (99%) of GBS-based SNPs was observed. This infers the robustness of GBS as a high-throughput assay for rapid large-scale mining and genotyping of genome-wide SNPs in chickpea with sub-optimal use of resources. With 23,798 genome-wide SNPs, a relatively high intra-specific polymorphic potential (49.5%) and broader molecular diversity (13-89%)/functional allelic diversity (18-77%) was apparent among 93 chickpea accessions, suggesting their tremendous applicability in rapid selection of desirable diverse accessions/inter-specific hybrids in chickpea crossbred varietal improvement program. The genome-wide SNPs revealed complex admixed domestication pattern, extensive LD estimates (0.54-0.68) and extended LD decay (400-500 kb) in a structured population inclusive of 93 accessions. These findings reflect the utility of our identified SNPs for subsequent genome-wide association study (GWAS) and selective sweep-based domestication trait dissection analysis to identify potential genomic loci (gene-associated targets) specifically regulating

  1. The Diversity of Alleles at the Hsd Locus in Natural Populations of Escherichia Coli

    PubMed Central

    Barcus, V. A.; Titheradge, AJB.; Murray, N. E.

    1995-01-01

    In enteric bacteria three discrete families of type I restriction and modification systems (IA, IB and ID) are encoded by alleles of the serB-linked hsd locus. Probes specific for each of the three familes were used to monitor the distribution of related systems in 37 of the 72 wild-type Escherichia coli strains comprising the ECOR collection. All 25 members of group A in this collection were screened; 12 were probe-positive, nine have hsd genes in the IA family, two in the IB and one in the ID. Twelve strains, representing all groups other than A, were screened; five were probe-positive, one has hsd genes in the IA family, one in the IB and three in the ID. The type ID genes are the first representatives of this family in E. coli, the probe-negative strains could have alternative families of hsd genes. The type IA and IB systems added at least five new specificites to the five already identified in natural isolates of E. coli. The distribution of alleles is inconsistent with the dendrogram of the bacterial strains derived from other criteria. This discrepancy and the dissimilar coding sequences of allelic hsd genes both imply lateral transfer of hsd genes. PMID:7498762

  2. Prevalence and phenotype consequence of FRAXA and FRAXE alleles in a large, ethnically diverse, special education-needs population.

    PubMed Central

    Crawford, D C; Meadows, K L; Newman, J L; Taft, L F; Pettay, D L; Gold, L B; Hersey, S J; Hinkle, E F; Stanfield, M L; Holmgreen, P; Yeargin-Allsopp, M; Boyle, C; Sherman, S L

    1999-01-01

    We conducted a large population-based survey of fragile X (FRAXA) syndrome in ethnically diverse metropolitan Atlanta. The eligible study population consisted of public school children, aged 7-10 years, in special education-needs (SEN) classes. The purpose of the study was to estimate the prevalence among whites and, for the first time, African Americans, among a non-clinically referred population. At present, 5 males with FRAXA syndrome (4 whites and 1 African American), among 1,979 tested males, and no females, among 872 tested females, were identified. All males with FRAXA syndrome were mentally retarded and had been diagnosed previously. The prevalence for FRAXA syndrome was estimated to be 1/3,460 (confidence interval [CI] 1/7,143-1/1,742) for the general white male population and 1/4, 048 (CI 1/16,260-1/1,244) for the general African American male population. We also compared the frequency of intermediate and premutation FRAXA alleles (41-199 repeats) and fragile XE syndrome alleles (31-199 repeats) in the SEN population with that in a control population, to determine if there was a possible phenotype consequence of such high-repeat alleles, as has been reported previously. No difference was observed between our case and control populations, and no difference was observed between populations when the probands were grouped by a rough estimate of IQ based on class placement. These results suggest that there is no phenotype consequence of larger alleles that would cause carriers to be placed in an SEN class. PMID:9973286

  3. Rapid Evolution of Major Histocompatibility Complex Class I Genes in Primates Generates New Disease Alleles in Humans via Hitchhiking Diversity

    PubMed Central

    Shiina, Takashi; Ota, Masao; Shimizu, Sayoko; Katsuyama, Yoshihiko; Hashimoto, Nami; Takasu, Miwa; Anzai, Tatsuya; Kulski, Jerzy K.; Kikkawa, Eri; Naruse, Taeko; Kimura, Natsuki; Yanagiya, Kazuyo; Watanabe, Atsushi; Hosomichi, Kazuyoshi; Kohara, Sakae; Iwamoto, Chie; Umehara, Yumi; Meyer, Alice; Wanner, Valérie; Sano, Kazumi; Macquin, Cécile; Ikeo, Kazuho; Tokunaga, Katsushi; Gojobori, Takashi; Inoko, Hidetoshi; Bahram, Seiamak

    2006-01-01

    A plausible explanation for many MHC-linked diseases is lacking. Sequencing of the MHC class I region (coding units or full contigs) in several human and nonhuman primate haplotypes allowed an analysis of single nucleotide variations (SNV) across this entire segment. This diversity was not evenly distributed. It was rather concentrated within two gene-rich clusters. These were each centered, but importantly not limited to, the antigen-presenting HLA-A and HLA-B/-C loci. Rapid evolution of MHC-I alleles, as evidenced by an unusually high number of haplotype-specific (hs) and hypervariable (hv) (which could not be traced to a single species or haplotype) SNVs within the classical MHC-I, seems to have not only hitchhiked alleles within nearby genes, but also hitchhiked deleterious mutations in these same unrelated loci. The overrepresentation of a fraction of these hvSNV (hv1SNV) along with hsSNV, as compared to those that appear to have been maintained throughout primate evolution (trans-species diversity; tsSNV; included within hv2SNV) tends to establish that the majority of the MHC polymorphism is de novo (species specific). This is most likely reminiscent of the fact that these hsSNV and hv1SNV have been selected in adaptation to the constantly evolving microbial antigenic repertoire. PMID:16702430

  4. Population diversity of B-locus alleles observed by high-resolution DNA typing.

    PubMed

    Fernandez-Viña, M; Lazaro, A M; Sun, Y; Miller, S; Forero, L; Stastny, P

    1995-03-01

    HLA B-locus typing by group-specific PCR and hybridization with SSOP was performed in 81 10th IHWS B cell lines and 334 selected subjects of our local panel, from four ethnic groups. Most of the B-locus serological specificities were well defined. However, some antigens like B41, B58, B56, the splits of B14, and some subtypes of B5, were not accurately assigned by serology. In the panel studied, we found 17 hybridization patterns that corresponded to probable new alleles. New patterns occurred in the four ethnic groups examined. Multiple subtypes of B35, B5, B15, B41, B44, B57, B58, B70, B14, B40, B22 were found in subjects of the same ethnic group. In view of the poor serological definition of some alleles, and the occurrence of multiple subtypes in the same ethnic population, it appears that high resolution B-locus typing may be an important addition for detection of potentially relevant HLA incompatibilities in transplantation. It should also be valuable for population studies and for the investigation of HLA associations with diseases.

  5. Genetic Diversity and Population Structure in a Legacy Collection of Spring Barley Landraces Adapted to a Wide Range of Climates

    PubMed Central

    Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

    2014-01-01

    Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type – and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

  6. Genetic diversity and population structure in a legacy collection of spring barley landraces adapted to a wide range of climates.

    PubMed

    Pasam, Raj K; Sharma, Rajiv; Walther, Alexander; Özkan, Hakan; Graner, Andreas; Kilian, Benjamin

    2014-01-01

    Global environmental change and increasing human population emphasize the urgent need for higher yielding and better adapted crop plants. One strategy to achieve this aim is to exploit the wealth of so called landraces of crop species, representing diverse traditional domesticated populations of locally adapted genotypes. In this study, we investigated a comprehensive set of 1485 spring barley landraces (Lrc1485) adapted to a wide range of climates, which were selected from one of the largest genebanks worldwide. The landraces originated from 5° to 62.5° N and 16° to 71° E. The whole collection was genotyped using 42 SSR markers to assess the genetic diversity and population structure. With an average allelic richness of 5.74 and 372 alleles, Lrc1485 harbours considerably more genetic diversity than the most polymorphic current GWAS panel for barley. Ten major clusters defined most of the population structure based on geographical origin, row type of the ear and caryopsis type - and were assigned to specific climate zones. The legacy core reference set Lrc648 established in this study will provide a long-lasting resource and a very valuable tool for the scientific community. Lrc648 is best suited for multi-environmental field testing to identify candidate genes underlying quantitative traits but also for allele mining approaches. PMID:25541702

  7. Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast.

    PubMed

    Pasino, Serena; Caratti, Stefano; Del Pero, Massimiliano; Santovito, Alfredo; Torre, Carlo; Robino, Carlo

    2011-09-01

    Twenty-one X-chromosomal short tandem repeat (STR) loci, including the six clusters of linked markers DXS10148-DXS10135-DXS8378 (Xp22), DXS7132-DXS10079-DXS10074 (Xq12), DXS6801-DXS6809-DXS6789 (Xq21), DXS7424-DXS101 (Xq22), DXS10103-HPRTB-DXS10101 (Xq26), DXS8377-DXS10146-DXS10134-DXS7423 (Xq28) and the loci DXS6800, GATA172D05 and DXS10011 were typed in a population sample from Ivory Coast (n=125; 51 men and 74 women). Allele and haplotype frequencies as well as linkage disequilibrium data for kinship calculations are provided. On the whole, no significant differences in the genetic variability of X-STR markers were observed between Ivorians and other sub-Saharan African populations belonging to the Niger-Kordofanian linguistic group. PMID:21717153

  8. Allele and haplotype diversity of X-chromosomal STRs in Ivory Coast.

    PubMed

    Pasino, Serena; Caratti, Stefano; Del Pero, Massimiliano; Santovito, Alfredo; Torre, Carlo; Robino, Carlo

    2011-09-01

    Twenty-one X-chromosomal short tandem repeat (STR) loci, including the six clusters of linked markers DXS10148-DXS10135-DXS8378 (Xp22), DXS7132-DXS10079-DXS10074 (Xq12), DXS6801-DXS6809-DXS6789 (Xq21), DXS7424-DXS101 (Xq22), DXS10103-HPRTB-DXS10101 (Xq26), DXS8377-DXS10146-DXS10134-DXS7423 (Xq28) and the loci DXS6800, GATA172D05 and DXS10011 were typed in a population sample from Ivory Coast (n=125; 51 men and 74 women). Allele and haplotype frequencies as well as linkage disequilibrium data for kinship calculations are provided. On the whole, no significant differences in the genetic variability of X-STR markers were observed between Ivorians and other sub-Saharan African populations belonging to the Niger-Kordofanian linguistic group.

  9. Diversity of HLA-B17 alleles and haplotypes in East Asians and a novel Cw6 allele (Cw*0604) associated with B*5701.

    PubMed

    Inoue, T; Ogawa, A; Tokunaga, K; Ishikawa, Y; Kashiwase, K; Tanaka, H; Park, M H; Jia, G J; Chimge, N O; Sideltseva, E W; Akaza, T; Tadokoro, K; Takahashi, T; Juji, T

    1999-06-01

    The distribution of HLA-B17 alleles and their association with HLA-A, -C and -DRB1 alleles were investigated in seven East Asian populations Japanese, South Korean, Chinese-Korean, Man, Northern Han, Mongolian and Buryat populations). The B17 alleles were identified from genomic DNA using group-specific polymerase chain reaction (PCR) followed by hybridization with sequence-specific oligonucleotide probes (SSOP). In all of these East Asian populations, except Japanese and Chinese-Koreans, B*5701 was detected and strongly associated with A*0101, Cw*0602 and DRB1*0701. In contrast, B*5801 was detected in all the seven populations and strongly associated with A*3303, Cw*0302, DRB1*0301 and DRB1*1302. The A*3303-Cw*0302-B*5801-DRB1*1302 haplotype was observed in South Korean, Chinese-Korean, Buryat and Japanese populations, while A*3303-Cw*0302-B*5801-DRB1*0301 was predominantly observed in the Mongolian population. A similar haplotype, A*0101-Cw*0302-B*5801-DRB1*1302, was observed in the Buryat population. A novel Cw6 allele, Cw*0604, was identified in the Man population. This Cw allele was observed on the haplotype A*0101-B*5701-DRB1*0701. Thus, we confirmed, at the sequence level, that the common haplotypes carrying B*5701 and B*5801 have been conserved and shared in East Asian populations.

  10. Molecular basis of the allelic inheritance of rabbit immunoglobulin VH allotypes: implications for the generation of antibody diversity.

    PubMed

    Knight, K L; Becker, R S

    1990-03-23

    Rabbits are unique in that their immunoglobulin VH regions bear allotypic markers encoded by allelic genes. The presence of these markers on most serum immunoglobulins is difficult to explain, as the germline contains several hundred VH genes. We cloned VH genes from normal rabbits of the VHa allotypes a1, a2, and a3 and from a mutant a2 rabbit, Alicia, which expresses almost no a2 allotype. The D-proximal VH gene VH1 of normal rabbits encoded prototype a1, a2, or a3 allotype VH regions in a1, a2, or a3 rabbits, respectively; VH1 was shown to be preferentially utilized in leukemic rabbit B cells. This VH1 gene was deleted from the germline of the Alicia rabbit. These data suggest that the allelic inheritance of a allotypes results from preferential utilization of VH1 in VDJ rearrangements. We suggest that antibody diversity in rabbit primarily results from somatic hypermutation and gene conversion.

  11. Allele- and Tir-Independent Functions of Intimin in Diverse Animal Infection Models

    PubMed Central

    Mallick, Emily M.; Brady, Michael J.; Luperchio, Steven A.; Vanguri, Vijay K.; Magoun, Loranne; Liu, Hui; Sheppard, Barbara J.; Mukherjee, Jean; Donohue-Rolfe, Art; Tzipori, Saul; Leong, John M.; Schauer, David B.

    2012-01-01

    Upon binding to intestinal epithelial cells, enterohemorrhagic Escherichia coli (EHEC), enteropathogenic E. coli (EPEC), and Citrobacter rodentium trigger formation of actin pedestals beneath bound bacteria. Pedestal formation has been associated with enhanced colonization, and requires intimin, an adhesin that binds to the bacterial effector translocated intimin receptor (Tir), which is translocated to the host cell membrane and promotes bacterial adherence and pedestal formation. Intimin has been suggested to also promote cell adhesion by binding one or more host receptors, and allelic differences in intimin have been associated with differences in tissue and host specificity. We assessed the function of EHEC, EPEC, or C. rodentium intimin, or a set of intimin derivatives with varying Tir-binding abilities in animal models of infection. We found that EPEC and EHEC intimin were functionally indistinguishable during infection of gnotobiotic piglets by EHEC, and that EPEC, EHEC, and C. rodentium intimin were functionally indistinguishable during infection of C57BL/6 mice by C. rodentium. A derivative of EHEC intimin that bound Tir but did not promote robust pedestal formation on cultured cells was unable to promote C. rodentium colonization of conventional mice, indicating that the ability to trigger actin assembly, not simply to bind Tir, is required for intimin-mediated intestinal colonization. Interestingly, streptomycin pre-treatment of mice eliminated the requirement for Tir but not intimin during colonization, and intimin derivatives that were defective in Tir-binding still promoted colonization of these mice. These results indicate that EPEC, EHEC, and C. rodentium intimin are functionally interchangeable during infection of gnotobiotic piglets or conventional C57BL/6 mice, and that whereas the ability to trigger Tir-mediated pedestal formation is essential for colonization of conventional mice, intimin provides a Tir-independent activity during colonization

  12. High genetic diversity and structured populations of the oriental fruit moth in its range of origin.

    PubMed

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

  13. High Genetic Diversity and Structured Populations of the Oriental Fruit Moth in Its Range of Origin

    PubMed Central

    Zheng, Yan; Peng, Xiong; Liu, Gaoming; Pan, Hongyan; Dorn, Silvia; Chen, Maohua

    2013-01-01

    The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies. PMID:24265692

  14. Compensatory Aspects of Allele Diversity at Immunoglobulin Loci: Gene Correlations in Rabbit Populations Devoid of Light Chain Diversity (Oryctolagus Cuniculus L.; Kerguelen Islands)

    PubMed Central

    van-der-Loo, W.; Bousses, P.; Arthur, C. P.; Chapuis, J. L.

    1996-01-01

    Is there a selective advantage of increased diversity at one immunoglobulin locus when diversity at another locus is low? A previous paper demonstrated excess heterozygosity at the rabbit light chain b locus when heterozygosity was low at the heavy chain constant region e locus. Here we consider the reverse situation by analyzing allele distributions at heavy chain loci in populations fixed for the light chain b locus. We analyzed the a locus that encodes the predominantly expressed heavy chain variable region, and the d and e loci that control different parts of the Ig gamma class constant region. While there was excess heterozygosity, genetic differentiation between localities was extensive and was most pronounced for females. This was in marked contrast with observations in areas where b-locus diversity was important and confirms a negative correlation between e- and b-locus heterozygosity. Trigenic disequilibria corresponded to a significant negative correlation between e- and a-locus heterozygosity due mainly to strong variation among localities within the context of pronounced (digenic) linkage disequilibria. Although substantial, the average increase in a/e-locus single heterozygosity implemented by higher order disequilibria within localities was not significant. PMID:8913759

  15. Genetic differentiation and reduced genetic diversity at the northern range edge of two species with different dispersal modes.

    PubMed

    Cahill, Abigail E; Levinton, Jeffrey S

    2016-01-01

    Theory predicts that genetic variation should be reduced at range margins, but empirical support is equivocal. Here, we used genotyping-by-sequencing technology to investigate genetic variation in central and marginal populations of two species in the marine gastropod genus Crepidula. These two species have different development and dispersal types and might therefore show different spatial patterns of genetic variation. Both allelic richness and the proportion of private alleles were highest in the most central populations of both species, and lower at the margin. The species with low dispersal, Crepidula convexa, showed high degrees of structure throughout the range that conform to the pattern found in previous studies using other molecular markers. The northernmost populations of the high-dispersing species, Crepidula fornicata, are distinct from more central populations, although this species has been previously observed to have little genetic structure over much of its range. Although genetic diversity was significantly lower at the range margin, the absolute reduction in diversity observed with these genomewide markers was slight, and it is not yet known whether there are functional consequences for the marginal populations. PMID:26615052

  16. Genetic differentiation and reduced genetic diversity at the northern range edge of two species with different dispersal modes.

    PubMed

    Cahill, Abigail E; Levinton, Jeffrey S

    2016-01-01

    Theory predicts that genetic variation should be reduced at range margins, but empirical support is equivocal. Here, we used genotyping-by-sequencing technology to investigate genetic variation in central and marginal populations of two species in the marine gastropod genus Crepidula. These two species have different development and dispersal types and might therefore show different spatial patterns of genetic variation. Both allelic richness and the proportion of private alleles were highest in the most central populations of both species, and lower at the margin. The species with low dispersal, Crepidula convexa, showed high degrees of structure throughout the range that conform to the pattern found in previous studies using other molecular markers. The northernmost populations of the high-dispersing species, Crepidula fornicata, are distinct from more central populations, although this species has been previously observed to have little genetic structure over much of its range. Although genetic diversity was significantly lower at the range margin, the absolute reduction in diversity observed with these genomewide markers was slight, and it is not yet known whether there are functional consequences for the marginal populations.

  17. Role of the B Allele of Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity

    PubMed Central

    Turnbull, Matthew L.; Wise, Helen M.; Nicol, Marlynne Q.; Smith, Nikki; Dunfee, Rebecca L.; Beard, Philippa M.; Jagger, Brett W.; Ligertwood, Yvonne; Hardisty, Gareth R.; Xiao, Haixia; Benton, Donald J.; Coburn, Alice M.; Paulo, Joao A.; Gygi, Steven P.; McCauley, John W.; Taubenberger, Jeffery K.; Lycett, Samantha J.; Weekes, Michael P.; Dutia, Bernadette M.

    2016-01-01

    ABSTRACT Two alleles of segment 8 (NS) circulate in nonchiropteran influenza A viruses. The A allele is found in avian and mammalian viruses, but the B allele is viewed as being almost exclusively found in avian viruses. This might reflect the fact that one or both of its encoded proteins (NS1 and NEP) are maladapted for replication in mammalian hosts. To test this, a number of clade A and B avian virus-derived NS segments were introduced into human H1N1 and H3N2 viruses. In no case was the peak virus titer substantially reduced following infection of various mammalian cell types. Exemplar reassortant viruses also replicated to similar titers in mice, although mice infected with viruses with the avian virus-derived segment 8s had reduced weight loss compared to that achieved in mice infected with the A/Puerto Rico/8/1934 (H1N1) parent. In vitro, the viruses coped similarly with type I interferons. Temporal proteomics analysis of cellular responses to infection showed that the avian virus-derived NS segments provoked lower levels of expression of interferon-stimulated genes in cells than wild type-derived NS segments. Thus, neither the A nor the B allele of avian virus-derived NS segments necessarily attenuates virus replication in a mammalian host, although the alleles can attenuate disease. Phylogenetic analyses identified 32 independent incursions of an avian virus-derived A allele into mammals, whereas 6 introductions of a B allele were identified. However, A-allele isolates from birds outnumbered B-allele isolates, and the relative rates of Aves-to-Mammalia transmission were not significantly different. We conclude that while the introduction of an avian virus segment 8 into mammals is a relatively rare event, the dogma of the B allele being especially restricted is misleading, with implications in the assessment of the pandemic potential of avian influenza viruses. IMPORTANCE Influenza A virus (IAV) can adapt to poultry and mammalian species, inflicting a

  18. Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea

    PubMed Central

    Bajaj, Deepak; Das, Shouvik; Badoni, Saurabh; Kumar, Vinod; Singh, Mohar; Bansal, Kailash C.; Tyagi, Akhilesh K.; Parida, Swarup K.

    2015-01-01

    We identified 82489 high-quality genome-wide SNPs from 93 wild and cultivated Cicer accessions through integrated reference genome- and de novo-based GBS assays. High intra- and inter-specific polymorphic potential (66–85%) and broader natural allelic diversity (6–64%) detected by genome-wide SNPs among accessions signify their efficacy for monitoring introgression and transferring target trait-regulating genomic (gene) regions/allelic variants from wild to cultivated Cicer gene pools for genetic improvement. The population-specific assignment of wild Cicer accessions pertaining to the primary gene pool are more influenced by geographical origin/phenotypic characteristics than species/gene-pools of origination. The functional significance of allelic variants (non-synonymous and regulatory SNPs) scanned from transcription factors and stress-responsive genes in differentiating wild accessions (with potential known sources of yield-contributing and stress tolerance traits) from cultivated desi and kabuli accessions, fine-mapping/map-based cloning of QTLs and determination of LD patterns across wild and cultivated gene-pools are suitably elucidated. The correlation between phenotypic (agromorphological traits) and molecular diversity-based admixed domestication patterns within six structured populations of wild and cultivated accessions via genome-wide SNPs was apparent. This suggests utility of whole genome SNPs as a potential resource for identifying naturally selected trait-regulating genomic targets/functional allelic variants adaptive to diverse agroclimatic regions for genetic enhancement of cultivated gene-pools. PMID:26208313

  19. MAIZE ALLELIC DIVERSITY PROJECT

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Of the estimated 250-300 races of maize, only 24 races are represented in materials utilized by the Germplasm Enhancement of Maize (GEM) project, a collaborative effort between USDA-ARS and public and private sector research scientists. This is largely a result of poor performance of many races in ...

  20. The diversity of bovine MHC class II DRB3 and DQA1 alleles in different herds of Japanese Black and Holstein cattle in Japan.

    PubMed

    Miyasaka, Taku; Takeshima, Shin-nosuke; Matsumoto, Yuki; Kobayashi, Naohiko; Matsuhashi, Tamako; Miyazaki, Yoshiyuki; Tanabe, Yoshihiro; Ishibashi, Kazuki; Sentsui, Hiroshi; Aida, Yoko

    2011-02-01

    In cattle, bovine leukocyte antigens (BoLAs) have been extensively used as markers for bovine diseases and immunological traits. In this study, we sequenced alleles of the BoLA class II loci, BoLA-DRB3 and BoLA-DQA1, from 650 Japanese cattle from six herds [three herds (507 animals) of Japanese Black cattle and three herds (143 animals) of Holstein cattle] using polymerase chain reaction-sequence-based typing (PCR-SBT) methods. We identified 26 previously reported distinct DRB3 alleles in the two populations: 22 in Japanese Black and 17 in Holstein. The number of DRB3 alleles detected in each herd ranged from 9 to 20. Next, we identified 15 previously reported distinct DQA1 alleles: 13 in Japanese Black and 10 in Holstein. The number of alleles in each herd ranged from 6 to 10. Thus, allelic divergence is significantly greater for DRB3 than for DQA1. A population tree on the basis of the frequencies of the DRB3 and DQA1 alleles showed that, although the genetic distance differed significantly between the two cattle breeds, it was closely related within the three herds of each breed. In addition, Wu-Kabat variability analysis indicated that the DRB3 gene was more polymorphic than the DQA1 gene in both breeds and in all herds, and that the majority of the hypervariable positions within both loci corresponded to pocket-forming residues. The DRB3 and DQA1 heterozygosity for both breeds within each herd were calculated based on the Hardy-Weinberg equilibrium. Only one Japanese Black herd showed a significant difference between the expected and observed heterozygosity at both loci. This is the first report presenting a detailed study of the allelic distribution of BoLA-DRB3 and -DQA1 genes in Japanese Black and Holstein cattle from different farms in Japan. These results may help to develop improved livestock breeding strategies in the future. PMID:20965236

  1. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

    PubMed Central

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

  2. Status of allele frequency and diversity of Plasmodium falciparum msp1, msp2 and glurp before implementation of an artemisinin-based combined therapy in Northwestern Colombia.

    PubMed Central

    Arango, Eliana; Carmona-Fonseca, Jaime

    2013-01-01

    Introduction: The status of msp1, msp2 and glurp allele frequency and the diversity of Plasmodium falciparum in Northwestern Colombia before the implementation of an artemisinin-combined therapy have been explored only by a few authors and in a relatively small number of samples from this highly endemic region. Objective: To evaluate the frequency of msp1, msp2, and glurp alleles and the diversity of P. falciparum in two Colombian regions before the use of an artemisinin-combined therapy. Methods: This study was part of a major anti-malarial efficacy trial designed as a random, clinically-controlled study for which 224 subjects were recruited. Region 2 of msp1 and msp2 (central region) were amplified by a nested PCR; glurp (region R2) was amplified by a semi-nested PCR. Results: For msp1, five genotypes were observed, representing the K1, MAD20, and RO33 allelic families. All samples corresponded to a MAD20 150 bp allele. For msp2 (IC family), two alleles were detected and for glurp, eight were observed. A total 33 haplotypes were detected. Conclusions: Analysis of glurpcan be used to successfully genotype parasite populations in the new studies in Colombia aimed at exploring Plasmodium spp population dynamics. In addition, analysis of msp1 and msp2 can also be of value for comparisons with past studies, but not when the objective is to study parasites obtained from the same patient in a reduced period of time; for instance, during treatment efficacy studies. PMID:24892236

  3. [Cultural diversity in Montreal: a range of public health challenges].

    PubMed

    Vissandjee, B; Hemlin, I; Gravel, S; Roy, S; Dupéré, S

    2005-09-01

    Increasing immigration to Quebec has brought to the surface the need for adapting its public health systems and services, particularly in the area of primary care. The challenge is to take the heterogeneous nature of the population into account and to integrate diverse values, experience and know-how into the development of programmes and delivery of services, whilst simultaneously respecting the values of the various care providers and the norms of the institutions in the host country. This article addresses the question of adaptation strategies for health services, and namely the development of prevention and heath promotion programmes in public health within the framework of primary health care services within the intercultural context of Montreal. The issue of adaptation falls within the perspective and mandate of the Quebec government's policy on health and well-being (La politique de santé et du bien-être, 1992). Furthermore, it is a response to frequent demands from various health professionals and groups concerned with the adaptation of public services with respect to intercultural relationships confronted with the emerging realities associated with immigration. The article provides a reflection on specific ways of adapting prevention and health promotion initiatives targeting cultural communities and those who are undergoing immigration procedures or transitions. It also examines the development of ethno-cultural or other indicators which make it possible to capture migration experiences and their health impact. Since the Quebec health and social services system is currently in the process of major reform, it is hoped that it will seize this opportunity in order to make health and social service centres accountable for the adaptation of their programmes and services to the diversity of the populations they serve. PMID:16285423

  4. Allelic diversity of S-RNase at the self-incompatibility locus in natural flowering cherry populations (Prunus lannesiana var. speciosa).

    PubMed

    Kato, S; Mukai, Y

    2004-03-01

    In the Rosaceae family, which includes Prunus, gametophytic self-incompatibility (GSI) is controlled by a single multiallelic locus (S-locus), and the S-locus product expressed in the pistils is a glycoprotein with ribonuclease activity (S-RNase). Two populations of flowering cherry (Prunus lannesiana var. speciosa), located on Hachijo Island in Japan's Izu Islands, were sampled, and S-allele diversity was surveyed based on the sequence polymorphism of S-RNase. A total of seven S-alleles were cloned and sequenced. The S-RNases of flowering cherry showed high homology to those of Prunus cultivars (P. avium and P. dulcis). In the phylogenetic tree, the S-RNases of flowering cherry and other Prunus cultivars formed a distinct group, but they did not form species-specific subgroups. The nucleotide substitution pattern in S-RNases of flowering cherry showed no excess of nonsynonymous substitutions relative to synonymous substitutions. However, the S-RNases of flowering cherry had a higher Ka/Ks ratio than those of other Prunus cultivars, and a subtle heterogeneity in the nucleotide substitution rates was observed among the Prunus species. The S-genotype of each individual was determined by Southern blotting of restriction enzyme-digested genomic DNA, using cDNA for S-RNase as a probe. A total of 22 S-alleles were identified. All individuals examined were heterozygous, as expected under GSI. The allele frequencies were, contrary to the expectation under GSI, significantly unequal. The two populations studied showed a high degree of overlap, with 18 shared alleles. However, the allele frequencies differed considerably between the two populations.

  5. High genetic diversity and distribution of Bubu-DQA alleles in swamp buffaloes (Bubalus bubalis carabanesis): identification of new Bubu-DQA loci and haplotypes.

    PubMed

    Mishra, S K; Niranjan, S K; Banerjee, B; Dubey, P K; Gonge, D S; Mishra, B P; Kataria, R S

    2016-07-01

    In this study, genetic diversity analysis of MHC class II-DQA locus helped in identification of 25 new Bubu-DQA nucleotide sequences in swamp buffaloes (Bubalus bubalis carabanesis, Bubu). Phylogenetic analysis revealed the distribution of the buffalo DQA sequences in two major clusters of DQA1 and DQA2 genes, sharing common lineages with corresponding cattle alleles, possibly due to trans-species evolution. However, a highly divergent sequence, Bubu-DQA*2501, homologous to cattle (BoLA) DQA3 allele, was identified, indicating the existence of an additional locus; putative DQA3 in buffalo. PCR-RFLP analysis revealed extensive duplication of DQA locus in swamp buffaloes, sharing DQA1, DQA2, and DQA3 alleles in different combinations in duplicated haplotypes. Higher dN than dS values and Wu-Kabat variability at peptide-binding regions in Bubu-DQA indicated high polymorphism with balancing selection. Levels of genetic diversity within DQA sequences and duplication in a small population of swamp buffalo indicate the genetic richness of the species, important for fitness. PMID:27177904

  6. Haplotype diversity of 13 RM Y-STRs in Chinese Han population and an update on the allele designation of DYF403S1.

    PubMed

    Zhang, Wenqiong; Xiao, Chao; Wei, Tian; Pan, Chao; Yi, Shaohua; Huang, Daixin

    2016-07-01

    Rapidly mutating Y-STRs (RM Y-STRs) have been paid much attention in recent years. The 13 RM Y-STRs have been proved to have substantially higher haplotype diversity and discrimination capacity than conventionally used Y-STRs, indicating the considerable power in paternal lineage differentiation. To investigate the haplotype diversity in Chinese Han population, we collected 252 unrelated male samples and tested the genotype of the 13 RM Y-STRs. Among 252 male individuals, a total of 250 haplotypes were observed in which only 2 haplotypes were shared by 2 males respectively. The haplotype diversity reached 0.999937 and the discrimination capacity was 99.21%, showing a great discrimination power in Chinese Han population. In addition, an update on the allele designation of DYF403S1 was proposed.

  7. [Spatial pattern of vegetation landscape diversity in longitudinal Range-Gorge Region, southwestern China].

    PubMed

    Pan, Tao; Wu, Shao-hong; Dai, Er-fu; Zhao, Dong-sheng; Yin, Yun-he

    2010-12-01

    Based on the China 1:1000000 vegetation type map, and by using GIS spatial analysis, the spatial pattern of major vegetation landscape diversity indices and its relationships with environmental factors in Longitudinal Range-Gorge Region (LRGR) were analyzed. The proper scale for studying the vegetation landscape diversity in LRGR was 2000 m. In the study region, an obvious regional difference was observed in the vegetation landscape diversity indices, exhibiting typical longitudinal "corridor" and latitudinal "barrier" characteristics. The correlations between the vegetation landscape diversity indices and environmental elements were significant, and the regional difference in the environmental elements was the main factor controlling the spatial pattern of vegetation landscape diversity indices. The "corridor-barrier" function of the longitudinal range-gorge terrain made a spatial redistribution of hydro-thermal conditions, being the main cause of the special pattern of the vegetation landscape diversity in LRGR.

  8. Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China.

    PubMed

    Wang, Y J; Zhang, N J; Chen, E; Chen, C J; Bu, Y H; Yu, P

    2016-05-01

    Previous studies indicate the distribution of major histocompatibility complex class I chain-related genes A (MICA) and B (MICB) alleles and haplotypes varies widely between different ethnic populations and geographic areas. It is meaningful to investigate allelic frequencies and establish a genetic database. In this study, we firstly reported the polymorphic variation of MICA/B in 187 healthy, unrelated Tujia individuals in Zhangjiajie region, China. Using polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (PCR-SBT), we identified eight MICA-sequence alleles, four MICA-short tandem repeat variants, and 13 MICB variants, of which MICA(∗)008:04 (29.41%), MICA(∗)A5 (29.68%), MICA(∗)A5.1 (29.68%) and MICB(∗)005:02 (39.57%) were the most frequent. Linkage disequilibrium analysis further revealed MICB(∗)005:02-MICA(∗)019 (13.10%) and MICB(∗)002-MICA(∗)008:04 (9.89%) as the most common two-locus haplotypes. Data comparison by neighbor-joining dendrograms and principal component analysis to verify allelic frequencies in other Chinese and Asia ethnic groups showed that the Zhangjiajie Tujias were genetically closer to the Guangdong Han population, based on MICA loci variability. Our results provide new information about the MICA/B gene polymorphism in Chinese Tujia population, which will form the basis for future studies on the potential role of MICA/B in allogeneic organ transplantation and disease susceptibility in related ethnic groups.

  9. Allele polymorphism and haplotype diversity of MICA/B in Tujia nationality of Zhangjiajie, Hunan Province, China.

    PubMed

    Wang, Y J; Zhang, N J; Chen, E; Chen, C J; Bu, Y H; Yu, P

    2016-05-01

    Previous studies indicate the distribution of major histocompatibility complex class I chain-related genes A (MICA) and B (MICB) alleles and haplotypes varies widely between different ethnic populations and geographic areas. It is meaningful to investigate allelic frequencies and establish a genetic database. In this study, we firstly reported the polymorphic variation of MICA/B in 187 healthy, unrelated Tujia individuals in Zhangjiajie region, China. Using polymerase chain reaction-sequence specific priming (PCR-SSP) and sequencing-based typing (PCR-SBT), we identified eight MICA-sequence alleles, four MICA-short tandem repeat variants, and 13 MICB variants, of which MICA(∗)008:04 (29.41%), MICA(∗)A5 (29.68%), MICA(∗)A5.1 (29.68%) and MICB(∗)005:02 (39.57%) were the most frequent. Linkage disequilibrium analysis further revealed MICB(∗)005:02-MICA(∗)019 (13.10%) and MICB(∗)002-MICA(∗)008:04 (9.89%) as the most common two-locus haplotypes. Data comparison by neighbor-joining dendrograms and principal component analysis to verify allelic frequencies in other Chinese and Asia ethnic groups showed that the Zhangjiajie Tujias were genetically closer to the Guangdong Han population, based on MICA loci variability. Our results provide new information about the MICA/B gene polymorphism in Chinese Tujia population, which will form the basis for future studies on the potential role of MICA/B in allogeneic organ transplantation and disease susceptibility in related ethnic groups. PMID:26972750

  10. An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis.

    PubMed

    Lin, Ching-Jung; Smibert, Peter; Zhao, Xiaoyu; Hu, Jennifer F; Ramroop, Johnny; Kellner, Stefanie M; Benton, Matthew A; Govind, Shubha; Dedon, Peter C; Sternglanz, Rolf; Lai, Eric C

    2015-12-01

    N(6)-threonylcarbamoyl-adenosine (t6A) is one of the few RNA modifications that is universally present in life. This modification occurs at high frequency at position 37 of most tRNAs that decode ANN codons, and stabilizes cognate anticodon-codon interactions. Nearly all genetic studies of the t6A pathway have focused on single-celled organisms. In this study, we report the isolation of an extensive allelic series in the Drosophila ortholog of the core t6A biosynthesis factor Kae1. kae1 hemizygous larvae exhibit decreases in t6A that correlate with allele strength; however, we still detect substantial t6A-modified tRNAs even during the extended larval phase of null alleles. Nevertheless, complementation of Drosophila Kae1 and other t6A factors in corresponding yeast null mutants demonstrates that these metazoan genes execute t6A synthesis. Turning to the biological consequences of t6A loss, we characterize prominent kae1 melanotic masses and show that they are associated with lymph gland overgrowth and ectopic generation of lamellocytes. On the other hand, kae1 mutants exhibit other phenotypes that reflect insufficient tissue growth. Interestingly, whole-tissue and clonal analyses show that strongly mitotic tissues such as imaginal discs are exquisitely sensitive to loss of kae1, whereas nonproliferating tissues are less affected. Indeed, despite overt requirements of t6A for growth of many tissues, certain strong kae1 alleles achieve and sustain enlarged body size during their extended larval phase. Our studies highlight tissue-specific requirements of the t6A pathway in a metazoan context and provide insights into the diverse biological roles of this fundamental RNA modification during animal development and disease.

  11. Several different lactase persistence associated alleles and high diversity of the lactase gene in the admixed Brazilian population.

    PubMed

    Friedrich, Deise C; Santos, Sidney E B; Ribeiro-dos-Santos, Ândrea K C; Hutz, Mara H

    2012-01-01

    Adult-type hypolactasia is a common phenotype caused by the lactase enzyme deficiency. The -13910 C>T polymorphism, located 14 Kb upstream of the lactase gene (LCT) in the MCM6 gene was associated with lactase persistence (LP) in Europeans. This polymorphism is rare in Africa but several other variants associated with lactase persistence were observed in Africans. The aims of this study were to identify polymorphisms in the MCM6 region associated with the lactase persistence phenotype and to determine the distribution of LCT gene haplotypes in 981 individuals from North, Northeast and South Brazil. These polymorphisms were genotyped by PCR based methods and sequencing. The -13779*C,-13910*T, -13937*A, -14010*C, -14011*T LP alleles previously described in the MCM6 gene region that acts as an enhancer for the LCT gene were identified in Brazilians. The most common LP allele was -13910*T. Its frequency was highly correlated with European ancestry in the Brazilian populations investigated. The -13910*T was higher (0.295) in southern Brazilians of European ancestry and lower (0.175) in the Northern admixed population. LCT haplotypes were derived from the 10 LCT SNPs genotyped. Overall twenty six haplotypes previously described were identified in the four Brazilian populations studied. The Multidimensional Scaling analysis showed that Belém, in the north, was closer to Amerindians. Northeastern and southern Afro-descendants were more related with Bantu-speaking South Africans whereas the Southern population with European ancestry grouped with Southern and Northern Europeans. This study shows a high variability considering the number of LCT haplotypes observed. Due to the highly admixed nature of the Brazilian populations, the diagnosis of hypolactasia in Brazil, based only in the investigation of the -13910*T allele is an oversimplification. PMID:23029545

  12. Several different lactase persistence associated alleles and high diversity of the lactase gene in the admixed Brazilian population.

    PubMed

    Friedrich, Deise C; Santos, Sidney E B; Ribeiro-dos-Santos, Ândrea K C; Hutz, Mara H

    2012-01-01

    Adult-type hypolactasia is a common phenotype caused by the lactase enzyme deficiency. The -13910 C>T polymorphism, located 14 Kb upstream of the lactase gene (LCT) in the MCM6 gene was associated with lactase persistence (LP) in Europeans. This polymorphism is rare in Africa but several other variants associated with lactase persistence were observed in Africans. The aims of this study were to identify polymorphisms in the MCM6 region associated with the lactase persistence phenotype and to determine the distribution of LCT gene haplotypes in 981 individuals from North, Northeast and South Brazil. These polymorphisms were genotyped by PCR based methods and sequencing. The -13779*C,-13910*T, -13937*A, -14010*C, -14011*T LP alleles previously described in the MCM6 gene region that acts as an enhancer for the LCT gene were identified in Brazilians. The most common LP allele was -13910*T. Its frequency was highly correlated with European ancestry in the Brazilian populations investigated. The -13910*T was higher (0.295) in southern Brazilians of European ancestry and lower (0.175) in the Northern admixed population. LCT haplotypes were derived from the 10 LCT SNPs genotyped. Overall twenty six haplotypes previously described were identified in the four Brazilian populations studied. The Multidimensional Scaling analysis showed that Belém, in the north, was closer to Amerindians. Northeastern and southern Afro-descendants were more related with Bantu-speaking South Africans whereas the Southern population with European ancestry grouped with Southern and Northern Europeans. This study shows a high variability considering the number of LCT haplotypes observed. Due to the highly admixed nature of the Brazilian populations, the diagnosis of hypolactasia in Brazil, based only in the investigation of the -13910*T allele is an oversimplification.

  13. Chromosomal diversity in tropical reef fishes is related to body size and depth range.

    PubMed

    Martinez, P A; Zurano, J P; Amado, T F; Penone, C; Betancur-R, R; Bidau, C J; Jacobina, U P

    2015-12-01

    Tropical reef fishes show contrasting patterns of karyotypic diversity. Some families have a high chromosomal conservatism while others show wide variation in karyotypic macrostructure. However, the influence of life-history traits on karyotypic diversity is largely unknown. Using phylogenetic comparative methods, we assessed the effects of larval and adult species traits on chromosomal diversity rates of 280 reef species in 24 families. We employed a novel approach to account for trait variation within families as well as phylogenetic uncertainties. We found a strong negative relationship between karyotypic diversity rates and body size and depth range. These results suggest that lineages with higher dispersal potential and gene flow possess lower karyotypic diversity. Taken together, these results provide evidence that biological traits might modulate the rate of karyotypic diversity in tropical reef fishes.

  14. Genomic diversity, population structure, and migration following rapid range expansion in the Balsam poplar, Populus balsamifera.

    PubMed

    Keller, Stephen R; Olson, Matthew S; Silim, Salim; Schroeder, William; Tiffin, Peter

    2010-03-01

    Rapid range expansions can cause pervasive changes in the genetic diversity and structure of populations. The postglacial history of the Balsam Poplar, Populus balsamifera, involved the colonization of most of northern North America, an area largely covered by continental ice sheets during the last glacial maximum. To characterize how this expansion shaped genomic diversity within and among populations, we developed 412 SNP markers that we assayed for a range-wide sample of 474 individuals sampled from 34 populations. We complemented the SNP data set with DNA sequence data from 11 nuclear loci from 94 individuals, and used coalescent analyses to estimate historical population size, demographic growth, and patterns of migration. Bayesian clustering identified three geographically separated demes found in the Northern, Central, and Eastern portions of the species' range. These demes varied significantly in nucleotide diversity, the abundance of private polymorphisms, and population substructure. Most measures supported the Central deme as descended from the primary refuge of diversity. Both SNPs and sequence data suggested recent population growth, and coalescent analyses of historical migration suggested a massive expansion from the Centre to the North and East. Collectively, these data demonstrate the strong influence that range expansions exert on genomic diversity, both within local populations and across the range. Our results suggest that an in-depth knowledge of nucleotide diversity following expansion requires sampling within multiple populations, and highlight the utility of combining insights from different data types in population genomic studies.

  15. Functional IL6R 358Ala allele impairs classical IL-6 receptor signaling and influences risk of diverse inflammatory diseases.

    PubMed

    Ferreira, Ricardo C; Freitag, Daniel F; Cutler, Antony J; Howson, Joanna M M; Rainbow, Daniel B; Smyth, Deborah J; Kaptoge, Stephen; Clarke, Pamela; Boreham, Charlotte; Coulson, Richard M; Pekalski, Marcin L; Chen, Wei-Min; Onengut-Gumuscu, Suna; Rich, Stephen S; Butterworth, Adam S; Malarstig, Anders; Danesh, John; Todd, John A

    2013-04-01

    Inflammation, which is directly regulated by interleukin-6 (IL-6) signaling, is implicated in the etiology of several chronic diseases. Although a common, non-synonymous variant in the IL-6 receptor gene (IL6R Asp358Ala; rs2228145 A>C) is associated with the risk of several common diseases, with the 358Ala allele conferring protection from coronary heart disease (CHD), rheumatoid arthritis (RA), atrial fibrillation (AF), abdominal aortic aneurysm (AAA), and increased susceptibility to asthma, the variant's effect on IL-6 signaling is not known. Here we provide evidence for the association of this non-synonymous variant with the risk of type 1 diabetes (T1D) in two independent populations and confirm that rs2228145 is the major determinant of the concentration of circulating soluble IL-6R (sIL-6R) levels (34.6% increase in sIL-6R per copy of the minor allele 358Ala; rs2228145 [C]). To further investigate the molecular mechanism of this variant, we analyzed expression of IL-6R in peripheral blood mononuclear cells (PBMCs) in 128 volunteers from the Cambridge BioResource. We demonstrate that, although 358Ala increases transcription of the soluble IL6R isoform (P = 8.3×10⁻²²) and not the membrane-bound isoform, 358Ala reduces surface expression of IL-6R on CD4+ T cells and monocytes (up to 28% reduction per allele; P≤5.6×10⁻²²). Importantly, reduced expression of membrane-bound IL-6R resulted in impaired IL-6 responsiveness, as measured by decreased phosphorylation of the transcription factors STAT3 and STAT1 following stimulation with IL-6 (P≤5.2×10⁻⁷). Our findings elucidate the regulation of IL-6 signaling by IL-6R, which is causally relevant to several complex diseases, identify mechanisms for new approaches to target the IL-6/IL-6R axis, and anticipate differences in treatment response to IL-6 therapies based on this common IL6R variant. PMID:23593036

  16. Allelic combinations of soybean maturity Loci E1, E2, E3 and E4 result in diversity of maturity and adaptation to different latitudes.

    PubMed

    Jiang, Bingjun; Nan, Haiyang; Gao, Youfei; Tang, Lili; Yue, Yanlei; Lu, Sijia; Ma, Liming; Cao, Dong; Sun, Shi; Wang, Jialin; Wu, Cunxiang; Yuan, Xiaohui; Hou, Wensheng; Kong, Fanjiang; Han, Tianfu; Liu, Baohui

    2014-01-01

    Soybean cultivars are extremely diverse in time to flowering and maturation as a result of various photoperiod sensitivities. The underlying molecular genetic mechanism is not fully clear, however, four maturity loci E1, E2, E3 and E4 have been molecularly identified. In this report, cultivars were selected with various photoperiod sensitivities from different ecological zones, which covered almost all maturity groups (MG) from MG 000 to MG VIII and MG X adapted from latitude N 18° to N 53°. They were planted in the field under natural daylength condition (ND) in Beijing, China or in pots under different photoperiod treatments. Maturity-related traits were then investigated. The four E maturity loci were genotyped at the molecular level. Our results suggested that these four E genes have different impacts on maturity and their allelic variations and combinations determine the diversification of soybean maturity and adaptation to different latitudes. The genetic mechanisms underlying photoperiod sensitivity and adaptation in wild soybean seemed unique from those in cultivated soybean. The allelic combinations and functional molecular markers for the four E loci will significantly assist molecular breeding towards high productivity.

  17. High and Distinct Range-Edge Genetic Diversity despite Local Bottlenecks

    PubMed Central

    Assis, Jorge; Castilho Coelho, Nelson; Alberto, Filipe; Valero, Myriam; Raimondi, Pete; Reed, Dan; Alvares Serrão, Ester

    2013-01-01

    The genetic consequences of living on the edge of distributional ranges have been the subject of a largely unresolved debate. Populations occurring along persistent low latitude ranges (rear-edge) are expected to retain high and unique genetic diversity. In contrast, currently less favourable environmental conditions limiting population size at such range-edges may have caused genetic erosion that prevails over past historical effects, with potential consequences on reducing future adaptive capacity. The present study provides an empirical test of whether population declines towards a peripheral range might be reflected on decreasing diversity and increasing population isolation and differentiation. We compare population genetic differentiation and diversity with trends in abundance along a latitudinal gradient towards the peripheral distribution range of Saccorhizapolyschides, a large brown seaweed that is the main structural species of kelp forests in SW Europe. Signatures of recent bottleneck events were also evaluated to determine whether the recently recorded distributional shifts had a negative influence on effective population size. Our findings show decreasing population density and increasing spatial fragmentation and local extinctions towards the southern edge. Genetic data revealed two well supported groups with a central contact zone. As predicted, higher differentiation and signs of bottlenecks were found at the southern edge region. However, a decrease in genetic diversity associated with this pattern was not verified. Surprisingly, genetic diversity increased towards the edge despite bottlenecks and much lower densities, suggesting that extinctions and recolonizations have not strongly reduced diversity or that diversity might have been even higher there in the past, a process of shifting genetic baselines. PMID:23967038

  18. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism.

    PubMed

    Hammond, John A; Guethlein, Lisbeth A; Norman, Paul J; Parham, Peter

    2012-12-01

    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals' classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

  19. Natural selection on marine carnivores elaborated a diverse family of classical MHC class I genes exhibiting haplotypic gene content variation and allelic polymorphism

    PubMed Central

    Norman, Paul J.; Parham, Peter

    2012-01-01

    Pinnipeds, marine carnivores, diverged from terrestrial carnivores ~45 million years ago, before their adaptation to marine environments. This lifestyle change exposed pinnipeds to different microbiota and pathogens, with probable impact on their MHC class I genes. Investigating this question, genomic sequences were determined for 71 MHC class I variants: 27 from harbor seal and 44 from gray seal. These variants form three MHC class I gene lineages, one comprising a pseudogene. The second, a candidate nonclassical MHC class I gene, comprises a nonpolymorphic transcribed gene related to dog DLA-79 and giant panda Aime-1906. The third is the diversity lineage, which includes 62 of the 71 seal MHC class I variants. All are transcribed, and they minimally represent six harbor and 12 gray seal MHC class I genes. Besides species-specific differences in gene number, seal MHC class I haplotypes exhibit gene content variation and allelic polymorphism. Patterns of sequence variation, and of positions for positively selected sites, indicate the diversity lineage genes are the seals’ classical MHC class I genes. Evidence that expansion of diversity lineage genes began before gray and harbor seals diverged is the presence in both species of two distinctive sublineages of diversity lineage genes. Pointing to further expansion following the divergence are the presence of species-specific genes and greater MHC class I diversity in gray seals than harbor seals. The elaboration of a complex variable family of classical MHC class I genes in pinnipeds contrasts with the single, highly polymorphic classical MHC class I gene of dog and giant panda, terrestrial carnivores. PMID:23001684

  20. HLA-B allele and haplotype diversity among Thai patients identified by PCR-SSOP: evidence for high risk of drug-induced hypersensitivity

    PubMed Central

    Puangpetch, Apichaya; Koomdee, Napatrupron; Chamnanphol, Montri; Jantararoungtong, Thawinee; Santon, Siwalee; Prommas, Santirhat; Hongkaew, Yaowaluck; Sukasem, Chonlaphat

    2015-01-01

    Background: There are 3 classes of HLA molecules; HLA class I, II and III, of which different classes have different functions. HLA-B gene which belongs to HLA class I play an important role predicting drug hypersensitivity. Materials and Methods: Nine hundred and eighty-six Thai subjects who registered at a pharmacogenomics laboratory were determined for HLA-B genotype using a two-stage sequence-specific oligonucleotide probe system (PCR-SSOP). Results: In this study, HLA-B alleles did not deviate from Hardy-Weinberg equilibrium (P > 0.05). The most common HLA-B alleles observed in this population were HLA-B*46:01 (11.51%), HLA-B*58:01 (8.62%), HLA-B*40:01 (8.22%), HLA-B*15:02 (8.16%) and HLA-B*13:01 (6.95%). This finding revealed that HLA-B allele frequency in the Thai population was consistent with the Chinese population (p > 0.05), however, differed from the Malaysian population (p < 0.05). The top five HLA-B genotypes were HLA-B*40:01/46:01 (2.13%), HLA-B*46:01/46:01 (2.03%), HLA-B*40:01/58:01 (2.03%), HLA-B*46:01/58:01 (1.93%) and HLA-B*15:02/46:01 (1.83%). This study found that 15.92% of Thai subjects carry HLA-B*15:02, which has been associated with carbamazepine-induced severe cutaneous adverse drug reactions (SCARs). Moreover, 16.33% of Thai subjects carry the HLA-B*58:01 allele, which has been associated with allopurinol-induced SCARs. Conclusion: This study demonstrates a high diversity of HLA-B polymorphisms in this Thai population. The high frequency of HLA-B pharmacogenomic markers in the population emphasizes the importance of such screening to predict/avoid drug hypersensitivity. PMID:25657656

  1. Functionally Divergent Alleles and Duplicated Loci Encoding an Acyltransferase Contribute to Acylsugar Metabolite Diversity in Solanum Trichomes[OPEN

    PubMed Central

    Schilmiller, Anthony L.; Moghe, Gaurav D.; Fan, Pengxiang; Ghosh, Banibrata; Ning, Jing; Jones, A. Daniel; Last, Robert L.

    2015-01-01

    Glandular trichomes from tomato (Solanum lycopersicum) and other species in the Solanaceae produce and secrete a mixture of O-acylsugars (aliphatic esters of sucrose and glucose) that contribute to insect defense. Despite their phylogenetic distribution and diversity, relatively little is known about how these specialized metabolites are synthesized. Mass spectrometric profiling of acylsugars in the S. lycopersicum x Solanum pennellii introgression lines identified a chromosome 11 locus containing a cluster of BAHD acyltransferases with one gene (named Sl-ASAT3) expressed in tip cells of type I trichomes where acylsugars are made. Sl-ASAT3 was shown to encode an acyl-CoA-dependent acyltransferase that catalyzes the transfer of short (four to five carbons) branched acyl chains to the furanose ring of di-acylsucrose acceptors to produce tri-acylsucroses, which can be further acetylated by Sl-ASAT4 (previously Sl-AT2). Among the wild tomatoes, diversity in furanose ring acyl chains on acylsucroses was most striking in Solanum habrochaites. S. habrochaites accessions from Ecuador and northern Peru produced acylsucroses with short (≤C5) or no acyl chains on the furanose ring. Accessions from central and southern Peru had the ability to add short or long (up to C12) acyl chains to the furanose ring. Multiple ASAT3-like sequences were found in most accessions, and their in vitro activities correlated with observed geographical diversity in acylsugar profiles. PMID:25862303

  2. Genetic diversity, haplotypes and allele groups of Duffy binding protein (PkDBPαII) of Plasmodium knowlesi clinical isolates from Peninsular Malaysia

    PubMed Central

    2014-01-01

    Background The monkey malaria parasite Plasmodium knowlesi is now recognized as the fifth species of Plasmodium that can cause human malaria. Like the region II of the Duffy binding protein of P. vivax (PvDBPII), the region II of the P. knowlesi Duffy binding protein (PkDBPαII) plays an essential role in the parasite’s invasion into the host’s erythrocyte. Numerous polymorphism studies have been carried out on PvDBPII, but none has been reported on PkDBPαII. In this study, the genetic diversity, haplotyes and allele groups of PkDBPαII of P. knowlesi clinical isolates from Peninsular Malaysia were investigated. Methods Blood samples from 20 knowlesi malaria patients and 2 wild monkeys (Macaca fascicularis) were used. These samples were collected between 2010 and 2012. The PkDBPαII region of the isolates was amplified by PCR, cloned into Escherichia coli, and sequenced. The genetic diversity, natural selection and haplotypes of PkDBPαII were analysed using MEGA5 and DnaSP ver. 5.10.00 programmes. Results Fifty-three PkDBPαII sequences from human infections and 6 from monkeys were obtained. Comparison at the nucleotide level against P. knowlesi strain H as reference sequence showed 52 synonymous and 76 nonsynonymous mutations. Analysis on the rate of these mutations indicated that PkDBPαII was under purifying (negative) selection. At the amino acid level, 36 different PkDBPαII haplotypes were identified. Twelve of the 20 human and 1 monkey blood samples had mixed haplotype infections. These haplotypes were clustered into 2 distinct allele groups. The majority of the haplotypes clustered into the large dominant group. Conclusions Our present study is the first to report the genetic diversity and natural selection of PkDBPαII. Hence, the haplotypes described in this report can be considered as novel. Although a high level of genetic diversity was observed, the PkDBPαII appeared to be under purifying selection. The distribution of the haplotypes was skewed

  3. Diversity of Bacillus cereus group strains is reflected in their broad range of pathogenicity and diverse ecological lifestyles.

    PubMed

    Ceuppens, Siele; Boon, Nico; Uyttendaele, Mieke

    2013-06-01

    Bacillus cereus comprises a highly versatile group of bacteria, which are of particular interest because of their capacity to cause disease. Emetic food poisoning is caused by the toxin cereulide produced during the growth of emetic B. cereus in food, while diarrhoeal food poisoning is the result of enterotoxin production by viable vegetative B. cereus cells in the small intestine, probably in the mucus layer and/or attached to the host's intestinal epithelium. The numbers of B. cereus causing disease are highly variable, depending on diverse factors linked to the host (age, diet, physiology and immunology), bacteria (cellular form, toxin genes and expression) and food (nutritional composition and meal characteristics). Bacillus cereus group strains show impressive ecological diversity, ranging from their saprophytic life cycle in soil to symbiotic (commensal and mutualistic) lifestyles near plant roots and in guts of insects and mammals to various pathogenic ones in diverse insect and mammalian hosts. During all these different ecological lifestyles, their toxins play important roles ranging from providing competitive advantages within microbial communities to inhibition of specific pathogenic organisms for their host and accomplishment of infections by damaging their host's tissues.

  4. Natural selection constrains neutral diversity across a wide range of species.

    PubMed

    Corbett-Detig, Russell B; Hartl, Daniel L; Sackton, Timothy B

    2015-04-01

    The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

  5. Multiple introductions boosted genetic diversity in the invasive range of black cherry (Prunus serotina; Rosaceae)

    PubMed Central

    Pairon, Marie; Petitpierre, Blaise; Campbell, Michael; Guisan, Antoine; Broennimann, Olivier; Baret, Philippe V.; Jacquemart, Anne-Laure; Besnard, Guillaume

    2010-01-01

    Background and Aims Black cherry (Prunus serotina) is a North American tree that is rapidly invading European forests. This species was introduced first as an ornamental plant then it was massively planted by foresters in many countries but its origins and the process of invasion remain poorly documented. Based on a genetic survey of both native and invasive ranges, the invasion history of black cherry was investigated by identifying putative source populations and then assessing the importance of multiple introductions on the maintenance of gene diversity. Methods Genetic variability and structure of 23 populations from the invasive range and 22 populations from the native range were analysed using eight nuclear microsatellite loci and five chloroplast DNA regions. Key Results Chloroplast DNA diversity suggests there were multiple introductions from a single geographic region (the north-eastern United States). A low reduction of genetic diversity was observed in the invasive range for both nuclear and plastid genomes. High propagule pressure including both the size and number of introductions shaped the genetic structure in Europe and boosted genetic diversity. Populations from Denmark, The Netherlands, Belgium and Germany showed high genetic diversity and low differentiation among populations, supporting the hypothesis that numerous introduction events, including multiple individuals and exchanges between sites, have taken place during two centuries of plantation. Conclusions This study postulates that the invasive black cherry has originated from east of the Appalachian Mountains (mainly the Allegheny plateau) and its invasiveness in north-western Europe is mainly due to multiple introductions containing high numbers of individuals. PMID:20400456

  6. Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community.

    PubMed

    Klümper, Uli; Riber, Leise; Dechesne, Arnaud; Sannazzarro, Analia; Hansen, Lars H; Sørensen, Søren J; Smets, Barth F

    2015-03-17

    Conjugal plasmids can provide microbes with full complements of new genes and constitute potent vehicles for horizontal gene transfer. Conjugal plasmid transfer is deemed responsible for the rapid spread of antibiotic resistance among microbes. While broad host range plasmids are known to transfer to diverse hosts in pure culture, the extent of their ability to transfer in the complex bacterial communities present in most habitats has not been comprehensively studied. Here, we isolated and characterized transconjugants with a degree of sensitivity not previously realized to investigate the transfer range of IncP- and IncPromA-type broad host range plasmids from three proteobacterial donors to a soil bacterial community. We identified transfer to many different recipients belonging to 11 different bacterial phyla. The prevalence of transconjugants belonging to diverse Gram-positive Firmicutes and Actinobacteria suggests that inter-Gram plasmid transfer of IncP-1 and IncPromA-type plasmids is a frequent phenomenon. While the plasmid receiving fractions of the community were both plasmid- and donor- dependent, we identified a core super-permissive fraction that could take up different plasmids from diverse donor strains. This fraction, comprising 80% of the identified transconjugants, thus has the potential to dominate IncP- and IncPromA-type plasmid transfer in soil. Our results demonstrate that these broad host range plasmids have a hitherto unrecognized potential to transfer readily to very diverse bacteria and can, therefore, directly connect large proportions of the soil bacterial gene pool. This finding reinforces the evolutionary and medical significances of these plasmids.

  7. Prevalence, genetic diversity, and host range of tectiviruses among members of the Bacillus cereus group.

    PubMed

    Gillis, Annika; Mahillon, Jacques

    2014-07-01

    GIL01, Bam35, GIL16, AP50, and Wip1 are tectiviruses preying on the Bacillus cereus group. Despite the significant contributions of phages in different biological processes, little is known about the dealings taking place between tectiviruses and their Gram-positive bacterial hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group by assessing their occurrence and genetic diversity and evaluating their host range. To study the occurrence of tectiviruses in the B. cereus group, 2,000 isolates were evaluated using primers designed to be specific to two variable regions detected in previously described elements. PCR and propagation tests revealed that tectivirus-like elements occurred in less than 3% of the isolates. Regardless of this limited distribution, several novel tectiviruses were found, and partial DNA sequencing indicated that a greater diversity exists within the family Tectiviridae. Analyses of the selected variable regions, along with their host range, showed that tectiviruses in the B. cereus group can be clustered mainly into two different groups: the ones infecting B. anthracis and those isolated from other B. cereus group members. In order to address the host range of some novel tectiviruses, 120 strains were tested for sensitivity. The results showed that all the tested tectiviruses produced lysis in at least one B. cereus sensu lato strain. Moreover, no simple relationship between the infection patterns of the tectiviruses and their diversity was found.

  8. Prevalence, Genetic Diversity, and Host Range of Tectiviruses among Members of the Bacillus cereus Group

    PubMed Central

    Gillis, Annika

    2014-01-01

    GIL01, Bam35, GIL16, AP50, and Wip1 are tectiviruses preying on the Bacillus cereus group. Despite the significant contributions of phages in different biological processes, little is known about the dealings taking place between tectiviruses and their Gram-positive bacterial hosts. Therefore, this work focuses on characterizing the interactions between tectiviruses and the B. cereus group by assessing their occurrence and genetic diversity and evaluating their host range. To study the occurrence of tectiviruses in the B. cereus group, 2,000 isolates were evaluated using primers designed to be specific to two variable regions detected in previously described elements. PCR and propagation tests revealed that tectivirus-like elements occurred in less than 3% of the isolates. Regardless of this limited distribution, several novel tectiviruses were found, and partial DNA sequencing indicated that a greater diversity exists within the family Tectiviridae. Analyses of the selected variable regions, along with their host range, showed that tectiviruses in the B. cereus group can be clustered mainly into two different groups: the ones infecting B. anthracis and those isolated from other B. cereus group members. In order to address the host range of some novel tectiviruses, 120 strains were tested for sensitivity. The results showed that all the tested tectiviruses produced lysis in at least one B. cereus sensu lato strain. Moreover, no simple relationship between the infection patterns of the tectiviruses and their diversity was found. PMID:24795369

  9. An invasive non-native mammal population conserves genetic diversity lost from its native range.

    PubMed

    Veale, A J; Holland, O J; McDonald, R A; Clout, M N; Gleeson, D M

    2015-05-01

    Invasive, non-native species are one of the major causes of global biodiversity loss. Although they are, by definition, successful in their non-native range, their populations generally show major reductions in their genetic diversity during the demographic bottleneck they experience during colonization. By investigating the mitochondrial genetic diversity of an invasive non-native species, the stoat Mustela erminea, in New Zealand and comparing it to diversity in the species' native range in Great Britain, we reveal the opposite effect. We demonstrate that the New Zealand stoat population contains four mitochondrial haplotypes that have not been found in the native range. Stoats in Britain rely heavily on introduced rabbits Oryctolagus cuniculus as their primary prey and were introduced to New Zealand in a misguided attempt at biological control of rabbits, which had also been introduced there. While invasive stoats have since decimated the New Zealand avifauna, native stoat populations were themselves decimated by the introduction to Britain of Myxoma virus as a control measure for rabbits. We highlight the irony that while introduced species (rabbits) and subsequent biocontrol (myxomatosis) have caused population crashes of native stoats, invasive stoats in New Zealand, which were also introduced for biological control, now contain more genetic haplotypes than their most likely native source. PMID:25655531

  10. Rescue of Progeria in Trichothiodystrophy by Homozygous Lethal Xpd Alleles

    PubMed Central

    Andressoo, Jaan-Olle; Jans, Judith; de Wit, Jan; Coin, Frederic; Hoogstraten, Deborah; van de Ven, Marieke; Toussaint, Wendy; Huijmans, Jan; Thio, H. Bing; van Leeuwen, Wibeke J; de Boer, Jan; Egly, Jean-Marc; Hoeijmakers, Jan H. J; van der Horst, Gijsbertus T. J; Mitchell, James R

    2006-01-01

    Although compound heterozygosity, or the presence of two different mutant alleles of the same gene, is common in human recessive disease, its potential to impact disease outcome has not been well documented. This is most likely because of the inherent difficulty in distinguishing specific biallelic effects from differences in environment or genetic background. We addressed the potential of different recessive alleles to contribute to the enigmatic pleiotropy associated with XPD recessive disorders in compound heterozygous mouse models. Alterations in this essential helicase, with functions in both DNA repair and basal transcription, result in diverse pathologies ranging from elevated UV sensitivity and cancer predisposition to accelerated segmental progeria. We report a variety of biallelic effects on organismal phenotype attributable to combinations of recessive Xpd alleles, including the following: (i) the ability of homozygous lethal Xpd alleles to ameliorate a variety of disease symptoms when their essential basal transcription function is supplied by a different disease-causing allele, (ii) differential developmental and tissue-specific functions of distinct Xpd allele products, and (iii) interallelic complementation, a phenomenon rarely reported at clinically relevant loci in mammals. Our data suggest a re-evaluation of the contribution of “null” alleles to XPD disorders and highlight the potential of combinations of recessive alleles to affect both normal and pathological phenotypic plasticity in mammals. PMID:17020410

  11. Bryophyte diversity and range size distribution along two altitudinal gradients: Continent vs. island

    NASA Astrophysics Data System (ADS)

    Ah-Peng, Claudine; Wilding, Nicholas; Kluge, Juergen; Descamps-Julien, Blandine; Bardat, Jacques; Chuah-Petiot, Min; Strasberg, Dominique; Hedderson, Terry A. J.

    2012-07-01

    We compare patterns of bryophyte diversity and variation in species altitudinal ranges between a continental and an island altitudinal gradient. We use our ecological data set along the highest summit (Piton des Neiges, 3069 m) of Réunion Island (Mascarene archipelago) and compare it to available published data of another high volcanic massif in Colombia (Nevado del Ruiz, 5321 m). The distribution of narrow-ranged and large-ranged species was investigated. We tested the effect of geometric constraints on species distribution along the two gradients by comparing empirical to predicted data using the Mid-Domain Null Programme (McCain, 2004). Species richness was comparable between the island and continental gradient for epiphytic bryophytes, 265 and 295 species respectively. The comparison between the two tropical high mountains demonstrates important differences in the distribution of range sizes with altitude and a dominance of species with small range sizes on the Réunion gradient. For the island gradient, mean altitudinal range increases with altitude whilst concurrently species richness decreases revealing a Rapoport effect in altitudinal distribution of bryophyte communities. Geometric constraints did not explain much of the species richness pattern for the island. Conversely, for the continental gradient, dominated by large-ranged species, geometric constraints could not be ruled out as a primary structuring feature for the species richness pattern. This study also highlights that the island's cloud forest hosts not only high species richness but also high number of rare species, which is of prime interest for conservation planners.

  12. Selection Criterion of Gauges for Vacuum Measurements of Systems with Diverse Ranges

    NASA Astrophysics Data System (ADS)

    Akram, H. M.; Fasih, A.

    Basically a vacuum gauge is a key that opens the secrets of a closed vacuum system, indicates what is happening inside the sealed makeup and has the facility to control it through evacuation system. But for the broad vacuum range, all the goings-on are not made known or commanded by a particular vacuum gauge. Consequently, various gauges of special types are used to accurately measure the vacuum of diverse ranges, together with the requisite services. Therefore, the selection of proper gauge in favor of exact vacuum metrology in conjunction with extra actions, for a particular vacuum work, is of primary importance. There are many factors that affect the appropriate gauge selection. In this paper, selection criterion for suitable vacuum gauge, supportive for accurate vacuum measurements and other critical functions of the required range, has briefly been discussed that can make the task of gauge selection simpler and exact.

  13. Cultivable bacterial diversity along the altitudinal zonation and vegetation range of tropical Eastern Himalaya.

    PubMed

    Lyngwi, Nathaniel A; Koijam, Khedarani; Sharma, D; Joshi, S R

    2013-03-01

    The Northeastern part of India sprawls over an area of 262 379km2 in the Eastern Himalayan range. This constitutes a biodiversity hotspot with high levels of biodiversity and endemism; unfortunately, is also a poorly known area, especially on its microbial diversity. In this study, we assessed cultivable soil bacterial diversity and distribution from lowlands to highlands (34 to 3 990m.a.s.l.). Soil physico-chemical parameters and forest types across the different altitudes were characterized and correlated with bacterial distribution and diversity. Microbes from the soil samples were grown in Nutrient, Muller Hinton and Luria-Bertani agar plates and were initially characterized using biochemical methods. Parameters like dehydrogenase and urease activities, temperature, moisture content, pH, carbon content, bulk density of the sampled soil were measured for each site. Representative isolates were also subjected to 16S rDNA sequence analysis. A total of 155 cultivable bacterial isolates were characterized which were analyzed for richness, evenness and diversity indices. The tropical and sub-tropical forests supported higher bacterial diversity compared to temperate pine, temperate conifer, and sub-alpine rhododendron forests. The 16S rRNA phylogenetic analysis revealed that Firmicutes was the most common group followed by Proteobacreria and Bacteroidetes. Species belonging to the genera Bacillus and Pseudomonas were the most abundant. Bacterial CFU showed positive but insignificant correlation with soil parameters like pH (r=0.208), soil temperature (r=0.303), ambient temperature (r=0.443), soil carbon content (r=0.525), soil bulk density (r=0.268), soil urease (r=0.549) and soil dehydrogenase (r=0.492). Altitude (r=-0.561) and soil moisture content (r=-0.051) showed negative correlation. Altitudinal gradient along with the vegetation and soil physico-chemical parameters were found to influence bacterial diversity and distribution. This study points out that this is

  14. Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape.

    PubMed

    Delourme, R; Bousset, L; Ermel, M; Duffé, P; Besnard, A L; Marquer, B; Fudal, I; Linglin, J; Chadœuf, J; Brun, H

    2014-10-01

    Quantitative resistance mediated by multiple genetic factors has been shown to increase the potential for durability of major resistance genes. This was demonstrated in the Leptosphaeria maculans/Brassica napus pathosystem in a 5year recurrent selection field experiment on lines harboring the qualitative resistance gene Rlm6 combined or not with quantitative resistance. The quantitative resistance limited the size of the virulent isolate population. In this study we continued this recurrent selection experiment in the same way to examine whether the pathogen population could adapt and render the major gene ineffective in the longer term. The cultivars Eurol, with a susceptible background, and Darmor, with quantitative resistance, were used. We confirmed that the combination of qualitative and quantitative resistance is an effective approach for controlling the pathogen epidemics over time. This combination did not prevent isolates virulent against the major gene from amplifying in the long term but the quantitative resistance significantly delayed for 5years the loss of effectiveness of the qualitative resistance and disease severity was maintained at a low level on the genotype with both types of resistance after the fungus population had adapted to the major gene. We also showed that diversity of AvrLm6 virulence alleles was comparable in isolates recovered after the recurrent selection on lines carrying either the major gene alone or in combination with quantitative resistance: a single repeat-induced point mutation and deletion events were observed in both situations. Breeding varieties which combine qualitative and quantitative resistance can effectively contribute to disease control by increasing the potential for durability of major resistance genes.

  15. Entomofaunal diversity of tree hole mosquitoes in Western and Eastern Ghats hill ranges of Tamilnadu, India.

    PubMed

    Senthamarai Selvan, P; Jebanesan, A; Reetha, D

    2016-07-01

    The distribution and abundance of various mosquito vectors is important in the determination of disease prevalence in disease endemic areas. The aim of the present study was to conduct regular entomological surveillance and to determine the relative abundance of tree hole mosquito species in Tamilnadu, India. In addition to this, the impact of weather-conditions on tree hole mosquito population were evaluated between June, 2014 and May, 2015. Six hills ranges viz., Anaimalai hills, Kodaikanal hills, Sitheri hills, Kolli hills, Yercaud hills, and Megamalai were selected, the immatures collected from tree holes by the help of suction tube. Collections were made at dusk and dawn at randomly selected 15 different tree species. The collected samples were stored and morphologically identified to species level in the laboratory. Mosquito diversity was calculated by Simpson's and Shannon-Weiner diversity indicies with spatial and temporal aspects. Over 2642 mosquitoes comprising the primary vectors of dengue, chickungunya, malaria, filariasis were identified. Other species collected from the fifteen sites in each hill during the study included Christophersiomyia annularis, Christophersiomyia thomsoni, Downsiomyia albolateralis, Downsiomyia nivea and Toxorhynchites splendens, etc. Study revealed high species diversity and relative density associated with different study sites. Based on the Shannon diversity index high number of species was recorded with Aedes pseudoalbopicta (0.0829) followed by Ae. aegypti (0.0805) and least species was recorded as Anopheles elegans (0.0059). The distribution of the primary vectors of DF along the high occurrence was evident with most study sites representing proportions of this vector population. This showed the high risk level associated with the livestock movement in amplification and circulation of the virus during the outbreaks. The findings of this study, therefore, demonstrated the potential vulnerability of nomadic communities to

  16. Maritime climate influence on chaparral composition and diversity in the coast range of central California

    PubMed Central

    Vasey, Michael C; Parker, V Thomas; Holl, Karen D; Loik, Michael E; Hiatt, Seth

    2014-01-01

    We investigated the hypothesis that maritime climatic factors associated with summer fog and low cloud stratus (summer marine layer) help explain the compositional diversity of chaparral in the coast range of central California. We randomly sampled chaparral species composition in 0.1-hectare plots along a coast-to-interior gradient. For each plot, climatic variables were estimated and soil samples were analyzed. We used Cluster Analysis and Principle Components Analysis to objectively categorize plots into climate zone groups. Climate variables, vegetation composition and various diversity measures were compared across climate zone groups using ANOVA and nonmetric multidimensional scaling. Differences in climatic variables that relate to summer moisture availability and winter freeze events explained the majority of variance in measured conditions and coincided with three chaparral assemblages: maritime (lowland coast where the summer marine layer was strongest), transition (upland coast with mild summer marine layer influence and greater winter precipitation), and interior sites that generally lacked late summer water availability from either source. Species turnover (β-diversity) was higher among maritime and transition sites than interior sites. Coastal chaparral differs from interior chaparral in having a higher obligate seeder to facultative seeder (resprouter) ratio and by being dominated by various Arctostaphylos species as opposed to the interior dominant, Adenostoma fasciculatum. The maritime climate influence along the California central coast is associated with patterns of woody plant composition and β-diversity among sites. Summer fog in coastal lowlands and higher winter precipitation in coastal uplands combine to lower late dry season water deficit in coastal chaparral and contribute to longer fire return intervals that are associated with obligate seeders and more local endemism. Soil nutrients are comparatively less important in explaining plant

  17. Maritime climate influence on chaparral composition and diversity in the coast range of central California.

    PubMed

    Vasey, Michael C; Parker, V Thomas; Holl, Karen D; Loik, Michael E; Hiatt, Seth

    2014-09-01

    We investigated the hypothesis that maritime climatic factors associated with summer fog and low cloud stratus (summer marine layer) help explain the compositional diversity of chaparral in the coast range of central California. We randomly sampled chaparral species composition in 0.1-hectare plots along a coast-to-interior gradient. For each plot, climatic variables were estimated and soil samples were analyzed. We used Cluster Analysis and Principle Components Analysis to objectively categorize plots into climate zone groups. Climate variables, vegetation composition and various diversity measures were compared across climate zone groups using ANOVA and nonmetric multidimensional scaling. Differences in climatic variables that relate to summer moisture availability and winter freeze events explained the majority of variance in measured conditions and coincided with three chaparral assemblages: maritime (lowland coast where the summer marine layer was strongest), transition (upland coast with mild summer marine layer influence and greater winter precipitation), and interior sites that generally lacked late summer water availability from either source. Species turnover (β-diversity) was higher among maritime and transition sites than interior sites. Coastal chaparral differs from interior chaparral in having a higher obligate seeder to facultative seeder (resprouter) ratio and by being dominated by various Arctostaphylos species as opposed to the interior dominant, Adenostoma fasciculatum. The maritime climate influence along the California central coast is associated with patterns of woody plant composition and β-diversity among sites. Summer fog in coastal lowlands and higher winter precipitation in coastal uplands combine to lower late dry season water deficit in coastal chaparral and contribute to longer fire return intervals that are associated with obligate seeders and more local endemism. Soil nutrients are comparatively less important in explaining plant

  18. Maritime climate influence on chaparral composition and diversity in the coast range of central California.

    PubMed

    Vasey, Michael C; Parker, V Thomas; Holl, Karen D; Loik, Michael E; Hiatt, Seth

    2014-09-01

    We investigated the hypothesis that maritime climatic factors associated with summer fog and low cloud stratus (summer marine layer) help explain the compositional diversity of chaparral in the coast range of central California. We randomly sampled chaparral species composition in 0.1-hectare plots along a coast-to-interior gradient. For each plot, climatic variables were estimated and soil samples were analyzed. We used Cluster Analysis and Principle Components Analysis to objectively categorize plots into climate zone groups. Climate variables, vegetation composition and various diversity measures were compared across climate zone groups using ANOVA and nonmetric multidimensional scaling. Differences in climatic variables that relate to summer moisture availability and winter freeze events explained the majority of variance in measured conditions and coincided with three chaparral assemblages: maritime (lowland coast where the summer marine layer was strongest), transition (upland coast with mild summer marine layer influence and greater winter precipitation), and interior sites that generally lacked late summer water availability from either source. Species turnover (β-diversity) was higher among maritime and transition sites than interior sites. Coastal chaparral differs from interior chaparral in having a higher obligate seeder to facultative seeder (resprouter) ratio and by being dominated by various Arctostaphylos species as opposed to the interior dominant, Adenostoma fasciculatum. The maritime climate influence along the California central coast is associated with patterns of woody plant composition and β-diversity among sites. Summer fog in coastal lowlands and higher winter precipitation in coastal uplands combine to lower late dry season water deficit in coastal chaparral and contribute to longer fire return intervals that are associated with obligate seeders and more local endemism. Soil nutrients are comparatively less important in explaining plant

  19. Entomofaunal diversity of tree hole mosquitoes in Western and Eastern Ghats hill ranges of Tamilnadu, India.

    PubMed

    Senthamarai Selvan, P; Jebanesan, A; Reetha, D

    2016-07-01

    The distribution and abundance of various mosquito vectors is important in the determination of disease prevalence in disease endemic areas. The aim of the present study was to conduct regular entomological surveillance and to determine the relative abundance of tree hole mosquito species in Tamilnadu, India. In addition to this, the impact of weather-conditions on tree hole mosquito population were evaluated between June, 2014 and May, 2015. Six hills ranges viz., Anaimalai hills, Kodaikanal hills, Sitheri hills, Kolli hills, Yercaud hills, and Megamalai were selected, the immatures collected from tree holes by the help of suction tube. Collections were made at dusk and dawn at randomly selected 15 different tree species. The collected samples were stored and morphologically identified to species level in the laboratory. Mosquito diversity was calculated by Simpson's and Shannon-Weiner diversity indicies with spatial and temporal aspects. Over 2642 mosquitoes comprising the primary vectors of dengue, chickungunya, malaria, filariasis were identified. Other species collected from the fifteen sites in each hill during the study included Christophersiomyia annularis, Christophersiomyia thomsoni, Downsiomyia albolateralis, Downsiomyia nivea and Toxorhynchites splendens, etc. Study revealed high species diversity and relative density associated with different study sites. Based on the Shannon diversity index high number of species was recorded with Aedes pseudoalbopicta (0.0829) followed by Ae. aegypti (0.0805) and least species was recorded as Anopheles elegans (0.0059). The distribution of the primary vectors of DF along the high occurrence was evident with most study sites representing proportions of this vector population. This showed the high risk level associated with the livestock movement in amplification and circulation of the virus during the outbreaks. The findings of this study, therefore, demonstrated the potential vulnerability of nomadic communities to

  20. Determinants of northerly range limits along the Himalayan bird diversity gradient.

    PubMed

    Price, Trevor D; Mohan, Dhananjai; Tietze, D Thomas; Hooper, Daniel M; Orme, C David L; Rasmussen, Pamela C

    2011-10-01

    The primary explanation for the latitudinal gradient in species diversity must lie in why species fail to expand ranges across different climatic regimes. Theories of species gradients based in niche conservatism assume that whole clades are confined to particular climatic regimes because the traits they share limit adaptation to alternative regimes. We assess these theories in an analysis of the twofold decline in bird species richness along the Himalayas from the southeast to the northwest. The presence of fewer species in the northwest is entirely due to a steep decline in the number of forest species; species occupying more open habitats show a reversed gradient. Forest species numbers are exceptionally high at midelevations (1,000-2,000 m) in the southeast, which experience a warm, wet climate not present in the northwest, and a high proportion of these species fail to expand their range to the northwest. Despite this, many species do have populations or close relatives that straddle different climatic regimes along altitudinal gradients and/or the regional gradient, implying that climate-based niche conservatism per se does not strongly constrain range limits. We argue that climate- and competition-mediated resource distributions are important in setting northerly range limits and show that one measure of forest resources (foliage density) is lower in the northwest. PMID:21956095

  1. Metabolomic unveiling of a diverse range of green tea (Camellia sinensis) metabolites dependent on geography.

    PubMed

    Lee, Jang-Eun; Lee, Bum-Jin; Chung, Jin-Oh; Kim, Hak-Nam; Kim, Eun-Hee; Jung, Sungheuk; Lee, Hyosang; Lee, Sang-Jun; Hong, Young-Shick

    2015-05-01

    Numerous factors such as geographical origin, cultivar, climate, cultural practices, and manufacturing processes influence the chemical compositions of tea, in the same way as growing conditions and grape variety affect wine quality. However, the relationships between these factors and tea chemical compositions are not well understood. In this study, a new approach for non-targeted or global analysis, i.e., metabolomics, which is highly reproducible and statistically effective in analysing a diverse range of compounds, was used to better understand the metabolome of Camellia sinensis and determine the influence of environmental factors, including geography, climate, and cultural practices, on tea-making. We found a strong correlation between environmental factors and the metabolome of green, white, and oolong teas from China, Japan, and South Korea. In particular, multivariate statistical analysis revealed strong inter-country and inter-city relationships in the levels of theanine and catechin derivatives found in green and white teas. This information might be useful for assessing tea quality or producing distinct tea products across different locations, and highlights simultaneous identification of diverse tea metabolites through an NMR-based metabolomics approach. PMID:25529705

  2. Metabolomic unveiling of a diverse range of green tea (Camellia sinensis) metabolites dependent on geography.

    PubMed

    Lee, Jang-Eun; Lee, Bum-Jin; Chung, Jin-Oh; Kim, Hak-Nam; Kim, Eun-Hee; Jung, Sungheuk; Lee, Hyosang; Lee, Sang-Jun; Hong, Young-Shick

    2015-05-01

    Numerous factors such as geographical origin, cultivar, climate, cultural practices, and manufacturing processes influence the chemical compositions of tea, in the same way as growing conditions and grape variety affect wine quality. However, the relationships between these factors and tea chemical compositions are not well understood. In this study, a new approach for non-targeted or global analysis, i.e., metabolomics, which is highly reproducible and statistically effective in analysing a diverse range of compounds, was used to better understand the metabolome of Camellia sinensis and determine the influence of environmental factors, including geography, climate, and cultural practices, on tea-making. We found a strong correlation between environmental factors and the metabolome of green, white, and oolong teas from China, Japan, and South Korea. In particular, multivariate statistical analysis revealed strong inter-country and inter-city relationships in the levels of theanine and catechin derivatives found in green and white teas. This information might be useful for assessing tea quality or producing distinct tea products across different locations, and highlights simultaneous identification of diverse tea metabolites through an NMR-based metabolomics approach.

  3. A DNA Metabarcoding Study of a Primate Dietary Diversity and Plasticity across Its Entire Fragmented Range

    PubMed Central

    Quéméré, Erwan; Hibert, Fabrice; Miquel, Christian; Lhuillier, Emeline; Rasolondraibe, Emmanuel; Champeau, Julie; Rabarivola, Clément; Nusbaumer, Louis; Chatelain, Cyrille; Gautier, Laurent; Ranirison, Patrick; Crouau-Roy, Brigitte; Taberlet, Pierre; Chikhi, Lounès

    2013-01-01

    In tropical regions, most primary ecosystems have been replaced by mosaic landscapes in which species must cope with a large shift in the distribution of their habitat and associated food resources. Primates are particularly vulnerable to habitat modifications. Most species persist in small fragments surrounded by complex human-mediated matrices whose structure and connectivity may strongly influence their dispersal and feeding behavior. Behavioral plasticity appears to be a crucial parameter governing the ability of organisms to exploit the resources offered by new matrix habitats and thus to persist in fragmented habitats. In this study, we were interested in the dietary plasticity of the golden-crowned sifaka (Propithecus tattersalli), an endangered species of lemur, found only in the Daraina region in north-eastern Madagascar. We used a DNA-based approach combining the barcoding concept and Illumina next-generation sequencing to (i) describe the species diet across its entire range and (ii) evaluate the influence of landscape heterogeneity on diet diversity and composition. Faeces from 96 individuals were sampled across the entire species range and their contents were analyzed using the trnL metabarcoding approach. In parallel, we built a large DNA reference database based on a checklist of the plant species of the Daraina region. Our results suggest that golden-crowned sifakas exhibit remarkable dietary diversity with at least 130 plant species belonging to 80 genera and 49 different families. We highlighted an influence of both habitat type and openness on diet composition suggesting a high flexibility of foraging strategies. Moreover, we observed the presence of numerous cultivated and naturalized plants in the faeces of groups living in forest edge areas. Overall, our findings support our initial expectation that P. tattersalli is able to cope with the current level of alteration of the landscape and confirm our previous results on the distribution and the

  4. Structures of and allelic diversity and relationships among the major outer membrane protein (ompA) genes of the four chlamydial species.

    PubMed

    Kaltenboeck, B; Kousoulas, K G; Storz, J

    1993-01-01

    DNA sequences coding for 81% of the ompA gene from 24 chlamydial strains, representing all chlamydial species, were determined from DNA amplified by polymerase chain reactions. Chlamydial strains of serovars and strains with similar chromosomal restriction fragment length polymorphism had identical ompA DNA sequences. The ompA sequences were segregated into 23 different ompA alleles and aligned with each other, and phylogenetic relationships among them were inferred by neighbor-joining and maximum parsimony analyses. The neighbor-joining method produced a single phylogram which was rooted at the branch between two major clusters. One cluster included all Chlamydia trachomatis ompA alleles (trachoma group). The second cluster was composed of three major groups of ompA alleles: psittacosis group (alleles MN, 6BC, A22/M, B577, LW508, FEPN, and GPIC), pneumonia group (Chlamydia pneumoniae AR388 with the allele KOALA), and polyarthritis group (ruminant and porcine chlamydial alleles LW613, 66P130, L71, and 1710S with propensity for polyarthritis). These groups were distinguished through specific DNA sequence signatures. Maximum parsimony analysis yielded two equally most parsimonious phylograms with topologies similar to the ompA tree of neighbor joining. Two phylograms constructed from chlamydial genomic DNA distances had topologies identical to that of the ompA phylogram with respect to branching of the chlamydial species. Human serovars of C. trachomatis with essentially identical genomes represented a single taxonomic unit, while they were divergent in the ompA tree. Consistent with the ompA phylogeny, the porcine isolate S45, previously considered to be Chlamydia psittaci, was identified as C. trachomatis through biochemical characteristics. These data demonstrate that chlamydial ompA allelic relationships, except for human serovars of C. trachomatis, are cognate with chromosomal phylogenies.

  5. Structures of and allelic diversity and relationships among the major outer membrane protein (ompA) genes of the four chlamydial species.

    PubMed Central

    Kaltenboeck, B; Kousoulas, K G; Storz, J

    1993-01-01

    DNA sequences coding for 81% of the ompA gene from 24 chlamydial strains, representing all chlamydial species, were determined from DNA amplified by polymerase chain reactions. Chlamydial strains of serovars and strains with similar chromosomal restriction fragment length polymorphism had identical ompA DNA sequences. The ompA sequences were segregated into 23 different ompA alleles and aligned with each other, and phylogenetic relationships among them were inferred by neighbor-joining and maximum parsimony analyses. The neighbor-joining method produced a single phylogram which was rooted at the branch between two major clusters. One cluster included all Chlamydia trachomatis ompA alleles (trachoma group). The second cluster was composed of three major groups of ompA alleles: psittacosis group (alleles MN, 6BC, A22/M, B577, LW508, FEPN, and GPIC), pneumonia group (Chlamydia pneumoniae AR388 with the allele KOALA), and polyarthritis group (ruminant and porcine chlamydial alleles LW613, 66P130, L71, and 1710S with propensity for polyarthritis). These groups were distinguished through specific DNA sequence signatures. Maximum parsimony analysis yielded two equally most parsimonious phylograms with topologies similar to the ompA tree of neighbor joining. Two phylograms constructed from chlamydial genomic DNA distances had topologies identical to that of the ompA phylogram with respect to branching of the chlamydial species. Human serovars of C. trachomatis with essentially identical genomes represented a single taxonomic unit, while they were divergent in the ompA tree. Consistent with the ompA phylogeny, the porcine isolate S45, previously considered to be Chlamydia psittaci, was identified as C. trachomatis through biochemical characteristics. These data demonstrate that chlamydial ompA allelic relationships, except for human serovars of C. trachomatis, are cognate with chromosomal phylogenies. Images PMID:8419295

  6. Increased species diversity and extended habitat range of sulfur-oxidizing Thiomicrospira spp.

    PubMed Central

    Brinkhoff, T; Muyzer, G

    1997-01-01

    We combined traditional cultivation methods and new molecular techniques to study the diversity and habitat range of bacteria of the genus Thiomicrospira. Specific primers were designed and used in the PCR to amplify the 16S ribosomal DNA (rDNA) of Thiomicrospira spp. and thus detect the presence of these bacteria in environmental samples and enrichment cultures. By using this genus-specific PCR, we were able to amplify 722-bp-long 16S rDNA fragments from different saltwater habitats as well as from a freshwater ecosystem. Furthermore, we were able to isolate most of these bacteria in pure culture by using enrichment cultures for chemolithoautotrophic sulfur-oxidizing bacteria. With denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA fragments followed by hybridization analysis with one of the primers as a genus-specific probe, it was possible to monitor the success of isolation. The combined approach resulted in the isolation of several chemolithoautotrophic bacteria from different habitats: e.g., a coastal sediment along the coast of Chile, a microbial mat of the hypersaline pond Solar Lake (Sinai, Egypt), and the saline spring Artern (Thuringia, Germany). In addition, four different isolates were obtained from sediment and water samples taken at Jadebusen, which is part of the German Waddensea. Comparative analysis of the nearly complete 16S rRNA sequences of these isolates indicated several new species, all grouping with the Thiomicrospira species of the gamma subdivision of the class Proteobacteria. A freshwater Thiomicrospira species could not be isolated, but sequence analysis of the PCR product obtained after amplification of the environmental DNA with the Thiomicrospira-specific primers revealed its phylogenetic affiliation. The study indicates an increased species diversity of Thiomicrospira and the ubiquity of this sulfur-oxidizing bacterium in habitats with reduced sulfur compounds. PMID:9327542

  7. Transformation and pp60v-src autophosphorylation correlate with SHC-GRB2 complex formation in rat and chicken cells expressing host-range and kinase-active, transformation-defective alleles of v-src.

    PubMed Central

    Verderame, M F; Guan, J L; Woods Ignatoski, K M

    1995-01-01

    The biochemical properties of several pp60v-src substrates believed to participate in src-mediated transformation were examined in cells expressing a kinase-active, transformation-defective v-src allele (v-src-F172 delta/Y416F) and its parental allele, v-src-F172 delta, a host-range--dependent allele that transforms chicken cells to a fusiform morphology, but does not transform rat cells. Because pp60v-src-F172 delta is dependent on autophosphorylation for transforming ability, these alleles provide a unique opportunity to examine the role of pp60v-src autophosphorylation in regulating substrate interactions. Increased pp125FAK tyrosine phosphorylation and high levels of pp60v-src-associated phosphotidylinositol-3' kinase activity were detected specifically in chicken cells exhibiting round, refractile transformation but not in cells transformed to a fusiform morphology. Increased pp125FAK kinase activity, but not increased pp125FAK tyrosine-phosphorylation correlated with pp60v-src autophosphorylation and increased anchorage-independent growth. Thus, pp125FAK and PI3'K may participate in morphological transformation by v-src. Furthermore, association of phosphorylated SHC with the adapter GRB2 correlated with increased anchorage-independent growth (and autophosphorylation) in both rat and chicken cells independent of the morphological phenotype induced. Therefore, host-range dependence for transformation may be regulated through association of SHC with GRB2, thus implicating SHC as a crucial substrate for src-dependent transformation. Images PMID:7579711

  8. Distribution of MICB diversity in the Zhejiang Han population: PCR sequence-based typing for exons 2-6 and identification of five novel MICB alleles.

    PubMed

    Ying, Yanling; He, Yanmin; Tao, Sudan; Han, Zhedong; Wang, Wei; Chen, Nanying; He, Junjun; Zhang, Wei; He, Ji; Zhu, Faming; Lv, Hangjun

    2013-07-01

    The polymorphism of major histocompatibility complex class I chain-related gene B (MICB) and variations in MICB alleles in a variety of populations have been characterized using several genotyping approaches. In the present study, a novel polymerase chain reaction sequence-based typing (PCR-SBT) method was established for the genotyping of MICB exons 2-6, and the allelic frequency of MICB in the Zhejiang Han population was investigated. Among 400 unrelated healthy Han individuals from Zhejiang Province, China, a total of 20 MICB alleles were identified, of which MICB*005:02:01, MICB*002:01:01, and MICB*004:01:01 were the most predominant alleles, with frequencies of 0.57375, 0.1225, and 0.08375, respectively. Nine MICB alleles were detected on only one occasion, giving a frequency of 0.00125. Of the 118 distinct MICB ∼ HLA-B haplotypes identified, 42 showed significant linkage disequilibrium (P < 0.05). Haplotypes MICB*005:02:01 ∼ B*46:01, MICB*005:02:01 ∼ B*40:01, and MICB*008 ∼ B*58:01 were the most common haplotypes, with frequencies of 0.0978, 0.0761, and 0.0616, respectively. Five novel alleles, MICB*005:07, MICB*005:08, MICB*027, MICB*028, and MICB*029 were identified. Compared with the MICB*005:02:01 sequence, a G > A substitution was observed at nucleotide position 210 in MICB*005:07, and a 1,134 T > C substitution in MICB*005:08 and an 862 G > A substitution in MICB*027 were detected. In addition, it appears that MICB*028 probably arose from MICB*004:01:01 with an A to G substitution at position 1,147 in exon 6. MICB*029 had a G > T transversion at nucleotide position 730 in exon 4, compared with that of MICB*002:01:01. On the basis of the new PCR-SBT assay, these observed results demonstrated MICB allelic variations in the Zhejiang Han population.

  9. High genetic diversity declines towards the geographic range periphery of Adonis vernalis, a Eurasian dry grassland plant.

    PubMed

    Hirsch, H; Wagner, V; Danihelka, J; Ruprecht, E; Sánchez-Gómez, P; Seifert, M; Hensen, I

    2015-11-01

    Genetic diversity is important for species' fitness and evolutionary processes but our knowledge on how it varies across a species' distribution range is limited. The abundant centre hypothesis (ACH) predicts that populations become smaller and more isolated towards the geographic range periphery - a pattern that in turn should be associated with decreasing genetic diversity and increasing genetic differentiation. We tested this hypothesis in Adonis vernalis, a dry grassland plant with an extensive Eurasian distribution. Its life-history traits and distribution characteristics suggest a low genetic diversity that decreases and a high genetic differentiation that increases towards the range edge. We analysed AFLP fingerprints in 28 populations along a 4698-km transect from the geographic range core in Russia to the western range periphery in Central and Western Europe. Contrary to our expectation, our analysis revealed high genetic diversity (range of proportion of polymorphic bands = 56-81%, He = 0.168-0.238) and low genetic differentiation across populations (Φ(ST) = 0.18). However, in congruence with the genetic predictions of the ACH, genetic diversity decreased and genetic differentiation increased towards the range periphery. Spanish populations were genetically distinct, suggesting a divergent post-glacial history in this region. The high genetic diversity and low genetic differentiation in the remaining A. vernalis populations is surprising given the species' life-history traits and points to the possibility that the species has been widely distributed in the studied region or that it has migrated from a diverse source in an East-West direction, in the past. PMID:26122089

  10. High genetic diversity declines towards the geographic range periphery of Adonis vernalis, a Eurasian dry grassland plant.

    PubMed

    Hirsch, H; Wagner, V; Danihelka, J; Ruprecht, E; Sánchez-Gómez, P; Seifert, M; Hensen, I

    2015-11-01

    Genetic diversity is important for species' fitness and evolutionary processes but our knowledge on how it varies across a species' distribution range is limited. The abundant centre hypothesis (ACH) predicts that populations become smaller and more isolated towards the geographic range periphery - a pattern that in turn should be associated with decreasing genetic diversity and increasing genetic differentiation. We tested this hypothesis in Adonis vernalis, a dry grassland plant with an extensive Eurasian distribution. Its life-history traits and distribution characteristics suggest a low genetic diversity that decreases and a high genetic differentiation that increases towards the range edge. We analysed AFLP fingerprints in 28 populations along a 4698-km transect from the geographic range core in Russia to the western range periphery in Central and Western Europe. Contrary to our expectation, our analysis revealed high genetic diversity (range of proportion of polymorphic bands = 56-81%, He = 0.168-0.238) and low genetic differentiation across populations (Φ(ST) = 0.18). However, in congruence with the genetic predictions of the ACH, genetic diversity decreased and genetic differentiation increased towards the range periphery. Spanish populations were genetically distinct, suggesting a divergent post-glacial history in this region. The high genetic diversity and low genetic differentiation in the remaining A. vernalis populations is surprising given the species' life-history traits and points to the possibility that the species has been widely distributed in the studied region or that it has migrated from a diverse source in an East-West direction, in the past.

  11. Diverse broad-host-range plasmids from freshwater carry few accessory genes.

    PubMed

    Brown, Celeste J; Sen, Diya; Yano, Hirokazu; Bauer, Matthew L; Rogers, Linda M; Van der Auwera, Geraldine A; Top, Eva M

    2013-12-01

    Broad-host-range self-transferable plasmids are known to facilitate bacterial adaptation by spreading genes between phylogenetically distinct hosts. These plasmids typically have a conserved backbone region and a variable accessory region that encodes host-beneficial traits. We do not know, however, how well plasmids that do not encode accessory functions can survive in nature. The goal of this study was to characterize the backbone and accessory gene content of plasmids that were captured from freshwater sources without selecting for a particular phenotype or cultivating their host. To do this, triparental matings were used such that the only required phenotype was the plasmid's ability to mobilize a nonconjugative plasmid. Based on complete genome sequences of 10 plasmids, only 5 carried identifiable accessory gene regions, and none carried antibiotic resistance genes. The plasmids belong to four known incompatibility groups (IncN, IncP-1, IncU, and IncW) and two potentially new groups. Eight of the plasmids were shown to have a broad host range, being able to transfer into alpha-, beta-, and gammaproteobacteria. Because of the absence of antibiotic resistance genes, we resampled one of the sites and compared the proportion of captured plasmids that conferred antibiotic resistance to their hosts with the proportion of such plasmids captured from the effluent of a local wastewater treatment plant. Few of the captured plasmids from either site encoded antibiotic resistance. A high diversity of plasmids that encode no or unknown accessory functions is thus readily found in freshwater habitats. The question remains how the plasmids persist in these microbial communities.

  12. Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

    PubMed

    Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

    2011-01-01

    The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

  13. Genetic diversity and host range studies of turnip curly top virus.

    PubMed

    Razavinejad, Sara; Heydarnejad, Jahangir; Kamali, Mehdi; Massumi, Hossain; Kraberger, Simona; Varsani, Arvind

    2013-04-01

    Turnip curly top virus (TCTV) is a unique geminivirus that has recently been characterised as infecting turnips in Iran. The genome of TCTV shares <68 % pairwise identity with other geminiviruses and has a genome organisation similar to that of curtoviruses and topocuvirus. The replication-associated protein (Rep) bears the highest similarity to curtovirus Reps (48.5-69.0 %); however, in the case of the capsid protein (CP), the extent of similarity is only 39.5-44.5 %. We constructed an agroinfectious clone of TCTV and undertook host range studies on ten plant species; in three species (turnip, sugar beet and cowpea), we detected infection which presents curly top symptoms in turnip and sugar beet. The efficiency of TCTV infection in agroinoculated turnip plants was 71.7 %, and the infection was successfully transmitted to 80 % of the healthy turnip plants used in the insect transmission studies by Circulifer haematoceps under greenhouse conditions. We also determined the genome sequence of 14 new TCTV isolates from southern Iran isolated from turnips. We observed ~13 % diversity amongst all the TCTV isolates and found evidence of recombination in the CP- and Rep-coding regions of the genomes.

  14. Genetic diversity and host range studies of turnip curly top virus.

    PubMed

    Razavinejad, Sara; Heydarnejad, Jahangir; Kamali, Mehdi; Massumi, Hossain; Kraberger, Simona; Varsani, Arvind

    2013-04-01

    Turnip curly top virus (TCTV) is a unique geminivirus that has recently been characterised as infecting turnips in Iran. The genome of TCTV shares <68 % pairwise identity with other geminiviruses and has a genome organisation similar to that of curtoviruses and topocuvirus. The replication-associated protein (Rep) bears the highest similarity to curtovirus Reps (48.5-69.0 %); however, in the case of the capsid protein (CP), the extent of similarity is only 39.5-44.5 %. We constructed an agroinfectious clone of TCTV and undertook host range studies on ten plant species; in three species (turnip, sugar beet and cowpea), we detected infection which presents curly top symptoms in turnip and sugar beet. The efficiency of TCTV infection in agroinoculated turnip plants was 71.7 %, and the infection was successfully transmitted to 80 % of the healthy turnip plants used in the insect transmission studies by Circulifer haematoceps under greenhouse conditions. We also determined the genome sequence of 14 new TCTV isolates from southern Iran isolated from turnips. We observed ~13 % diversity amongst all the TCTV isolates and found evidence of recombination in the CP- and Rep-coding regions of the genomes. PMID:23225113

  15. Genetic diversity, host range, and distribution of tomato yellow leaf curl virus in Iran.

    PubMed

    Shirazi, M; Mozafari, J; Rakhshandehroo, F; Shams-Bakhsh, M

    2014-01-01

    Tomato yellow leaf curl virus (TYLCV) is considered one of the most important tomato pathogens in tropical and subtropical regions including Iran. During the years 2007 to 2009, a total number of 510 symptomatic and asymptomatic vegetable, ornamental and weed samples were collected from fields and greenhouses in ten provinces of Iran. Symptoms included stunting, yellowing, leaf curl and flower senescence. PCR with specific primers showed TYLCV infection in 184 samples (36%) such as cucumber, pepper, tomato and several weeds from seven provinces. Based on the geographical origin, host range and symptoms, twenty three representative isolates were selected for phylogenetic analysis. An amplicon with a size about 608 base pair (bp) comprising partial sequence of the coat (CP) and movement protein (MP) coding regions of the viral genome was sequenced and compared with the corresponding selected sequences available in GenBank for Iran and worldwide. Phylogenetic analyses on the basis of the nucleotide sequences indicated two geographically separated clades. Isolates collected from Hormozgan, Khuzestan and Kerman provinces were grouped together with other Iranian isolates including TYLCV-Ir2, TYLCV-Kahnooj, and an isolate from Oman. It was also revealed that isolates collected from Boushehr, Fars, Tehran, and Isfahan placed close to the Iranian isolate TYLCV-Abadeh and isolates from Israel and Egypt. No correlation was found between the genetic variation and the host species, but selected Iranian isolates were grouped on the basis of the geographical origins. Results of this study indicated a high genetic diversity among Iranian TYLCV isolates. PMID:24957717

  16. Cross-Scale Analysis of the Region Effect on Vascular Plant Species Diversity in Southern and Northern European Mountain Ranges

    PubMed Central

    Lenoir, Jonathan; Gégout, Jean-Claude; Guisan, Antoine; Vittoz, Pascal; Wohlgemuth, Thomas; Zimmermann, Niklaus E.; Dullinger, Stefan; Pauli, Harald; Willner, Wolfgang; Grytnes, John-Arvid; Virtanen, Risto; Svenning, Jens-Christian

    2010-01-01

    Background The divergent glacial histories of southern and northern Europe affect present-day species diversity at coarse-grained scales in these two regions, but do these effects also penetrate to the more fine-grained scales of local communities? Methodology/Principal Findings We carried out a cross-scale analysis to address this question for vascular plants in two mountain regions, the Alps in southern Europe and the Scandes in northern Europe, using environmentally paired vegetation plots in the two regions (n = 403 in each region) to quantify four diversity components: (i) total number of species occurring in a region (total γ-diversity), (ii) number of species that could occur in a target plot after environmental filtering (habitat-specific γ-diversity), (iii) pair-wise species compositional turnover between plots (plot-to-plot β-diversity) and (iv) number of species present per plot (plot α-diversity). We found strong region effects on total γ-diversity, habitat-specific γ-diversity and plot-to-plot β-diversity, with a greater diversity in the Alps even towards distances smaller than 50 m between plots. In contrast, there was a slightly greater plot α-diversity in the Scandes, but with a tendency towards contrasting region effects on high and low soil-acidity plots. Conclusions/Significance We conclude that there are strong regional differences between coarse-grained (landscape- to regional-scale) diversity components of the flora in the Alps and the Scandes mountain ranges, but that these differences do not necessarily penetrate to the finest-grained (plot-scale) diversity component, at least not on acidic soils. Our findings are consistent with the contrasting regional Quaternary histories, but we also consider alternative explanatory models. Notably, ecological sorting and habitat connectivity may play a role in the unexpected limited or reversed region effect on plot α-diversity, and may also affect the larger-scale diversity components. For

  17. The differentially regulated genes TvQR1 and TvPirin of the parasitic plant Triphysaria exhibit distinctive natural allelic diversity

    PubMed Central

    2013-01-01

    evolved highly distinct roles for haustorium formation. Unlike TvPirin, TvQR1 might have been under diversifying selection to maintain a diverse collection of polymorphisms, which might be related to the recognition of an assortment of HIF and non-HIF quinones as substrates for successful haustorial establishment in a wide range of host plants. PMID:23419068

  18. Mitochondrial DNA genetic diversity and LCT-13910 and deltaF508 CFTR alleles typing in the medieval sample from Poland.

    PubMed

    Płoszaj, T; Jerszyńska, B; Jędrychowska-Dańska, K; Lewandowska, M; Kubiak, D; Grzywnowicz, K; Masłowska, A; Witas, H W

    2015-06-01

    We attempted to confirm the resemblance of a local medieval population and to reconstruct their contribution to the formation of the modern Polish population at the DNA level. The HVR I mtDNA sequence and two nuclear alleles, LCT-13910C/T SNP and deltaF508 CFTR, were chosen as markers since the distribution of selected nuclear alleles varies among ethnic groups. A total of 47 specimens were selected from a medieval cemetery in Cedynia (located in the western Polish lowland). Regarding the HVR I profile, the analyzed population differed from the present-day population (P = 0.045, F(st) = 0.0103), in contrast to lactase persistence (LP) based on the LCT-13910T allele, thus indicating the lack of notable frequency changes of this allele during the last millennium (P = 0.141). The sequence of the HVR I mtDNA fragment allowed to identify six major haplogroups including H, U5, T, K, and HV0 within the medieval population of Cedynia which are common in today's central Europe. An analysis of haplogroup frequency and its comparison with modern European populations shows that the studied medieval population is more closely related to Finno-Ugric populations than to the present Polish population. Identification of less common haplogroups, i.e., Z and U2, both atypical of the modern Polish population and of Asian origin, provides evidence for some kind of connections between the studied and foreign populations. Furthermore, a comparison of the available aDNA sequences from medieval Europe suggests that populations differed from one another and a number of data from other locations are required to find out more about the features of the medieval gene pool profile. PMID:25896719

  19. Mitochondrial DNA genetic diversity and LCT-13910 and deltaF508 CFTR alleles typing in the medieval sample from Poland.

    PubMed

    Płoszaj, T; Jerszyńska, B; Jędrychowska-Dańska, K; Lewandowska, M; Kubiak, D; Grzywnowicz, K; Masłowska, A; Witas, H W

    2015-06-01

    We attempted to confirm the resemblance of a local medieval population and to reconstruct their contribution to the formation of the modern Polish population at the DNA level. The HVR I mtDNA sequence and two nuclear alleles, LCT-13910C/T SNP and deltaF508 CFTR, were chosen as markers since the distribution of selected nuclear alleles varies among ethnic groups. A total of 47 specimens were selected from a medieval cemetery in Cedynia (located in the western Polish lowland). Regarding the HVR I profile, the analyzed population differed from the present-day population (P = 0.045, F(st) = 0.0103), in contrast to lactase persistence (LP) based on the LCT-13910T allele, thus indicating the lack of notable frequency changes of this allele during the last millennium (P = 0.141). The sequence of the HVR I mtDNA fragment allowed to identify six major haplogroups including H, U5, T, K, and HV0 within the medieval population of Cedynia which are common in today's central Europe. An analysis of haplogroup frequency and its comparison with modern European populations shows that the studied medieval population is more closely related to Finno-Ugric populations than to the present Polish population. Identification of less common haplogroups, i.e., Z and U2, both atypical of the modern Polish population and of Asian origin, provides evidence for some kind of connections between the studied and foreign populations. Furthermore, a comparison of the available aDNA sequences from medieval Europe suggests that populations differed from one another and a number of data from other locations are required to find out more about the features of the medieval gene pool profile.

  20. Allele and haplotype frequencies of HLA-A, B, C, DRB1 and DQB1 genes in polytransfused patients in ethnically diverse populations from Brazil.

    PubMed

    Rodrigues, C; Macedo, L C; Bruder, A V; Quintero, F d C; de Alencar, J B; Sell, A M; Visentainer, J E L

    2015-10-01

    The red blood transfusion is a practice often used in patients with haematological and oncological diseases. However, the investigation of human leucocyte antigen (HLA) system frequency in these individuals is of great importance because multiple transfusions may lead to HLA alloimmunization. Brazil is a country that was colonized by many other ethnicities, leading to a mixed ethnicity and regionalized population. In view of the importance of HLA typing in these patients, the aim of this study was to investigate the allele and haplotype frequencies from polytransfused patients from three different regions from Brazil. HLA-A, HLA-B, HLA-C, HLA-DRB1 and HLA-DQB1 genotyping of 366 patients was performed by PCR-SSO, based on the Luminex technology (One Lambda(®) ), and the anti-HLA class I and class II antibodies were analysed using LabScreen Single Antigen Antibody Detection (One Lambda, Inc.). Allele and haplotype frequencies of polytransfused patients of three regions from Brazil were obtained using the Arlequin program. The most frequent allele frequencies observed were HLA-A*02, A*03, B*15, B*35, B*51, C*07, C*04, C*03, DRB1*13, DRB1*11, DRB1*07, DRB1*03, DRB1*01, DQB1*03, DQB1*02, DQB1*06 and DQB1*05. There were differences between the groups for allele variants HLA-B*57 (between Group 1 and Group 2) and HLA-C*12 (between Group 1 and Group 3). The most frequent haplotypes found in the sample were HLA-A*01B*08DRB1*03, DRBI*07DQB1*02, DRB1*01DQB1*05, DRB1*13DQB1*06 and A*02B*35. HLA class I and II antibodies were detected in 77.9% and 63.9% patients, respectively, while the both alloantibodies were detected in 62 (50.9%) patients. In conclusion, the HLA typing for polytransfused patients in each region has a great importance, as seen in this study; individuals from different regions from Brazil have HLA distribution not completely homogeneous.

  1. Patterns of bacterial diversity across a range of Antarctic terrestrial habitats.

    PubMed

    Yergeau, Etienne; Newsham, Kevin K; Pearce, David A; Kowalchuk, George A

    2007-11-01

    Although soil-borne bacteria represent the world's greatest source of biological diversity, it is not well understood whether extreme environmental conditions, such as those found in Antarctic habitats, result in reduced soil-borne microbial diversity. To address this issue, patterns of bacterial diversity were studied in soils sampled along a > 3200 km southern polar transect spanning a gradient of increased climate severity over 27 degrees of latitude. Vegetated and fell-field plots were sampled at the Falkland (51 degrees S), South Georgia (54 degrees S), Signy (60 degrees S) and Anchorage Islands (67 degrees S), while bare frost-sorted soil polygons were examined at Fossil Bluff (71 degrees S), Mars Oasis (72 degrees S), Coal Nunatak (72 degrees S) and the Ellsworth Mountains (78 degrees S). Bacterial 16S rRNA gene sequences were recovered subsequent to direct DNA extraction from soil, polymerase chain reaction amplification and cloning. Although bacterial diversity was observed to decline with increased latitude, habitat-specific patterns appeared to also be important. Namely, a negative relationship was found between bacterial diversity and latitude for fell-field soils, but no such pattern was observed for vegetated sites. The Mars Oasis site, previously identified as a biodiversity hotspot within this region, proved exceptional within the study transect, with unusually high bacterial diversity. In independent analyses, geographical distance and vegetation cover were found to significantly influence bacterial community composition. These results provide insight into the factors shaping the composition of bacterial communities in Antarctic terrestrial habitats and support the notion that bacterial diversity declines with increased climatic severity.

  2. Patterns of bacterial diversity across a range of Antarctic terrestrial habitats.

    PubMed

    Yergeau, Etienne; Newsham, Kevin K; Pearce, David A; Kowalchuk, George A

    2007-11-01

    Although soil-borne bacteria represent the world's greatest source of biological diversity, it is not well understood whether extreme environmental conditions, such as those found in Antarctic habitats, result in reduced soil-borne microbial diversity. To address this issue, patterns of bacterial diversity were studied in soils sampled along a > 3200 km southern polar transect spanning a gradient of increased climate severity over 27 degrees of latitude. Vegetated and fell-field plots were sampled at the Falkland (51 degrees S), South Georgia (54 degrees S), Signy (60 degrees S) and Anchorage Islands (67 degrees S), while bare frost-sorted soil polygons were examined at Fossil Bluff (71 degrees S), Mars Oasis (72 degrees S), Coal Nunatak (72 degrees S) and the Ellsworth Mountains (78 degrees S). Bacterial 16S rRNA gene sequences were recovered subsequent to direct DNA extraction from soil, polymerase chain reaction amplification and cloning. Although bacterial diversity was observed to decline with increased latitude, habitat-specific patterns appeared to also be important. Namely, a negative relationship was found between bacterial diversity and latitude for fell-field soils, but no such pattern was observed for vegetated sites. The Mars Oasis site, previously identified as a biodiversity hotspot within this region, proved exceptional within the study transect, with unusually high bacterial diversity. In independent analyses, geographical distance and vegetation cover were found to significantly influence bacterial community composition. These results provide insight into the factors shaping the composition of bacterial communities in Antarctic terrestrial habitats and support the notion that bacterial diversity declines with increased climatic severity. PMID:17922752

  3. High prevalence and diversity of pre-CTXΦ alleles in the environmental Vibrio cholerae O1 and O139 strains in the Zhujiang River estuary.

    PubMed

    Wang, Duochun; Wang, Xiaomei; Li, Baisheng; Deng, Xiaoling; Tan, Hailing; Diao, Baowei; Chen, Jingdiao; Ke, Bixia; Zhong, Haojie; Zhou, Haijian; Ke, Changwen; Kan, Biao

    2014-06-01

    Toxigenic conversion of environmental Vibrio cholerae strains through lysogenic infection by the phage CTXΦ is an important step in the emergence of new pathogenic clones. The precursor form of the CTXΦ phage, pre-CTXΦ, does not carry the cholera toxin gene. During our investigation, we frequently found pre-CTXΦ prophages in non-toxigenic isolates in the serogroups of O1 and O139 strains in the Zhujiang estuary. We observed high amounts of sequence variation of rstR and gIII(CTX) in the pre-CTXΦ alleles as well as in the tcpA sequences within the strains. In addition, a new pre-CTXΦ allele, with a novel rstR sequence type and hybrid RS2, was identified. Our findings show that active, complicated gene recombination and horizontal transfer of pre-CTXΦs occurs within V. cholerae environmental strains, which creates a complex intermediate pool for the generation of toxigenic clones in the estuarine environment. PMID:24983529

  4. MHC class II diversity of koala (Phascolarctos cinereus) populations across their range.

    PubMed

    Lau, Q; Jaratlerdsiri, W; Griffith, J E; Gongora, J; Higgins, D P

    2014-10-01

    Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity.

  5. MHC class II diversity of koala (Phascolarctos cinereus) populations across their range

    PubMed Central

    Lau, Q; Jaratlerdsiri, W; Griffith, J E; Gongora, J; Higgins, D P

    2014-01-01

    Major histocompatibility complex class II (MHCII) genes code for proteins that bind and present antigenic peptides and trigger the adaptive immune response. We present a broad geographical study of MHCII DA β1 (DAB) and DB β1 (DBB) variants of the koala (Phascolarctos cinereus; n=191) from 12 populations across eastern Australia, with a total of 13 DAB and 7 DBB variants found. We identified greater MHCII variation and, possibly, additional gene copies in koala populations in the north (Queensland and New South Wales) relative to the south (Victoria), confirmed by STRUCTURE analyses and genetic differentiation using analysis of molecular variance. The higher MHCII diversity in the north relative to south could potentially be attributed to (i) significant founder effect in Victorian populations linked to historical translocation of bottlenecked koala populations and (ii) increased pathogen-driven balancing selection and/or local genetic drift in the north. Low MHCII genetic diversity in koalas from the south could reduce their potential response to disease, although the three DAB variants found in the south had substantial sequence divergence between variants. This study assessing MHCII diversity in the koala with historical translocations in some populations contributes to understanding the effects of population translocations on functional genetic diversity. PMID:24690756

  6. Contrasting Influences of Geographic Range and Distribution of Populations on Patterns of Genetic Diversity in Two Sympatric Pilbara Acacias

    PubMed Central

    Levy, E.; Byrne, M.; Coates, D. J.; Macdonald, B. M.; McArthur, S.; van Leeuwen, S.

    2016-01-01

    The influence of geographic range on species persistence has long been of interest and there is a need for a better understanding of the genetic consequences for species with restricted distributions, particularly with the increasing rate of global species extinctions. However, the genetic effects of restricted range are often confounded by the impacts of population distribution. We compared chloroplast and nuclear genetic diversity and differentiation in two acacias, the restricted, patchily distributed Acacia atkinsiana and the widespread, semi-continuously distributed A. ancistrocarpa. Lower intra-population diversity and higher differentiation between populations were seen in A. atkinsiana compared to its widespread congener, A. ancistrocarpa. There was little evidence of geographical influences on population genetic structure in A. ancistrocarpa whereas A. atkinsiana exhibited nuclear genetic structure with isolation by distance, differentiation of near-coastal populations from those in the ranges, and differentiation of peripheral populations from those in the centre of the distribution. These results are consistent with expectations of the effect of geographic range and population distribution on genetic diversity, but indicate that distribution of populations rather than geographic range has influenced the observed genetic structure. The contrasting patterns observed here demonstrate that conservation approaches for species management and ecological restoration need to consider the distribution of populations in geographically restricted species. PMID:27768703

  7. Selective pressure for allelic diversity in SeM of Streptococcus equi does not affect immunoreactive proteins SzPSe or Se18.9.

    PubMed

    Ijaz, Muhammad; Velineni, Sridhar; Timoney, John F

    2011-07-01

    Streptococcus equi, a clone or biovar of an ancestral Streptococcus zooepidemicus of Lancefield group C causes equine strangles, a highly contagious tonsillitis and lymphadenitis of the head and neck. At least 74 alleles based on N-terminal amino acid sequence of the anti-phagocytic SeM have been observed among isolates of S. equi from N. America, Europe and Japan. A d(N)/d(S) ratio of 5.93 for the 5' region of sem is indicative of positive selective pressure. The aim of this study was to determine whether variations in SeM were accompanied by variations in the surface exposed SzPSe and secreted Se18.9, both of which bind to equine tonsillar epithelium and, along with SeM, elicit strong nasopharyngeal IgA responses during convalescence. Sequences of genes for these proteins from 25 S. equi expressing 19 different SeM alleles isolated over 40 years in different countries were compared. No variation was observed in szpse, except for an Australian isolate with a deletion of a single repeat in the 3' end of the gene. Interestingly, only two SNP loci were detected in se18.9 compared to 93 and 55 in sem and szpse, respectively. The high frequency of nucleotide substitutions in szpse may be related to its mosaic structure since this gene in S. zooepidemicus exists in a variety of combinations of sequence segments and has a central hypervariable region that includes exogenous DNA sequence based on an atypical G-C percentage. In summary, the results of this study document very different responses of streptococcal genes for 3 immunoreactive proteins to selection pressure of the nasopharyngeal mucosal immune response.

  8. Silage Collected from Dairy Farms Harbors an Abundance of Listeriaphages with Considerable Host Range and Genome Size Diversity

    PubMed Central

    Vongkamjan, Kitiya; Switt, Andrea Moreno; den Bakker, Henk C.; Fortes, Esther D.

    2012-01-01

    Since the food-borne pathogen Listeria monocytogenes is common in dairy farm environments, it is likely that phages infecting this bacterium (“listeriaphages”) are abundant on dairy farms. To better understand the ecology and diversity of listeriaphages on dairy farms and to develop a diverse phage collection for further studies, silage samples collected on two dairy farms were screened for L. monocytogenes and listeriaphages. While only 4.5% of silage samples tested positive for L. monocytogenes, 47.8% of samples were positive for listeriaphages, containing up to >1.5 × 104 PFU/g. Host range characterization of the 114 phage isolates obtained, with a reference set of 13 L. monocytogenes strains representing the nine major serotypes and four lineages, revealed considerable host range diversity; phage isolates were classified into nine lysis groups. While one serotype 3c strain was not lysed by any phage isolates, serotype 4 strains were highly susceptible to phages and were lysed by 63.2 to 88.6% of phages tested. Overall, 12.3% of phage isolates showed a narrow host range (lysing 1 to 5 strains), while 28.9% of phages represented broad host range (lysing ≥11 strains). Genome sizes of the phage isolates were estimated to range from approximately 26 to 140 kb. The extensive host range and genomic diversity of phages observed here suggest an important role of phages in the ecology of L. monocytogenes on dairy farms. In addition, the phage collection developed here has the potential to facilitate further development of phage-based biocontrol strategies (e.g., in silage) and other phage-based tools. PMID:23042180

  9. Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae).

    PubMed

    Shirk, R Y; Hamrick, J L; Zhang, C; Qiang, S

    2014-05-01

    Genetic diversity, and thus the adaptive potential of invasive populations, is largely based on three factors: patterns of genetic diversity in the species' native range, the number and location of introductions and the number of founding individuals per introduction. Specifically, reductions in genetic diversity ('founder effects') should be stronger for species with low within-population diversity in their native range and few introductions of few individuals to the invasive range. We test these predictions with Geranium carolinianum, a winter annual herb native to North America and invasive in China. We measure the extent of founder effects using allozymes and microsatellites, and ask whether this is consistent with its colonization history and patterns of diversity in the native range. In the native range, genetic diversity is higher and structure is lower than expected based on life history traits. In China, our results provide evidence for multiple introductions near Nanjing, Jiangsu province, with subsequent range expansion to the west and south. Patterns of genetic diversity across China reveal weak founder effects that are driven largely by low-diversity populations at the expansion front, away from the introduction location. This suggests that reduced diversity in China has resulted from successive founder events during range expansion, and that the loss of genetic diversity in the Nanjing area was mitigated by multiple introductions from diverse source populations. This has implications for the future of G. carolinianum in China, as continued gene flow among populations should eventually increase genetic diversity within the more recently founded populations.

  10. Cryptic diversity among Western Palearctic tree frogs: postglacial range expansion, range limits, and secondary contacts of three European tree frog lineages (Hyla arborea group).

    PubMed

    Stöck, Matthias; Dufresnes, Christophe; Litvinchuk, Spartak N; Lymberakis, Petros; Biollay, Sébastien; Berroneau, Matthieu; Borzée, Amaël; Ghali, Karim; Ogielska, Maria; Perrin, Nicolas

    2012-10-01

    We characterize divergence times, intraspecific diversity and distributions for recently recognized lineages within the Hyla arborea species group, based on mitochondrial and nuclear sequences from 160 localities spanning its whole distribution. Lineages of H. arborea, H. orientalis, H. molleri have at least Pliocene age, supporting species level divergence. The genetically uniform Iberian H. molleri, although largely isolated by the Pyrenees, is parapatric to H. arborea, with evidence for successful hybridization in a small Aquitanian corridor (southwestern France), where the distribution also overlaps with H. meridionalis. The genetically uniform H. arborea, spread from Crete to Brittany, exhibits molecular signatures of a postglacial range expansion. It meets different mtDNA clades of H. orientalis in NE-Greece, along the Carpathians, and in Poland along the Vistula River (there including hybridization). The East-European H. orientalis is strongly structured genetically. Five geographic mitochondrial clades are recognized, with a molecular signature of postglacial range expansions for the clade that reached the most northern latitudes. Hybridization with H. savignyi is suggested in southwestern Turkey. Thus, cryptic diversity in these Pliocene Hyla lineages covers three extremes: a genetically poor, quasi-Iberian endemic (H. molleri), a more uniform species distributed from the Balkans to Western Europe (H. arborea), and a well-structured Asia Minor-Eastern European species (H. orientalis). PMID:22652054

  11. Genetic diversity and structuring across the range of a widely distributed ladybird: focus on rear-edge populations phenotypically divergent.

    PubMed

    Lecompte, Émilie; Bouanani, Mohand-Ameziane; Magro, Alexandra; Crouau-Roy, Brigitte

    2016-08-01

    Population genetics and phenotypic structures are often predicted to vary along the geographic range of a species. This phenomenon would be accentuated for species with large range areas, with discontinuities and marginal populations. We herein compare the genetic patterns of central populations of Coccinella septempunctata L. with those of two phenotypically differentiated populations considered as rear-edge populations and subspecies based on phenotype (Algeria and Japan). According to the central-marginal model and expected characteristics of rear-edge populations, we hypothesize that these rear-edge populations have (1) a reduced genetic diversity, resulting from their relative isolation over long periods of time, (2) a higher population genetic differentiation, explained by low contemporary gene flow levels, and (3) a relationship between genetic diversity characteristics and phenotypes, due to historical isolation and/or local adaptation. Based on genotyping of 28 populations for 18 microsatellite markers, several levels of regional genetic diversity and differentiation are observed between and within populations, according to their localization: low within-population genetic diversity and higher genetic differentiation of rear-edge populations. The genetic structuring clearly dissociates the Algerian and Eastern Asia populations from the others. Geographical patterns of genetic diversity and differentiation support the hypothesis of the central-marginal model. The pattern observed is in agreement with the phenotypic structure across species range. A clear genetic break between populations of Algeria, the Eastern Asia, and the remaining populations is a dominant feature of the data. Differential local adaptations, absence of gene flow between marginal and central populations, and/or incapacity to mate after colonization, have contributed to their distinct genotypic and phenotypic characteristics. PMID:27551401

  12. Adenovirus and Herpesvirus Diversity in Free-Ranging Great Apes in the Sangha Region of the Republic of Congo

    PubMed Central

    Seimon, Tracie A.; Olson, Sarah H.; Lee, Kerry Jo; Rosen, Gail; Ondzie, Alain; Cameron, Kenneth; Reed, Patricia; Anthony, Simon J.; Joly, Damien O.; McAloose, Denise; Lipkin, W. Ian

    2015-01-01

    Infectious diseases have caused die-offs in both free-ranging gorillas and chimpanzees. Understanding pathogen diversity and disease ecology is therefore critical for conserving these endangered animals. To determine viral diversity in free-ranging, non-habituated gorillas and chimpanzees in the Republic of Congo, genetic testing was performed on great-ape fecal samples collected near Odzala-Kokoua National Park. Samples were analyzed to determine ape species, identify individuals in the population, and to test for the presence of herpesviruses, adenoviruses, poxviruses, bocaviruses, flaviviruses, paramyxoviruses, coronaviruses, filoviruses, and simian immunodeficiency virus (SIV). We identified 19 DNA viruses representing two viral families, Herpesviridae and Adenoviridae, of which three herpesviruses had not been previously described. Co-detections of multiple herpesviruses and/or adenoviruses were present in both gorillas and chimpanzees. Cytomegalovirus (CMV) and lymphocryptovirus (LCV) were found primarily in the context of co-association with each other and adenoviruses. Using viral discovery curves for herpesviruses and adenoviruses, the total viral richness in the sample population of gorillas and chimpanzees was estimated to be a minimum of 23 viruses, corresponding to a detection rate of 83%. These findings represent the first description of DNA viral diversity in feces from free-ranging gorillas and chimpanzees in or near the Odzala-Kokoua National Park and form a basis for understanding the types of viruses circulating among great apes in this region. PMID:25781992

  13. Crop-weed interactions in the Beta vulgaris complex at a local scale: allelic diversity and gene flow within sugar beet fields.

    PubMed

    Viard, F.; Bernard, J.; Desplanque, B.

    2002-03-01

    Crop-wild hybrids and weed beets are the main source of agronomic concern for sugar beet production all over Europe. In order to understand the dynamics of crop-wild interactions and the evolution of weediness in Beta vulgaris, we investigated genetic features of bolting individuals occurring at a local scale, i.e. within two sugar beet fields of the French northern area of sugar beet production. By analysing ploidy level, mitochondrial DNA and microsatellite polymorphism, the genetic diversity and the genetic relationships among three different classes of individuals (variety, in-row and out-row weed-beets) from a given field were examined. Such genetic analyses provide a unique opportunity to obtain evidence for the weeds origin and the evolutionary hypotheses previously stated. All the individuals shared in common the Svulg mitochondrial haplotype, and thus a common maternal origin. Conversely, the large genetic diversity at microsatellite loci highlighted the large diversity of the pollinator plants (cultivated and wild plants) during the-seed production process, as well as during the further evolution of weed beets in the sugar production area.

  14. Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants.

    PubMed

    Moreau, Corrie S; Bell, Charles D

    2013-08-01

    Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a "museum" where older lineages persist through evolutionary time or as a "cradle" where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139-158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood-based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high-current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity.

  15. Molecular phylogeny reveals high diversity, geographic structure and limited ranges in neotenic net-winged beetles platerodrilus (coleoptera: lycidae).

    PubMed

    Masek, Michal; Palata, Vaclav; Bray, Timothy C; Bocak, Ladislav

    2014-01-01

    The neotenic Platerodrilus net-winged beetles have strongly modified development where females do not pupate and retain larval morphology when sexually mature. As a result, dispersal propensity of females is extremely low and the lineage can be used for reconstruction of ancient dispersal and vicariance patterns and identification of centres of diversity. We identified three deep lineages in Platerodrilus occurring predominantly in (1) Borneo and the Philippines, (2) continental Asia, and (3) Sumatra, the Malay Peninsula and Java. We document limited ranges of all species of Platerodrilus and complete species level turnover between the Sunda Islands and even between individual mountain regions in Sumatra. Few dispersal events were recovered among the major geographical regions despite long evolutionary history of occurrence; all of them were dated at the early phase of Platerodrilus diversification up to the end of Miocene and no exchange of island faunas was identified during the Pliocene and Pleistocene despite the frequently exposed Sunda Shelf as sea levels fluctuated with each glacial cycle. We observed high diversity in the regions with persisting humid tropical forests during cool periods. The origins of multiple species were inferred in Sumatra soon after the island emerged and the mountain range uplifted 15 million years ago with the speciation rate lower since then. We suppose that the extremely low dispersal propensity makes Platerodrilus a valuable indicator of uninterrupted persistence of rainforests over a long time span. Additionally, if the diversity of these neotenic lineages is to be protected, a high dense system of protected areas would be necessary.

  16. Long-range high-speed visible light communication system over 100-m outdoor transmission utilizing receiver diversity technology

    NASA Astrophysics Data System (ADS)

    Wang, Yiguang; Huang, Xingxing; Shi, Jianyang; Wang, Yuan-quan; Chi, Nan

    2016-05-01

    Visible light communication (VLC) has no doubt become a promising candidate for future wireless communications due to the increasing trends in the usage of light-emitting diodes (LEDs). In addition to indoor high-speed wireless access and positioning applications, VLC usage in outdoor scenarios, such as vehicle networks and intelligent transportation systems, are also attracting significant interest. However, the complex outdoor environment and ambient noise are the key challenges for long-range high-speed VLC outdoor applications. To improve system performance and transmission distance, we propose to use receiver diversity technology in an outdoor VLC system. Maximal ratio combining-based receiver diversity technology is utilized in two receivers to achieve the maximal signal-to-noise ratio. A 400-Mb/s VLC transmission using a phosphor-based white LED and a 1-Gb/s wavelength division multiplexing VLC transmission using a red-green-blue LED are both successfully achieved over a 100-m outdoor distance with the bit error rate below the 7% forward error correction limit of 3.8×10-3. To the best of our knowledge, this is the highest data rate at 100-m outdoor VLC transmission ever achieved. The experimental results clearly prove the benefit and feasibility of receiver diversity technology for long-range high-speed outdoor VLC systems.

  17. Enumeration and diversity of campylobacters and bacteriophages isolated during the rearing cycles of free-range and organic chickens.

    PubMed

    El-Shibiny, A; Connerton, P L; Connerton, I F

    2005-03-01

    Campylobacters and Campylobacter-specific bacteriophages were isolated and enumerated during the rearing cycle of free-range (56 days) and organic chickens (73 days) at 3-day intervals from hatching until slaughter. In both flocks Campylobacter jejuni was the initial colonizer but Campylobacter coli was detected more frequently from 5 weeks of age. The diversity of the Campylobacter isolates was examined by pulsed-field gel electrophoresis of SmaI-digested genomic DNA and antimicrobial resistance typing. Bacteriophages were isolated from 51% (19 of 37 birds) of Campylobacter-positive organic birds (log10 2.5 to log10 5.7 PFU/g of cecal contents). The bacteriophages were all typical group III Campylobacter bacteriophages in terms of genomic size but could be characterized in terms of their host range and placed into five different groups. In contrast to the organic birds, anti-Campylobacter activity (bacteriocin-like) was observed in 26% (10 of 38 birds) of Campylobacter-positive free-range birds, and only one bacteriophage was isolated. Appearance of either bacteriophages or anti-Campylobacter activity was associated with changes in the levels of colonization and the predominant genotypes and species isolated. The frequency and potential influence of naturally occurring bacteriophages and/or inhibitory substances on the diversity and fluctuations of populations of campylobacters have not previously been reported in either free-range or organic chickens.

  18. Genetic diversity and differentiation in a wide ranging anadromous fish, American shad (Alosa sapidissima), is correlated with latitude.

    PubMed

    Hasselman, Daniel J; Ricard, Daniel; Bentzen, Paul

    2013-03-01

    Studies that span entire species ranges can provide insight into the relative roles of historical contingency and contemporary factors that influence population structure and can reveal patterns of genetic variation that might otherwise go undetected. American shad is a wide ranging anadromous clupeid fish that exhibits variation in demographic histories and reproductive strategies (both semelparity and iteroparity) and provides a unique perspective on the evolutionary processes that govern the genetic architecture of anadromous fishes. Using 13 microsatellite loci, we examined the magnitude and spatial distribution of genetic variation among 33 populations across the species' range to (i) determine whether signals of historical demography persist among contemporary populations and (ii) assess the effect of different reproductive strategies on population structure. Patterns of genetic diversity and differentiation among populations varied widely and reflect the differential influences of historical demography, microevolutionary processes and anthropogenic factors across the species' range. Sequential reductions of diversity with latitude among formerly glaciated rivers are consistent with stepwise postglacial colonization and successive population founder events. Weak differentiation among U.S. iteroparous populations may be a consequence of human-mediated gene flow, while weak differentiation among semelparous populations probably reflects natural gene flow. Evidence for an effect of reproductive strategy on population structure suggests an important role for environmental variation and suggests that the factors that are responsible for shaping American shad life history patterns may also influence population genetic structure.

  19. Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment.

    PubMed

    Rowe, Will; Verner-Jeffreys, David W; Baker-Austin, Craig; Ryan, Jim J; Maskell, Duncan J; Pearce, Gareth P

    2016-01-01

    The aquatic environment has been implicated as a reservoir for antimicrobial resistance genes (ARGs). In order to identify sources that are contributing to these gene reservoirs, it is crucial to assess effluents that are entering the aquatic environment. Here we describe a metagenomic assessment for two types of effluent entering a river catchment. We investigated the diversity and abundance of resistance genes, mobile genetic elements (MGEs) and pathogenic bacteria. Findings were normalised to a background sample of river source water. Our results show that effluent contributed an array of genes to the river catchment, the most abundant being tetracycline resistance genes tetC and tetW from farm effluents and the sulfonamide resistance gene sul2 from wastewater treatment plant (WWTP) effluents. In nine separate samples taken across 3 years, we found 53 different genes conferring resistance to seven classes of antimicrobial. Compared to the background sample taken up river from effluent entry, the average abundance of genes was three times greater in the farm effluent and two times greater in the WWTP effluent. We conclude that effluents disperse ARGs, MGEs and pathogenic bacteria within a river catchment, thereby contributing to environmental reservoirs of ARGs.

  20. Allele mining across DREB1A and DREB1B in diverse rice genotypes suggest a highly conserved pathway inducible by low temperature.

    PubMed

    Challam, Clarissa; Ghosh, Tapu; Rai, Mayank; Tyagi, Wricha

    2015-06-01

    Low temperature stress is one of the major limiting factors affecting rice productivity in higher altitudes. DREB1A and DREB1B, are two transcription factors that have been reported to play key regulatory role in low temperature tolerance. In order to understand whether natural genetic variation in these two loci leads to cold tolerance or susceptibility, OsDREB1A and OsDREB1B were targeted across several rice genotypes showing differential response to low temperature. Expression data suggests induction of gene expression in shoots in response to low temperature in both tolerant and susceptible genotypes. Upon sequence analysis of 20 rice genotypes, eight nucleotide changes were identified including two in the coding region and six in the 5'UTR. None of the discovered novel variations lie in the conserved region of the genes under study, thereby causing little or no changes in putative function of the corresponding proteins. In silico analysis using a diverse set of 400 O. sativa revealed much lower nucleotide diversity estimates across two DREB loci and one other gene (MYB2) involved in DREB pathway than those observed for other rice genes. None of the changes showed association with seedling stage cold tolerance, suggesting that nucleotide changes in DREB loci are unlikely to contribute to low temperature tolerance. So far, data concerning the physiological role and regulation of DREB1 in different genetic background are very limited; it is to be expected that they will be studied extensively in the near future. PMID:26174670

  1. Nature reserves: Do they capture the full range of America's biological diversity?

    USGS Publications Warehouse

    Scott, J.M.; Davis, Frank W.; McGhie, R.G.; Wright, R.G.; Groves, C.; Estes, James

    2001-01-01

    Less than 6% of the coterminous United States is in nature reserves. Assessment of the occurrence of nature reserves across ranges of elevation and soil productivity classes indicates that nature reserves are most frequently found at higher elevations and on less productive soils. The distribution of plants and animals suggests that the greatest number of species is found at lower elevations. A preliminary assessment of the occurrence of mapped land cover types indicates that ???60% of mapped cover types have <10% of their area in nature reserves Land ownership patterns show that areas of lower elevation and more productive soils are most often privately owned and already extensively converted to urban and agricultural uses. Thus any effort to establish a system of nature reserves that captures the full geographical and ecological range of cover types and species must fully engage the private sector.

  2. Foliar phosphite application has minor phytotoxic impacts across a diverse range of conifers and woody angiosperms.

    PubMed

    Scott, Peter; Bader, Martin Karl-Friedrich; Williams, Nari Michelle

    2016-10-01

    Phytophthora plant pathogens cause tremendous damage in planted and natural systems worldwide. Phosphite is one of the only effective chemicals to control broad-scale Phytophthora disease. Little work has been done on the phytotoxic effects of phosphite application on plant communities especially in combination with plant physiological impacts. Here, we tested the phytotoxic impact of phosphite applied as foliar spray at 0, 12, 24 and 48 kg a.i. ha(-1) . Eighteen-month-old saplings of 13 conifer and angiosperm species native to New Zealand, and two exotic coniferous species were treated and the development of necrotic tissue and chlorophyll-a-fluorescence parameters (optimal quantum yield, Fv /Fm ; effective quantum yield of photosystem II, ΦPSII ) were assessed. In addition, stomatal conductance (gs ) was measured on a subset of six species. Significant necrosis assessed by digital image analysis occurred in only three species: in the lauraceous canopy tree Beilschmiedia tawa (8-14%) and the understory shrub Dodonaea viscosa (5-7%) across phosphite concentrations and solely at the highest concentration in the myrtaceous pioneer shrub Leptospermum scoparium (66%). In non-necrotic tissue, Fv /Fm , ΦPSII and gs remained unaffected by the phosphite treatment. Overall, our findings suggest minor phytotoxic effects resulting from foliar phosphite application across diverse taxa and regardless of concentration. This study supports the large-scale use of phosphite as a management tool to control plant diseases caused by Phytophthora pathogens in plantations and natural ecosystems. Long-term studies are required to ascertain potential ecological impacts of repeated phosphite applications. PMID:26968132

  3. Methicillin resistance gene diversity in staphylococci isolated from captive and free-ranging wallabies

    PubMed Central

    Chen, Michelle M. S.; Boardman, Wayne S. J.; Brown, Melissa H.

    2016-01-01

    Background Infection with methicillin-resistant staphylococci (MRS) can be life-threatening in humans and its presence in animals is a cause for public health concern. The aim of this study was to measure the prevalence of MRS in captive and free-ranging wallabies over a 16-month period in South Australia, Australia. Materials and methods Eighty-nine purified staphylococcal isolates recovered from 98 captive and free-ranging wallabies' anterior nasal swabs were used in this study. All isolates were tested for the presence of the mecA, mecA1, and mecC genes. Multiplex PCR-directed SCCmec-typing, ccrB-typing, and determination of the minimal inhibitory concentration of oxacillin were performed on mec-positive isolates. Results and discussion In total, 11 non-Staphylococcus aureus MRS were isolated from 7 out of 98 animals, corresponding to a 7.1% carriage rate. The SCCmec types I, III, and V were identified by multiplex PCR and sequencing of the ccrB gene. This is the first report of MRS carriage in both captive and free-ranging wallabies in Australia. These data demonstrate a low prevalence of MRS and no association between wallaby captivity status and MRS carriage could be assigned. These animals may act as a reservoir for the exchange of genetic elements between staphylococci. Furthermore, the mecA genes of animal isolates were identical to that found in human MRS strains and thus the possibility of zoonotic transfer must be considered. PMID:27193419

  4. Extensive genetic diversity and endemism across the global range of the oceanic copepod Pleuromamma abdominalis

    NASA Astrophysics Data System (ADS)

    Hirai, Junya; Tsuda, Atsushi; Goetze, Erica

    2015-11-01

    Many oceanic zooplankton species have been described as cosmopolitan in distribution; however, recent molecular work has detected species complexity with highly divergent genetic lineages within several of these taxa. To further resolve the species complexity within these ecologically-important and widespread species, we performed both molecular and morphological analyses of the oceanic copepod Pleuromamma abdominalis using a comprehensive collection of material from 944 individuals collected at 46 sites across the global ocean. Phylogenetic analyses of mitochondrial cytochrome oxidase subunit I (mtCOI) sequences detected eighteen divergent evolutionary lineages within P. abdominalis, with an additional four singleton specimens that were also genetically divergent. Two phylogenetically distinct groups, PLAB1 and PLAB2, were supported by concordant sequence variation in the nuclear large subunit ribosomal RNA gene (nLSU). Within PLAB1, two mtCOI clades, 1a-1 and 1b-1 were observed, and each clade contained geographically distinct sub-clades 1a-2 and 1b-2. PLAB2 was composed of sixteen well-supported mtCOI clades (2a-2p) as well as four singletons. High genetic divergence among the mtCOI lineages within both PLAB1 and PLAB2, ranging between 9.2-11.2% and 4.3-18.9% K2P distances respectively, suggests the presence of additional species within these groups. Significant differences were observed in the presence and shape of antennule spines of adult females between sympatric clades with genetic distances greater than 5.7-7.0% (K2P). The biogeographic distributions of mtCOI clades indicated greater specialization to particular oceanographic provinces than observed in the nominal species P. abdominalis, with mtCOI clades ranging from antitropical in subtropical waters of all three ocean basins (Atlantic, Pacific and Indian; clade 1b-1 and 2a) to taxa that are endemic to a particular ocean region, for example restricted to equatorial waters of the Atlantic Ocean (clade 1b

  5. Broad-host-range plasmids from agricultural soils have IncP-1 backbones with diverse accessory genes.

    PubMed

    Sen, Diya; Van der Auwera, Geraldine A; Rogers, Linda M; Thomas, Christopher M; Brown, Celeste J; Top, Eva M

    2011-11-01

    Broad-host-range plasmids are known to spread genes between distinct phylogenetic groups of bacteria. These genes often code for resistances to antibiotics and heavy metals or degradation of pollutants. Although some broad-host-range plasmids have been extensively studied, their evolutionary history and genetic diversity remain largely unknown. The goal of this study was to analyze and compare the genomes of 12 broad-host-range plasmids that were previously isolated from Norwegian soils by exogenous plasmid isolation and that encode mercury resistance. Complete nucleotide sequencing followed by phylogenetic analyses based on the relaxase gene traI showed that all the plasmids belong to one of two subgroups (β and ε) of the well-studied incompatibility group IncP-1. A diverse array of accessory genes was found to be involved in resistance to antimicrobials (streptomycin, spectinomycin, and sulfonamides), degradation of herbicides (2,4-dichlorophenoxyacetic acid and 2,4-dichlorophenoxypropionic acid), and a putative new catabolic pathway. Intramolecular transposition of insertion sequences followed by deletion was found to contribute to the diversity of some of these plasmids. The previous observation that the insertion sites of a Tn501-related element are identical in four IncP-1β plasmids (pJP4, pB10, R906, and R772) was further extended to three more IncP-1β plasmids (pAKD15, pAKD18, and pAKD29). We proposed a hypothesis for the evolution of these Tn501-bearing IncP-1β plasmids that predicts recent diversification followed by worldwide spread. Our study increases the available collection of complete IncP-1 plasmid genome sequences by 50% and will aid future studies to enhance our understanding of the evolution and function of this important plasmid family.

  6. Triatoma dimidiata (Latreille, 1811): a review of its diversity across its geographic range and the relationship among populations.

    PubMed

    Dorn, Patricia L; Monroy, Carlota; Curtis, Andrew

    2007-03-01

    Due to its vast diversity the Chagas vector, Triatoma dimidiata, has been merged and split into species and subspecies since its first description in 1811. Across its geographic range from Southern Mexico to Northern Peru populations differ in their biology and ethology in many ways including those that directly affect vector capacity and competence. Recent phenetic and genetic data suggest that T. dimidiata can be divided into at least three clades and in fact may be a polytypic species or species complex. To effectively target this vector, it will be necessary to clearly understand how "T. dimidiata" is genetically partitioned both at the taxonomic and population level.

  7. Evidence of rapid change in genetic structure and diversity during range expansion in a recovering large terrestrial carnivore

    PubMed Central

    Hagen, Snorre B.; Kopatz, Alexander; Aspi, Jouni; Kojola, Ilpo; Eiken, Hans Geir

    2015-01-01

    Recovery of natural populations occurs often with simultaneous or subsequent range expansions. According to population genetic theory, genetic structuring emerges at the expansion front together with decreasing genetic diversity, owing to multiple founder events. Thereupon, as the expansion proceeds and connectivity among populations is established, homogenization and a resurgence of genetic diversity are to be expected. Few studies have used a fine temporal scale combined with genetic sampling to track range expansions as they proceed in wild animal populations. As a natural experiment, the historical eradication of large terrestrial carnivores followed by their recovery and recolonization may facilitate empirical tests of these ideas. Here, using brown bear (Ursus arctos) as model species, we tested predictions from genetic theory of range expansion. Individuals from all over Finland were genotyped for every year between 1996 and 2010 using 12 validated autosomal microsatellite markers. A latitudinal shift of about 110 km was observed in the distribution and delineation of genetic clusters during this period. As the range expansion proceeded, we found, as theory predicts, that the degree of genetic structure decreased, and that both genetic variation and admixture increased. The genetic consequences of range expansions may first be detected after multiple generations, but we found major changes in genetic composition after just 1.5 generations, accompanied by population growth and increased migration. These rapid genetic changes suggest an ongoing concerted action of geographical and demographic expansion combined with substantial immigration of bears from Russia during the recovery of brown bears within the large ecosystem of northern Europe. PMID:25904665

  8. European Invasion of North American Pinus strobus at Large and Fine Scales: High Genetic Diversity and Fine-Scale Genetic Clustering over Time in the Adventive Range

    PubMed Central

    Mandák, Bohumil; Hadincová, Věroslava; Mahelka, Václav; Wildová, Radka

    2013-01-01

    Background North American Pinus strobus is a highly invasive tree species in Central Europe. Using ten polymorphic microsatellite loci we compared various aspects of the large-scale genetic diversity of individuals from 30 sites in the native distribution range with those from 30 sites in the European adventive distribution range. To investigate the ascertained pattern of genetic diversity of this intercontinental comparison further, we surveyed fine-scale genetic diversity patterns and changes over time within four highly invasive populations in the adventive range. Results Our data show that at the large scale the genetic diversity found within the relatively small adventive range in Central Europe, surprisingly, equals the diversity found within the sampled area in the native range, which is about thirty times larger. Bayesian assignment grouped individuals into two genetic clusters separating North American native populations from the European, non-native populations, without any strong genetic structure shown over either range. In the case of the fine scale, our comparison of genetic diversity parameters among the localities and age classes yielded no evidence of genetic diversity increase over time. We found that SGS differed across age classes within the populations under study. Old trees in general completely lacked any SGS, which increased over time and reached its maximum in the sapling stage. Conclusions Based on (1) the absence of difference in genetic diversity between the native and adventive ranges, together with the lack of structure in the native range, and (2) the lack of any evidence of any temporal increase in genetic diversity at four highly invasive populations in the adventive range, we conclude that population amalgamation probably first happened in the native range, prior to introduction. In such case, there would have been no need for multiple introductions from previously isolated populations, but only several introductions from

  9. Bacterial Physiological Diversity in the Rhizosphere of Range Plants in Response to Retorted Shale Stress

    PubMed Central

    Metzger, W. C.; Klein, D. A.; Redente, E. F.

    1986-01-01

    Bacterial populations were isolated from the soil-root interface and root-free regions of Agropyron smithii Rydb. and Atriplex canescens (Pursh) Nutt. grown in soil, retorted shale, or soil over shale. Bacteria isolated from retorted shale exhibited a wider range of tolerance to alkalinity and salinity and decreased growth on amino acid substrates compared with bacteria from soil and soil-over-shale environments. Exoenzyme production was only slightly affected by growth medium treatment. Viable bacterial populations were higher in the rhizosphere and rhizoplane of plants grown in retorted shale than in plants grown in soil or soil over shale. In addition, a greater number of physiological groups of rhizosphere bacteria was observed in retorted shale compared with soil alone. Two patterns of community similarity were observed in comparisons of bacteria from soil over shale with those from soil and retorted-shale environments. Root-associated populations from soil over shale had a higher proportion of physiological groups in common with those from the soil control than with those from the retorted-shale treatment. However, in non-rhizosphere populations, bacterial groups from soil over shale more closely resembled the physiological groups from retorted shale. PMID:16347169

  10. Sandfly-borne phleboviruses of Eurasia and Africa: epidemiology, genetic diversity, geographic range, control measures.

    PubMed

    Alkan, Cigdem; Bichaud, Laurence; de Lamballerie, Xavier; Alten, Bulent; Gould, Ernest A; Charrel, Rémi N

    2013-10-01

    Sandfly-borne phleboviruses may cause a transient febrile illness (sandfly fever) or more severe neuroinvasive disease. In the Old World, they are vectored by phlebotomine flies, which are widely distributed in the Mediterranean basin, North Africa, the Indian subcontinent, the Middle East and central Asia. High seroprevalence rates have been recorded in humans and domestic animals in areas where sandflies are present. Most published studies have focused on phlebovirus infections of travelers and of soldiers stationed in endemic areas, but the health impact on local populations should not be underestimated, as seroprevalence studies indicate massive circulation of these viruses, even if disease is seldom documented. Except for Toscana virus, which shows a marked neurotropism and is a leading cause of aseptic meningitis in endemic regions, phlebovirus infections are inadequately considered by physicians and are generally underestimated. However, several properties of these viruses suggest that they will extend their geographic range. First, changes in the areas occupied by sandflies as a result of climate change have a direct impact on the epidemiology of associated human and animal diseases. Second, phleboviruses exhibit a high mutation rate, and their tri-segmented genome is prone to reassortment and recombination. Third, distinct virus strains can be transmitted by the same arthropod species. Recent studies have documented the distribution of sandfly-borne phleboviruses in Western Europe, but data for Eastern Europe, the Middle East and Africa are very limited. With the goal of filling knowledge gaps and planning new research programs, we have examined available information and present it as a comprehensive review, with a specific focus on understudied regions. We also discuss the need to conduct studies aimed at developing new antiviral drugs and vaccines.

  11. Diverse sources for igneous blocks in Franciscan melanges, California Coast Ranges

    SciTech Connect

    MacPherson, G.J. ); Phipps, S.P. ); Grossman, J.N. )

    1990-11-01

    Igneous blocks in Franciscan melanges are of three chemical-petrologic types: (1) tholeiitic basalts of both arc and spreading center origin, with depletions in light relative to heavy rare-earth elements, 3% > TiO{sub 2} > 1%, high Y/Zr and Y/Ti ratios, and relict augites that generally have low Al and Ti and well-defined iron-enrichment trends; (2) basalts of probable seamount origin with marked enrichments in light relative to heavy rare-earth elements, 5% > TiO{sub 2} > 1%, lower Y/Zr and Y/Ti than (1), and Ti-Al-rich augites showing little if any iron-enrichment trends; and (3) hypabyssal intrusives having SiO{sub 2} > 52%, TiO{sub 2} < 1%, flat or only slightly fractionated rare-earth-abundance patterns, and diopsidic augites that are very low in Ti and Al and show no iron-enrichment trends. All of the blocks are metamorphosed; most are undeformed pumpellyite-bearing greenstones, and a few contain sodic amphibole {plus minus} lawsonite {plus minus} sodic pyroxene. The melanges are probably olistostromal in origin, deriving their igneous block detritus both from the downgoing Pacific plate (ocean floor basalts and seamounts) and from the hanging wall of the Franciscan trench (basalts and arc-related silic intrusive rocks). The silicic intrusive rocks and some of the basalts are eroded fragments of the fore-arc crust that ultimately become the Coast Range Ophiolite. These fragments were incorporated into the Franciscan trench fill and subducted. Results suggest that the igneous blocks in ophiolitic melanges provide important information about melange formation and about the tectonics and paleogeography of the regions in which the melanges are found.

  12. Ecology and genetic diversity of the dense-flowered orchid, Neotinea maculata, at the centre and edge of its range

    PubMed Central

    Duffy, Karl J.; Scopece, Giovanni; Cozzolino, Salvatore; Fay, Michael F.; Smith, Rhian J.; Stout, Jane C.

    2009-01-01

    Background and Aims Species may occur over a wide geographical range within which populations can display large variation in reproductive success and genetic diversity. Neotinea maculata is a rare orchid of conservation concern at the edge of its range in Ireland, where it occurs in small populations. However, it is relatively common throughout the Mediterranean region. Here, factors that affect rarity of N. maculata in Ireland are investigated by comparing Irish populations with those found in Italy, where it is more common. Methods Vegetation communities, breeding system and genetic diversity were compared using three amplified fragment length polymorphism (AFLP) primer pairs in populations in Ireland and Italy. Vegetation was quantified using quadrats taken along transects in study populations, and hand pollination experiments were performed to assess reliance of N. maculata on pollinators in both Irish and Italian populations. Key Results Neotinea maculata occupies different vegetation communities in Italian and Irish populations. Breeding system experiments show that N. maculata is 100 % autogamous, and there are no differences in fruit and seed production in selfed, outcrossed and unmanipulated plants. AFLP markers revealed that Irish and Italian populations have similar genetic diversity and are distinct from each other. Conclusions Neotinea maculata does not suffer any negative effects of autogamous reproduction; it self-pollinates and sets seed readily in the absence of pollinators. It occupies a variety of habitats in both Ireland and Italy; however, Irish populations are small and rare and should be conserved. This could be due to climatic factors and the absence of suitable soil mycorrhizas to allow recruitment from seed. PMID:18940852

  13. Genetic structure at range edge: low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations.

    PubMed

    Arnaud-Haond, S; Teixeira, S; Massa, S I; Billot, C; Saenger, P; Coupland, G; Duarte, C M; Serrão, E A

    2006-10-01

    Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species' distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes. PMID:17032254

  14. Nucleotide variation and identification of novel blast resistance alleles of Pib by allele mining strategy.

    PubMed

    Ramkumar, G; Madhav, M S; Devi, S J S Rama; Prasad, M S; Babu, V Ravindra

    2015-04-01

    Pib is one of significant rice blast resistant genes, which provides resistance to wide range of isolates of rice blast pathogen, Magnaporthe oryzae. Identification and isolation of novel and beneficial alleles help in crop enhancement. Allele mining is one of the best strategies for dissecting the allelic variations at candidate gene and identification of novel alleles. Hence, in the present study, Pib was analyzed by allele mining strategy, and coding and non-coding (upstream and intron) regions were examined to identify novel Pib alleles. Allelic sequences comparison revealed that nucleotide polymorphisms at coding regions affected the amino acid sequences, while the polymorphism at upstream (non-coding) region affected the motifs arrangements. Pib alleles from resistant landraces, Sercher and Krengosa showed better resistance than Pib donor variety, might be due to acquired mutations, especially at LRR region. The evolutionary distance, Ka/Ks and phylogenetic analyzes also supported these results. Transcription factor binding motif analysis revealed that Pib (Sr) had a unique motif (DPBFCOREDCDC3), while five different motifs differentiated the resistance and susceptible Pib alleles. As the Pib is an inducible gene, the identified differential motifs helps to understand the Pib expression mechanism. The identified novel Pib resistant alleles, which showed high resistance to the rice blast, can be used directly in blast resistance breeding program as alternative Pib resistant sources.

  15. Microstrip Antennas with Polarization Diversity across a Wide Frequency Range and Phased Array Antennas for Radar and Satellite Communications

    NASA Astrophysics Data System (ADS)

    Ho, Kevin Ming-Jiang

    The thesis comprises of 3 projects; an L-band microstrip antenna with frequency agility and polarization diversity, X-band phased array antennas incorporating commercially packaged RFIC phased array chips, and studies for Ku/Ka-band shared aperture antenna array. The first project features the use of commercially packaged RF-MEMS SPDT switches, that boasts of high reliability, high linearity, low losses, hermetically packaged and fully compatible for SMTA processes for mass-assembly and production. Using the switches in a novel manner for the feed network, microstrip antennas with polarization diversity are presented. Frequency agility is achieved with the use of tuning diodes to provide capacitive loading to the antenna element. Additional inductance effects from surface-mounted capacitors, and its impact, is introduced. Theoretical cross-polarization of probe-fed antenna elements is presented for both linear and circular polarized microstrip antennas. Designs and measurements are presented, for microstrip antennas with polarization diversity, wide frequency tuning range, and both features. Replacement of the tuning diodes with commercially-packaged high Q RF MEMS tunable capacitors will allow for significant improvements to the radiation efficiency. In another project, multi-channel CMOS RFIC phased-array receiver chips are assembled in QFN packages and directly integrated on the same multi-layered PCB stack-up with the antenna arrays. Problems of isolation from the PCB-QFN interface, and potential performance degradation on antenna array from the use of commercial-grade laminates for assembly requirements, namely potential scan blindness and radiation efficiency, are presented. Causes for apparent drift of dielectric constant for microstrip circuits, and high conductor losses observed in measurements, are introduced. Finally, studies are performed for the design of a Ku/Ka-Band shared aperture array. Different approaches for developing dual-band shared apertures

  16. Firing Range Soils Yield a Diverse Array of Fungal Isolates Capable of Organic Acid Production and Pb Mineral Solubilization

    PubMed Central

    Sullivan, Tarah S.; Gottel, Neil R.; Basta, Nicholas; Jardine, Philip M.

    2012-01-01

    Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil−1. We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter−1 (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health. PMID:22729539

  17. The Role of the Jasmonate Response in Plant Susceptibility to Diverse Pathogens with a Range of Lifestyles1[w

    PubMed Central

    Thaler, Jennifer S.; Owen, Blythe; Higgins, Verna J.

    2004-01-01

    Plants defend themselves against attack from insects and pathogens with various resistance strategies. The jasmonate and salicylate signaling pathways are two induced responses that protect plants against these attackers. Knowledge of the range of organisms that are affected by each response is important for understanding how plants coordinate their defenses against multiple attackers and the generality of effect of different resistance mechanisms. The jasmonate response is known to protect plants against a wide range of insect herbivores; in this study, we examined the role of the jasmonate response in susceptibility to eight pathogens with diverse lifestyles in the laboratory and field. Recent biochemical models suggest that the lifestyle of the pathogen (necrotroph versus biotroph) should predict whether the jasmonate response will be involved in resistance. We tested this by examining the susceptibility of wild-type (cv Castlemart with no known genes for resistance to the pathogens used) and jasmonate-deficient mutant tomato (Lycopersicon esculentum) plants (def1) and by employing rescue treatments of the mutant. Plant susceptibility to five of the eight pathogens we examined was reduced by the jasmonate response, including two bacteria (Pseudomonas syringae and Xanthomonas campestris), two fungi (Verticillium dahliae and Fusarium oxysporum f. sp. lycopersici), and an oomycete (Phytophthora infestans). Susceptibility to three fungi was unaffected (Cladosporium fulvum, Oidium neolycopersici, and Septoria lycopersici). Our results indicate that the jasmonate response reduces damage by a wide range of pathogens from different lifestyles, a result that contrasts with the emerging picture of diseases on Arabidopsis. Thus, the generality of jasmonate-based resistance of tomato challenges the view that ecologically distinct plant parasites are resisted via different mechanisms. PMID:15133157

  18. Firing range soils yield a diverse array of fungal isolates capable of organic acid production and Pb mineral solubilization.

    PubMed

    Sullivan, Tarah S; Gottel, Neil R; Basta, Nicholas; Jardine, Philip M; Schadt, Christopher W

    2012-09-01

    Anthropogenic sources of lead contamination in soils include mining and smelting activities, effluents and wastes, agricultural pesticides, domestic garbage dumps, and shooting ranges. While Pb is typically considered relatively insoluble in the soil environment, some fungi may potentially contribute to mobilization of heavy metal cations by means of secretion of low-molecular-weight organic acids (LMWOAs). We sought to better understand the potential for metal mobilization within an indigenous fungal community at an abandoned shooting range in Oak Ridge, TN, where soil Pb contamination levels ranged from 24 to >2,700 mg Pb kg dry soil(-1). We utilized culture-based assays to determine organic acid secretion and Pb-carbonate dissolution of a diverse collection of soil fungal isolates derived from the site and verified isolate distribution patterns within the community by 28S rRNA gene analysis of whole soils. The fungal isolates examined included both ascomycetes and basidiomycetes that excreted high levels (up to 27 mM) of a mixture of LMWOAs, including oxalic and citric acids, and several isolates demonstrated a marked ability to dissolve Pb-carbonate at high concentrations up to 10.5 g liter(-1) (18.5 mM) in laboratory assays. Fungi within the indigenous community of these highly Pb-contaminated soils are capable of LMWOA secretion at levels greater than those of well-studied model organisms, such as Aspergillus niger. Additionally, these organisms were found in high relative abundance (>1%) in some of the most heavily contaminated soils. Our data highlight the need to understand more about autochthonous fungal communities at Pb-contaminated sites and how they may impact Pb biogeochemistry, solubility, and bioavailability, thus consequently potentially impacting human and ecosystem health.

  19. Assessing potential modifications to the activated sludge process to improve simultaneous removal of a diverse range of micropollutants.

    PubMed

    Petrie, Bruce; McAdam, Ewan J; Lester, John N; Cartmell, Elise

    2014-10-01

    It is proposed that wastewater treatment facilities meet legislated discharge limits for a range of micropollutants. However, the heterogeneity of these micropollutants in wastewaters make removal difficult to predict since their chemistry is so diverse. In this study, a range of organic and inorganic micropollutants known to be preferentially removed via different mechanisms were selected to challenge the activated sludge process (ASP) and determine its potential to achieve simultaneous micropollutant removal. At a fixed hydraulic retention time (HRT) of 8 h, the influence of an increase in solids retention time (SRT) on removal was evaluated. Maximum achievable micropollutant removal was recorded for all chemicals (estrogens, nonylphenolics and metals) at the highest SRT studied (27 days). Also, optimisation of HRT by extension to 24 h further augmented organic biodegradation. Most notable was the enhancement in removal of the considerably recalcitrant synthetic estrogen 17α-ethinylestradiol which increased to 65 ± 19%. Regression analysis indicates that this enhanced micropollutant behaviour is ostensibly related to the concomitant reduction in food: microorganism ratio. Interestingly, extended HRT also initiated nonylphenol biodegradation which has not been consistently observed previously in real wastewaters. However, extending HRT increased the solubilisation of particulate bound metals, increasing effluent aqueous metals concentrations (i.e., 0.45 μm filtered) by >100%. This is significant as only the aqueous metal phase is to be considered for environmental compliance. Consequently, identification of an optimum process condition for generic micropollutant removal is expected to favour a more integrated approach where upstream process unit optimisation (i.e., primary sedimentation) is demanded to reduce loading of the particle bound metal phase onto the ASP, thereby enabling longer HRT in the ASP to be considered for optimum removal of organic

  20. High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis.

    PubMed

    Halbert, Kristin M K; Goetze, Erica; Carlon, David B

    2013-01-01

    Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3-17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species' boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide.

  1. Species History Masks the Effects of Human-Induced Range Loss – Unexpected Genetic Diversity in the Endangered Giant Mayfly Palingenia longicauda

    PubMed Central

    Bálint, Miklós; Málnás, Kristóf; Nowak, Carsten; Geismar, Jutta; Váncsa, Éva; Polyák, László; Lengyel, Szabolcs; Haase, Peter

    2012-01-01

    Freshwater biodiversity has declined dramatically in Europe in recent decades. Because of massive habitat pollution and morphological degradation of water bodies, many once widespread species persist in small fractions of their original range. These range contractions are generally believed to be accompanied by loss of intraspecific genetic diversity, due to the reduction of effective population sizes and the extinction of regional genetic lineages. We aimed to assess the loss of genetic diversity and its significance for future potential reintroduction of the long-tailed mayfly Palingenia longicauda (Olivier), which experienced approximately 98% range loss during the past century. Analysis of 936 bp of mitochondrial DNA of 245 extant specimens across the current range revealed a surprisingly large number of haplotypes (87), and a high level of haplotype diversity (). In contrast, historic specimens (6) from the lost range (Rhine catchment) were not differentiated from the extant Rába population (, ), despite considerable geographic distance separating the two rivers. These observations can be explained by an overlap of the current with the historic (Pleistocene) refugia of the species. Most likely, the massive recent range loss mainly affected the range which was occupied by rapid post-glacial dispersal. We conclude that massive range losses do not necessarily coincide with genetic impoverishment and that a species' history must be considered when estimating loss of genetic diversity. The assessment of spatial genetic structures and prior phylogeographic information seems essential to conserve once widespread species. PMID:22412844

  2. Effects of historical climate change, habitat connectivity, and vicariance on genetic structure and diversity across the range of the Red Tree Vole (Phenacomys longicaudus) in the Pacific Northwest United States

    USGS Publications Warehouse

    Miller, Mark P.; Bellinger, R.M.; Forsman, E.D.; Haig, Susan M.

    2006-01-01

    Phylogeographical analyses conducted in the Pacific Northwestern United States have often revealed concordant patterns of genetic diversity among taxa. These studies demonstrate distinct North/South genetic discontinuities that have been attributed to Pleistocene glaciation. We examined phylogeographical patterns of red tree voles (Phenacomys longicaudus) in western Oregon by analysing mitochondrial control region sequences for 169 individuals from 18 areas across the species' range. Cytochrome b sequences were also analysed from a subset of our samples to confirm the presence of major haplotype groups. Phylogenetic network analyses suggested the presence of two haplotype groups corresponding to northern and southern regions of P. longicaudus' range. Spatial genetic analyses (samova and Genetic Landscape Shapes) of control region sequences demonstrated a primary genetic discontinuity separating northern and southern sampling areas, while a secondary discontinuity separated northern sampling areas into eastern and western groups divided by the Willamette Valley. The North/South discontinuity likely corresponds to a region of secondary contact between lineages rather than an overt barrier. Although the Cordilleran ice sheet (maximum a??12 000 years ago) did not move southward to directly affect the region occupied by P. longicaudus, climate change during glaciation fragmented the forest landscape that it inhabits. Signatures of historical fragmentation were reflected by positive associations between latitude and variables such as Tajima's D and patterns associated with location-specific alleles. Genetic distances between southern sampling areas were smaller, suggesting that forest fragmentation was reduced in southern vs. northern regions.

  3. Petrogenesis of Triassic granites from the Nanling Range in South China: Implications for geochemical diversity in granites

    NASA Astrophysics Data System (ADS)

    Gao, Peng; Zhao, Zi-Fu; Zheng, Yong-Fei

    2014-12-01

    A combined study of whole-rock major-trace elements and Sr-Nd isotopes, zircon U-Pb ages, Hf and O isotopes as well as biotite geochemistry was carried out for Triassic granite intrusions from the Nanling Range in South China. The results provide insights into the effects of source composition and melting conditions on the geochemical diversity of granites. The granites of interest are peraluminous, and contain primary muscovite and tourmaline. They are characterized by high zircon δ18O values of > 9.0‰, high initial 87Sr/86Sr values of ~ 0.7200, and homogeneous εNd(t) values of - 11.3 to - 9.8, as well as variable zircon εHf(t) values of - 12.2 to - 5.8. Biotite geochemistry is similar to that of common peraluminous granites. An integrated interpretation of these petrological, mineralogical and geochemical data indicates that these granites were derived from partial melting of metasedimentary rocks under variable physicochemical conditions. The differences in whole-rock and biotite geochemistry between the intrusions are ascribed to the variable effects of source heterogeneity and melting temperature. The Luxi intrusion exhibits higher contents of MgO, FeOT, TiO2 and CaO than common melts derived from metasedimentary rocks, tight variations in major-trace elements and homogeneous Sr-Nd isotopic compositions, and homogeneous biotite composition with high Mg# [= Mg / (Mg + Fe) in molar] and lower whole-rock A/CNK values [= Al2O3 / (CaO + Na2O + K2O) in molar]. These can be explained by originating from a relatively mafic metasedimentary source. On the other hand, the geochemical diversity of granites can be caused by the difference in melting temperature in addition to the source heterogeneity. This is suggested by the Xiazhuang and Fucheng intrusions which exhibit similar range of SiO2. Nevertheless, the Fucheng intrusion is ferroan, and high in TiO2, (Na2O + K2O)/CaO, TiO2/MgO, Ga/Al and Zr + Nb + Ce + Y, but low in CaO, MgO and Mg#. Most of its major

  4. High Cryptic Diversity across the Global Range of the Migratory Planktonic Copepods Pleuromamma piseki and P. gracilis

    PubMed Central

    Halbert, Kristin M. K.; Goetze, Erica; Carlon, David B.

    2013-01-01

    Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide. PMID:24167556

  5. Allelic Richness following Population Founding Events – A Stochastic Modeling Framework Incorporating Gene Flow and Genetic Drift

    PubMed Central

    Greenbaum, Gili; Templeton, Alan R.; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the “One Migrant per Generation” rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution. PMID:25526062

  6. Allelic richness following population founding events--a stochastic modeling framework incorporating gene flow and genetic drift.

    PubMed

    Greenbaum, Gili; Templeton, Alan R; Zarmi, Yair; Bar-David, Shirli

    2014-01-01

    Allelic richness (number of alleles) is a measure of genetic diversity indicative of a population's long-term potential for adaptability and persistence. It is used less commonly than heterozygosity as a genetic diversity measure, partially because it is more mathematically difficult to take into account the stochastic process of genetic drift for allelic richness. This paper presents a stochastic model for the allelic richness of a newly founded population experiencing genetic drift and gene flow. The model follows the dynamics of alleles lost during the founder event and simulates the effect of gene flow on maintenance and recovery of allelic richness. The probability of an allele's presence in the population was identified as the relevant statistical property for a meaningful interpretation of allelic richness. A method is discussed that combines the probability of allele presence with a population's allele frequency spectrum to provide predictions for allele recovery. The model's analysis provides insights into the dynamics of allelic richness following a founder event, taking into account gene flow and the allele frequency spectrum. Furthermore, the model indicates that the "One Migrant per Generation" rule, a commonly used conservation guideline related to heterozygosity, may be inadequate for addressing preservation of diversity at the allelic level. This highlights the importance of distinguishing between heterozygosity and allelic richness as measures of genetic diversity, since focusing merely on the preservation of heterozygosity might not be enough to adequately preserve allelic richness, which is crucial for species persistence and evolution.

  7. Interpreting sperm DNA damage in a diverse range of mammalian sperm by means of the two-tailed comet assay

    PubMed Central

    Cortés-Gutiérrez, Elva I.; López-Fernández, Carmen; Fernández, José Luis; Dávila-Rodríguez, Martha I.; Johnston, Stephen D.; Gosálvez, Jaime

    2014-01-01

    allow for the simultaneous evaluation of DSBs and SSBs in mammalian spermatozoa. Here we have compiled a retrospective overview of how the TT-comet assay has been used to investigate the structure and function of sperm DNA across a diverse range of mammalian species (eutheria, metatheria, and prototheria). When conducted as part of the TT-comet assay, we illustrate (a) how the alkaline comet single assay has been used to help understand the constitutive and transient changes in DNA structure associated with chromatin packing, (b) the capacity of the TT-comet to differentiate between the presence of SSBs and DSBs (c) and the possible implications of SSBs or DSBs for the assessment of infertility. PMID:25505901

  8. Interpreting sperm DNA damage in a diverse range of mammalian sperm by means of the two-tailed comet assay.

    PubMed

    Cortés-Gutiérrez, Elva I; López-Fernández, Carmen; Fernández, José Luis; Dávila-Rodríguez, Martha I; Johnston, Stephen D; Gosálvez, Jaime

    2014-01-01

    the simultaneous evaluation of DSBs and SSBs in mammalian spermatozoa. Here we have compiled a retrospective overview of how the TT-comet assay has been used to investigate the structure and function of sperm DNA across a diverse range of mammalian species (eutheria, metatheria, and prototheria). When conducted as part of the TT-comet assay, we illustrate (a) how the alkaline comet single assay has been used to help understand the constitutive and transient changes in DNA structure associated with chromatin packing, (b) the capacity of the TT-comet to differentiate between the presence of SSBs and DSBs (c) and the possible implications of SSBs or DSBs for the assessment of infertility.

  9. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection

    PubMed Central

    Sams, Aaron J.; Hawks, John; Keinan, Alon

    2015-01-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles. PMID:25467111

  10. The utility of ancient human DNA for improving allele age estimates, with implications for demographic models and tests of natural selection.

    PubMed

    Sams, Aaron J; Hawks, John; Keinan, Alon

    2015-02-01

    The age of polymorphic alleles in humans is often estimated from population genetic patterns in extant human populations, such as allele frequencies, linkage disequilibrium, and rate of mutations. Ancient DNA can improve the accuracy of such estimates, as well as facilitate testing the validity of demographic models underlying many population genetic methods. Specifically, the presence of an allele in a genome derived from an ancient sample testifies that the allele is at least as old as that sample. In this study, we consider a common method for estimating allele age based on allele frequency as applied to variants from the US National Institutes of Health (NIH) Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project. We view these estimates in the context of the presence or absence of each allele in the genomes of the 5300 year old Tyrolean Iceman, Ötzi, and of the 50,000 year old Altai Neandertal. Our results illuminate the accuracy of these estimates and their sensitivity to demographic events that were not included in the model underlying age estimation. Specifically, allele presence in the Iceman genome provides a good fit of allele age estimates to the expectation based on the age of that specimen. The equivalent based on the Neandertal genome leads to a poorer fit. This is likely due in part to the older age of the Neandertal and the older time of the split between modern humans and Neandertals, but also due to gene flow from Neandertals to modern humans not being considered in the underlying demographic model. Thus, the incorporation of ancient DNA can improve allele age estimation, demographic modeling, and tests of natural selection. Our results also point to the importance of considering a more diverse set of ancient samples for understanding the geographic and temporal range of individual alleles.

  11. Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limits.

    PubMed

    Lind, Curtis E; Evans, Brad S; Taylor, Joseph J U; Jerry, Dean R

    2007-12-01

    Intraspecific genetic diversity governs the potential of species to prevail in the face of environmental or ecological challenges; therefore, its protection is critical. The Indo-Australian Archipelago (IAA) is a significant reservoir of the world's marine biodiversity and a region of high conservation priority. Yet, despite indications that the IAA may harbour greater intraspecific variation, multiple-locus genetic diversity data are limited. We investigated microsatellite DNA variation in Pinctada maxima populations from the IAA to elucidate potential factors influencing levels of genetic diversity in the region. Results indicate that genetic diversity decreases as the geographical distance away from central Indonesia increases, and that populations located towards the centre of P. maxima's range are more genetically diverse than those located peripherally (P < 0.01). Significant partitioning of genetic variation was identified (F(ST) = 0.027; R(ST) = 0.023, P < 0.001) and indicates that historical biogeographical episodes or oceanographic factors have shaped present population genetic structure. We propose that the genetic diversity peak in P. maxima populations may be due to (i) an abundance of suitable habitat within the IAA, meaning larger, more temporally stable populations can be maintained and are less likely to encounter genetic bottlenecks; and/or (ii) the close proximity of biogeographical barriers around central Indonesia results in increased genetic diversity in the region because of admixture of genetically divergent populations. We encourage further genetic diversity studies of IAA marine biota to confirm whether this region has a significant role in maintaining intraspecific diversity, which will greatly assist the planning and efficacy of future conservation efforts.

  12. Comparative analysis of genetic diversity between Qinghai-Tibetan wild and Chinese landrace barley.

    PubMed

    Gong, Xue; Westcott, Sharon; Li, Chengdao; Yan, Guijun; Lance, Reg; Sun, Dongfa

    2009-10-01

    Fifty-two SSR markers were used to evaluate the genetic diversity of 33 Qinghai-Tibetan wild barley accessions, 56 landraces collected primarily from other parts of China, and 1 Israeli wild barley accession. At the 52 SSR loci, 206 alleles were detected for the 90 accessions, among which 111 were common alleles. The number of alleles per locus ranged from 1 to 9, with an average of 4.0. Polymorphism information content (PIC) values ranged from 0 to 0.856 among all the markers, with an average of 0.547. The PIC value of Qinghai-Tibetan wild barley varied from 0 to 0.813 with an average of 0.543, while in landraces, the markers showed a range of 0 to 0.790 with an average of 0.490. The SSR markers could clearly differentiate the Qinghai-Tibetan wild barley from the landraces. Twenty-four unique alleles were observed in Qinghai-Tibetan wild barley, and the frequency of unique alleles in Qinghai-Tibetan wild barley was about 2.1 times higher than that in the landraces, on average. Five of the 7 chromosomes had more unique alleles in the Qinghai-Tibetan wild barley, but chromosome 2H had more unique alleles in the landraces. The presence of many unique alleles may reflect the adaptation of this barley germplasm to diverse environments and production systems. PMID:19935909

  13. Genetic diversity in three groups of barley germplasm assessed by simple sequence repeats.

    PubMed

    Matus, I A; Hayes, P M

    2002-12-01

    Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm. PMID:12502254

  14. A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.

    PubMed

    Yuasa, Isao; Jin, Feng; Harihara, Shinji; Matsusue, Aya; Fujihara, Junko; Takeshita, Haruo; Akane, Atsushi; Umetsu, Kazuo; Saitou, Naruya; Chattopadhyay, Prasanta K

    2013-09-01

    Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper anthropological and forensic understanding of iSTR, 1161 additional individuals from 11 Asian populations were investigated. Group H alleles of iSTR and c.1217A allele of a SNP in exon 11 of the CFI gene were associated with each other and were almost entirely confined to East Asian populations. Han Chinese in Changsha, southern China, showed the highest frequency for East Asian-specific group H alleles (0.201) among 15 populations. Group H alleles were observed to decrease gradually from south to north in 11 East Asian populations. This expansion of group H alleles provides evidence that southern China and Southeast Asia are a hotspot of Asian diversity and a genetic reservoir of Asians after they entered East Asia. The expected heterozygosity values of iSTR ranged from 0.927 in Thais to 0.874 in Oroqens, higher than those of an STR in the fibrinogen alpha chain (FGA) gene on chromosome 4q. Thus, iSTR is a useful marker for anthropological and forensic genetics.

  15. A noncomplementation screen for quantitative trait alleles in saccharomyces cerevisiae.

    PubMed

    Kim, Hyun Seok; Huh, Juyoung; Riles, Linda; Reyes, Alejandro; Fay, Justin C

    2012-07-01

    Both linkage and linkage disequilibrium mapping provide well-defined approaches to mapping quantitative trait alleles. However, alleles of small effect are particularly difficult to refine to individual genes and causative mutations. Quantitative noncomplementation provides a means of directly testing individual genes for quantitative trait alleles in a fixed genetic background. Here, we implement a genome-wide noncomplementation screen for quantitative trait alleles that affect colony color or size by using the yeast deletion collection. As proof of principle, we find a previously known allele of CYS4 that affects colony color and a novel allele of CTT1 that affects resistance to hydrogen peroxide. To screen nearly 4700 genes in nine diverse yeast strains, we developed a high-throughput robotic plating assay to quantify colony color and size. Although we found hundreds of candidate alleles, reciprocal hemizygosity analysis of a select subset revealed that many of the candidates were false positives, in part the result of background-dependent haploinsufficiency or second-site mutations within the yeast deletion collection. Our results highlight the difficulty of identifying small-effect alleles but support the use of noncomplementation as a rapid means of identifying quantitative trait alleles of large effect. PMID:22870398

  16. Functional Significance of Single Nucleotide Polymorphisms in the Lactase Gene in Diverse United States Subjects and Evidence for a Novel Lactase Persistence Allele at -13909 in Those of European Ancestry

    PubMed Central

    Baffour-Awuah, Nana Yaa; Fleet, Sarah; Baker, Susan S.; Butler, Johannah L.; Campbell, Catarina; Tischfield, Samuel; Mitchell, Paul D.; Moon, Jennifer E.; Allende-Richter, Sophie; Fishman, Laurie; Bousvaros, Athos; Fox, Victor; Kuokkanen, Mikko; Montgomery, Robert K.; Grand, Richard J.; Hirschhorn, Joel N.

    2014-01-01

    Objectives Recent data from mainly homogeneous European and African populations implicate a 140 bp region 5′ to the transcriptional start site of LCT (the lactase gene) as a regulatory site for lactase persistence and non-persistence. As there are no studies of United States non-homogeneous populations, we performed genotype/phenotype analysis of the -13910 and -22018 LCT SNPs in New England children, mostly of European ancestry. Methods Duodenal biopsies were processed for disaccharidase activities, RNA quantification by RT-PCR, allelic expression ratios by PCR, and genotyping and SNP analysis. Results were compared to clinical information. Results Lactase activity and mRNA levels, as well as sucrase-to-lactase ratios of enzyme activity and mRNA, showed robust correlations with genotype. None of the other LCT SNPs showed as strong a correlation with enzyme or mRNA activities as did -13910. Data were consistent with the -13910 being the causal sequence variant rather than -22018. Four individuals heterozygous for -13910T/C had allelic expression patterns similar to individuals with -13910C/C genotypes; of these, 2 showed equal LCT expression from the 2 alleles and a novel variant (-13909C>A) associated with lactase persistence. Conclusion The identification of -13910C/C genotype is very likely to predict lactase non-persistence, consistent with prior published studies. A -13910T/T genotype will frequently, but not perfectly, predict lactase persistence in this mixed European-ancestry population; a -13910T/C genotype will not predict the phenotype. A long, rare haplotype in 2 individuals with -13910T/C genotype but equal allele-specific expression contains a novel lactase persistence allele present at -13909. PMID:25625576

  17. A limit to the divergent allele advantage model supported by variable pathogen recognition across HLA-DRB1 allele lineages.

    PubMed

    Lau, Q; Yasukochi, Y; Satta, Y

    2015-11-01

    Genetic diversity in human leukocyte antigen (HLA) molecules is thought to have arisen from the co-evolution between host and pathogen and maintained by balancing selection. Heterozygote advantage is a common proposed scenario for maintaining high levels of diversity in HLA genes, and extending from this, the divergent allele advantage (DAA) model suggests that individuals with more divergent HLA alleles bind and recognize a wider array of antigens. While the DAA model seems biologically suitable for driving HLA diversity, there is likely an upper threshold to the amount of sequence divergence. We used peptide-binding and pathogen-recognition capacity of DRB1 alleles as a model to further explore the DAA model; within the DRB1 locus, we examined binding predictions based on two distinct phylogenetic groups (denoted group A and B) previously identified based on non-peptide-binding region (PBR) nucleotide sequences. Predictions in this study support that group A allele and group B allele lineages have contrasting binding/recognition capacity, with only the latter supporting the DAA model. Furthermore, computer simulations revealed an inconsistency in the DAA model alone with observed extent of polymorphisms, supporting that the DAA model could only work effectively in combination with other mechanisms. Overall, we support that the mechanisms driving HLA diversity are non-exclusive. By investigating the relationships among HLA alleles, and pathogens recognized, we can provide further insights into the mechanisms on how humans have adapted to infectious diseases over time.

  18. Multiple and mass introductions from limited origins: genetic diversity and structure of Solidago altissima in the native and invaded range.

    PubMed

    Sakata, Yuzu; Itami, Joanne; Isagi, Yuji; Ohgushi, Takayuki

    2015-11-01

    Understanding the origins and diversity of invasive species can reveal introduction and invasion pathways, and inform an effective management of invasive species. Tall goldenrod, Solidago altissima, is a herbaceous perennial plant native to North America and it has become a widespread invasive weed in East Asian countries. We used microsatellite and chloroplast DNA markers to obtain information on neutral processes and on genetic diversity in native and invaded populations of S. altissima and to infer how it invaded and spread in Japan. We found that introduced (n = 12) and native (n = 20) populations had similar levels of genetic diversity at nuclear SSR loci. Genetic structure analysis indicated that at least two independent colonization events gave rise to current S. altissima populations in Japan. The majority (68%) of the Japanese S. altissima were genetically similar and likely shared a common origin from a single or a small number of populations from the southern USA populations, while the populations in Hokkaido were suggested to arise from a different source. Our results suggest that multiple and mass introductions have contributed to the persistence and rapid adaptation of S. altissima promoting its widespread establishment throughout Japan. PMID:26423999

  19. Multiple and mass introductions from limited origins: genetic diversity and structure of Solidago altissima in the native and invaded range.

    PubMed

    Sakata, Yuzu; Itami, Joanne; Isagi, Yuji; Ohgushi, Takayuki

    2015-11-01

    Understanding the origins and diversity of invasive species can reveal introduction and invasion pathways, and inform an effective management of invasive species. Tall goldenrod, Solidago altissima, is a herbaceous perennial plant native to North America and it has become a widespread invasive weed in East Asian countries. We used microsatellite and chloroplast DNA markers to obtain information on neutral processes and on genetic diversity in native and invaded populations of S. altissima and to infer how it invaded and spread in Japan. We found that introduced (n = 12) and native (n = 20) populations had similar levels of genetic diversity at nuclear SSR loci. Genetic structure analysis indicated that at least two independent colonization events gave rise to current S. altissima populations in Japan. The majority (68%) of the Japanese S. altissima were genetically similar and likely shared a common origin from a single or a small number of populations from the southern USA populations, while the populations in Hokkaido were suggested to arise from a different source. Our results suggest that multiple and mass introductions have contributed to the persistence and rapid adaptation of S. altissima promoting its widespread establishment throughout Japan.

  20. Prevalence, Genetic Characterization, and 18S Small Subunit Ribosomal RNA Diversity of Trypanosoma rangeli in Triatomine and Mammal Hosts in Endemic Areas for Chagas Disease in Ecuador.

    PubMed

    Ocaña-Mayorga, Sofia; Aguirre-Villacis, Fernanda; Pinto, C Miguel; Vallejo, Gustavo A; Grijalva, Mario J

    2015-12-01

    Trypanosoma rangeli is a nonpathogenic parasite for humans; however, its medical importance relies in its similarity and overlapping distribution with Trypanosoma cruzi, causal agent of Chagas disease in the Americas. The genetic diversity of T. rangeli and its association with host species (triatomines and mammals) has been identified along Central and the South America; however, it has not included data of isolates from Ecuador. This study reports infection with T. rangeli in 18 genera of mammal hosts and five species of triatomines in three environments (domestic, peridomestic, and sylvatic). Higher infection rates were found in the sylvatic environment, in close association with Rhodnius ecuadoriensis. The results of this study extend the range of hosts infected with this parasite and the geographic range of the T. rangeli genotype KP1(-)/lineage C in South America. It was not possible to detect variation on T. rangeli from the central coastal region and southern Ecuador with the analysis of the small subunit ribosomal RNA (SSU-rRNA) gene, even though these areas are ecologically different and a phenotypic subdivision of R. ecuadoriensis has been found. R. ecuadoriensis is considered one of the most important vectors for Chagas disease transmission in Ecuador due to its wide distribution and adaptability to diverse environments. An extensive knowledge of the trypanosomes circulating in this species of triatomine, and associated mammal hosts, is important for delineating transmission dynamics and preventive measures in the endemic areas of Ecuador and Northern Peru. PMID:26645579

  1. Comparison of genetic diversity of the invasive weed Rubus alceifolius poir. (Rosaceae) in its native range and in areas of introduction, using amplified fragment length polymorphism (AFLP) markers.

    PubMed

    Amsellem, L; Noyer, J L; Le Bourgeois, T; Hossaert-McKey, M

    2000-04-01

    Theory predicts that colonization of new areas will be associated with population bottlenecks that reduce within-population genetic diversity and increase genetic differentiation among populations. This should be especially true for weedy plant species, which are often characterized by self-compatible breeding systems and vegetative propagation. To test this prediction, and to evaluate alternative scenarios for the history of introduction, the genetic diversity of Rubus alceifolius was studied with amplified fragment length polymorphism (AFLP) markers in its native range in southeast Asia and in several areas where this plant has been introduced and is now a serious weed (Indian Ocean islands, Australia). In its native range, R. alceifolius showed great genetic variability within populations and among geographically close populations (populations sampled ranging from northern Vietnam to Java). In Madagascar, genetic variability was somewhat lower than in its native range, but still considerable. Each population sampled in the other Indian Ocean islands (Mayotte, La Réunion, Mauritius) was characterized by a single different genotype of R. alceifolius for the markers studied, and closely related to individuals from Madagascar. Queensland populations also included only a single genotype, identical to that found in Mauritius. These results suggest that R. alceifolius was first introduced into Madagascar, perhaps on multiple occasions, and that Madagascan individuals were the immediate source of plants that colonized other areas of introduction. Successive nested founder events appear to have resulted in cumulative reduction in genetic diversity. Possible explanations for the monoclonality of R. alceifolius in many areas of introduction are discussed.

  2. Retention of agronomically important variation in germplasm core collections: implications for allele mining

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to d...

  3. Analysis of population structure and genetic diversity of Egyptian and exotic rice (Oryza sativa L.) genotypes.

    PubMed

    Salem, Khaled F M; Sallam, Ahmed

    2016-01-01

    Understanding the population structure and genetic diversity is a very important goal to improve the economic value of crops. In rice, a loss of genetic diversity in the last few centuries is observed. To address this challenge, a set of 22 lines from three different regions - India (two), and Philippines (six), and Egypt (14) - were used to assess the genetic diversity and the features of population structure. These genotypes were analyzed using 106 SSR alleles that showed a clear polymorphism among the lines. Genetic diversity was estimated based on the number of different alleles, polymorphism information content (PIC), and gene diversity. A total of 106 SSR alleles was identified from the 23 SSR loci and used to study the population structure and carry out a cluster analysis. All SSR loci showed a wide range of the number of different alleles extended from two (one loci) to seven alleles (three loci). Five and eight loci showed high PIC and gene diversity (≥0.70), respectively. The results of population structure are in agreement with cluster analysis results. Both analyses revealed two different subpopulations (G1 and G2) with different genetic properties in number of private alleles, number of different alleles (Na), number of effective alleles (Ne), expected heterozygosity (He), and Shannon's Information Index (SII). Our findings indicate that five SSR loci (RM 111, RM 307, RM 22, RM 19, and RM 271) could be used in breeding programs to enhance the marker-assisted selection through QTL mapping and association studies. A high genetic diversity found between genotypes which can be exploited to improve and produce rice cultivars for important traits (e.g. high agronomic features and tolerance to biotic or/and abiotic stresses).

  4. Genetic Diversity and Ecological Niche Modelling of Wild Barley: Refugia, Large-Scale Post-LGM Range Expansion and Limited Mid-Future Climate Threats?

    PubMed Central

    Russell, Joanne; van Zonneveld, Maarten; Dawson, Ian K.; Booth, Allan; Waugh, Robbie; Steffenson, Brian

    2014-01-01

    Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum) in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare). Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR) and chloroplast-derived (5 cpSSR) markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM) and mid-term future (anthropogenic scenario A2, the 2080s) climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security. PMID:24505252

  5. Allelic variation contributes to bacterial host specificity.

    PubMed

    Yue, Min; Han, Xiangan; De Masi, Leon; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S; Fraser, George P; Zhao, Shaohua; McDermott, Patrick F; Weill, François-Xavier; Mainil, Jacques G; Arze, Cesar; Fricke, W Florian; Edwards, Robert A; Brisson, Dustin; Zhang, Nancy R; Rankin, Shelley C; Schifferli, Dieter M

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  6. Allelic variation contributes to bacterial host specificity

    SciTech Connect

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.

  7. Allelic variation contributes to bacterial host specificity

    DOE PAGES

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; et al

    2015-10-30

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population andmore » functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. In conclusion, together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts.« less

  8. Allelic variation contributes to bacterial host specificity

    PubMed Central

    Yue, Min; Han, Xiangan; Masi, Leon De; Zhu, Chunhong; Ma, Xun; Zhang, Junjie; Wu, Renwei; Schmieder, Robert; Kaushik, Radhey S.; Fraser, George P.; Zhao, Shaohua; McDermott, Patrick F.; Weill, François-Xavier; Mainil, Jacques G.; Arze, Cesar; Fricke, W. Florian; Edwards, Robert A.; Brisson, Dustin; Zhang, Nancy R.; Rankin, Shelley C.; Schifferli, Dieter M.

    2015-01-01

    Understanding the molecular parameters that regulate cross-species transmission and host adaptation of potential pathogens is crucial to control emerging infectious disease. Although microbial pathotype diversity is conventionally associated with gene gain or loss, the role of pathoadaptive nonsynonymous single-nucleotide polymorphisms (nsSNPs) has not been systematically evaluated. Here, our genome-wide analysis of core genes within Salmonella enterica serovar Typhimurium genomes reveals a high degree of allelic variation in surface-exposed molecules, including adhesins that promote host colonization. Subsequent multinomial logistic regression, MultiPhen and Random Forest analyses of known/suspected adhesins from 580 independent Typhimurium isolates identifies distinct host-specific nsSNP signatures. Moreover, population and functional analyses of host-associated nsSNPs for FimH, the type 1 fimbrial adhesin, highlights the role of key allelic residues in host-specific adherence in vitro. Together, our data provide the first concrete evidence that functional differences between allelic variants of bacterial proteins likely contribute to pathoadaption to diverse hosts. PMID:26515720

  9. Metabolic profiling of a range of peach fruit varieties reveals high metabolic diversity and commonalities and differences during ripening.

    PubMed

    Monti, Laura L; Bustamante, Claudia A; Osorio, Sonia; Gabilondo, Julieta; Borsani, Julia; Lauxmann, Martin A; Maulión, Evangelina; Valentini, Gabriel; Budde, Claudio O; Fernie, Alisdair R; Lara, María V; Drincovich, María F

    2016-01-01

    Peach (Prunus persica) fruits from different varieties display differential organoleptic and nutritional properties, characteristics related to their chemical composition. Here, chemical biodiversity of peach fruits from fifteen varieties, at harvest and after post-harvest ripening, was explored by gas chromatography-mass spectrometry. Metabolic profiling revealed that metabolites involved in organoleptic properties (sugars, organic and amino acids), stress tolerance (raffinose, galactinol, maltitol), and with nutritional properties (amino, caffeoylquinic and dehydroascorbic acids) displayed variety-dependent levels. Peach varieties clustered into four groups: two groups of early-harvest varieties with higher amino acid levels; two groups of mid- and late-harvest varieties with higher maltose levels. Further separation was mostly dependent on organic acids/raffinose levels. Variety-dependent and independent metabolic changes associated with ripening were detected; which contribute to chemical diversity or can be used as ripening markers, respectively. The great variety-dependent diversity in the content of metabolites that define fruit quality reinforces metabolomics usage as a tool to assist fruit quality improvement in peach.

  10. Evidence for selection maintaining MHC diversity in a rodent species despite strong density fluctuations.

    PubMed

    Schuster, Andrea C; Herde, Antje; Mazzoni, Camila J; Eccard, Jana A; Sommer, Simone

    2016-07-01

    Strong spatiotemporal variation in population size often leads to reduced genetic diversity limiting the adaptive potential of individual populations. Key genes of adaptive variation are encoded by the immune genes of the major histocompatibility complex (MHC) playing an essential role in parasite resistance. How MHC variation persists in rodent populations that regularly experience population bottlenecks remains an important topic in evolutionary genetics. We analysed the consequences of strong population fluctuations on MHC class II DRB exon 2 diversity in two distant common vole (Microtus arvalis) populations in three consecutive years using a high-throughput sequencing approach. In 143 individuals, we detected 25 nucleotide alleles translating into 14 unique amino acid MHC alleles belonging to at least three loci. Thus, the overall allelic diversity and amino acid distance among the remaining MHC alleles, used as a surrogate for the range of pathogenic antigens that can be presented to T-cells, are still remarkably high. Both study populations did not show significant population differentiation between years, but significant differences were found between sites. We concluded that selection processes seem to be strong enough to maintain moderate levels of MHC diversity in our study populations outcompeting genetic drift, as the same MHC alleles were conserved between years. Differences in allele frequencies between populations might be the outcome of different local parasite pressures and/or genetic drift. Further understanding of how pathogens vary across space and time will be crucial to further elucidate the mechanisms maintaining MHC diversity in cyclic populations. PMID:27225422

  11. Inferring the age of a fixed beneficial allele.

    PubMed

    Ormond, Louise; Foll, Matthieu; Ewing, Gregory B; Pfeifer, Susanne P; Jensen, Jeffrey D

    2016-01-01

    Estimating the age and strength of beneficial alleles is central to understanding how adaptation proceeds in response to changing environmental conditions. Several haplotype-based estimators exist for inferring the age of segregating beneficial mutations. Here, we develop an approximate Bayesian-based approach that rather estimates these parameters for fixed beneficial mutations in single populations. We integrate a range of existing diversity, site frequency spectrum, haplotype- and linkage disequilibrium-based summary statistics. We show that for strong selective sweeps on de novo mutations the method can estimate allele age and selection strength even in nonequilibrium demographic scenarios. We extend our approach to models of selection on standing variation, and co-infer the frequency at which selection began to act upon the mutation. Finally, we apply our method to estimate the age and selection strength of a previously identified mutation underpinning cryptic colour adaptation in a wild deer mouse population, and compare our findings with previously published estimates as well as with geological data pertaining to the presumed shift in selective pressure. PMID:26576754

  12. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots

    PubMed Central

    Baker, Christopher L.; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M.; Paigen, Kenneth

    2015-01-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9 +/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  13. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape. PMID:26368021

  14. Multimer Formation Explains Allelic Suppression of PRDM9 Recombination Hotspots.

    PubMed

    Baker, Christopher L; Petkova, Pavlina; Walker, Michael; Flachs, Petr; Mihola, Ondrej; Trachtulec, Zdenek; Petkov, Petko M; Paigen, Kenneth

    2015-09-01

    Genetic recombination during meiosis functions to increase genetic diversity, promotes elimination of deleterious alleles, and helps assure proper segregation of chromatids. Mammalian recombination events are concentrated at specialized sites, termed hotspots, whose locations are determined by PRDM9, a zinc finger DNA-binding histone methyltransferase. Prdm9 is highly polymorphic with most alleles activating their own set of hotspots. In populations exhibiting high frequencies of heterozygosity, questions remain about the influences different alleles have in heterozygous individuals where the two variant forms of PRDM9 typically do not activate equivalent populations of hotspots. We now find that, in addition to activating its own hotspots, the presence of one Prdm9 allele can modify the activity of hotspots activated by the other allele. PRDM9 function is also dosage sensitive; Prdm9+/- heterozygous null mice have reduced numbers and less active hotspots and increased numbers of aberrant germ cells. In mice carrying two Prdm9 alleles, there is allelic competition; the stronger Prdm9 allele can partially or entirely suppress chromatin modification and recombination at hotspots of the weaker allele. In cell cultures, PRDM9 protein variants form functional heteromeric complexes which can bind hotspots sequences. When a heteromeric complex binds at a hotspot of one PRDM9 variant, the other PRDM9 variant, which would otherwise not bind, can still methylate hotspot nucleosomes. We propose that in heterozygous individuals the underlying molecular mechanism of allelic suppression results from formation of PRDM9 heteromers, where the DNA binding activity of one protein variant dominantly directs recombination initiation towards its own hotspots, effectively titrating down recombination by the other protein variant. In natural populations with many heterozygous individuals, allelic competition will influence the recombination landscape.

  15. Allelic loss in colorectal carcinoma

    SciTech Connect

    Kern, S.E.; Fearon, E.R.; Tersmette, K.W.F.; Enterline, J.P.; Vogelstein, B.; Hamilton, S.R. ); Leppert, M.; Nakamura, Yusuke; White, R. )

    1989-06-02

    Clinical and pathological associations with molecular genetic alterations were studied in colorectal carcinomas from 83 patients. Fractional allelic loss, a measure of allelic deletions throughout the genome, and allelic deletions of specific chromosomal arms (the short arm of 17 and long arm of 18) each provided independent prognostic information by multivariate analysis when considered individually with Dukes' classification. Distant metastasis was significantly associated with high fractional allelic loss and with deletions of 17p and 18q. Mutations of ras proto-oncogenes and deletions of 5q had no prognostic importance. Statistically significant associations were also found between allelic losses and a family history of cancer, left-sided tumor location, and absence of extracellular tumor mucin. Allelic deletion analysis thus identified subsets of colorectal carcinoma with increased predilection for distant metastasis and cancer-related death. Further studies may define a subset of genetic alterations that can be used clinically to help assess prognosis.

  16. Analysis of the distribution of HLA-A alleles in populations from five continents.

    PubMed

    Middleton, D; Williams, F; Meenagh, A; Daar, A S; Gorodezky, C; Hammond, M; Nascimento, E; Briceno, I; Perez, M P

    2000-10-01

    The variation and frequency of HLA-A genotypes were established by PCR-SSOP typing in diverse geographically distributed populations: Brazilian, Colombian Kogui, Cuban, Mexican, Omani, Singapore Chinese, and South African Zulu. HLA-A allelic families with only one allele were identified for HLA-A*01, -A*23, -A*25, -A*31, -A*32, -A*36, -A*43, -A*69, -A*80; and with two alleles for HLA-A*03, -A*11, -A*26, -A*29, -A*33, -A*34, and -A*66. Greater variation was detected for HLA-A*02, -A*24, and -A*68 allele families. Colombian Kogui and Mexican Seris showed the least diversity with respect to HLA-A alleles, albeit with small numbers tested, with only four and five HLA-A alleles identified, respectively. It would appear by their presence in all populations studied, either rural or indigenous, that certain alleles are very important in pathogen peptide presentation. PMID:11082518

  17. Analysis of the distribution of HLA-A alleles in populations from five continents.

    PubMed

    Middleton, D; Williams, F; Meenagh, A; Daar, A S; Gorodezky, C; Hammond, M; Nascimento, E; Briceno, I; Perez, M P

    2000-10-01

    The variation and frequency of HLA-A genotypes were established by PCR-SSOP typing in diverse geographically distributed populations: Brazilian, Colombian Kogui, Cuban, Mexican, Omani, Singapore Chinese, and South African Zulu. HLA-A allelic families with only one allele were identified for HLA-A*01, -A*23, -A*25, -A*31, -A*32, -A*36, -A*43, -A*69, -A*80; and with two alleles for HLA-A*03, -A*11, -A*26, -A*29, -A*33, -A*34, and -A*66. Greater variation was detected for HLA-A*02, -A*24, and -A*68 allele families. Colombian Kogui and Mexican Seris showed the least diversity with respect to HLA-A alleles, albeit with small numbers tested, with only four and five HLA-A alleles identified, respectively. It would appear by their presence in all populations studied, either rural or indigenous, that certain alleles are very important in pathogen peptide presentation.

  18. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    PubMed

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity.

  19. Phylogeography of postglacial range expansion in Juglans mandshurica (Juglandaceae) reveals no evidence of bottleneck, loss of genetic diversity, or isolation by distance in the leading-edge populations.

    PubMed

    Wang, Wen-Ting; Xu, Bing; Zhang, Da-Yong; Bai, Wei-Ning

    2016-09-01

    The past studies of postglacial recolonization patterns in high latitude regions have revealed a significant role of dispersal capacity in shaping the genetic diversity and population structure of temperate trees. However, most of these studies have focused on species with long-distance dispersal followed by exponential population growth and were therefore unable to reveal the patterns in the case of a gradual expansion. Here we studied the impacts of postglacial range expansions on the distribution of genetic diversity in the Manchurian walnut (Juglans mandshurica), a common tree of East Asian cool-temperate deciduous forests that apparently lacks long-distance seed dispersal ability. The genetic diversity and structure of 19 natural walnut populations in Northeast China and the Korean Peninsula were examined using 17 nuclear simple sequence repeat (SSR) loci. Potential habitats under current and past climatic conditions were predicted using the ecological niche modelling (ENM) method. Bayesian clustering analysis revealed three groups, which were inferred to have diverged through multiple glacial-interglacial cycles in multiple refugia during the Quaternary Period. ENM estimated a southward range shift at the LGM, but high suitability scores still occurred in the western parts of the Changbai Mountains (Northeast China), the Korean peninsula and the exposed seafloor of the Yellow Sea. In contrast to most other cool-temperate trees co-occurring in the same region, the Manchurian walnut did not show any evidence of a population bottleneck, loss of genetic diversity or isolation by distance during the postglacial expansion. Our study clearly indicates that current northern populations originated from one glacial lineage and recolonization via a gradually advancing front due to the lack of a long-distance seed dispersal mechanism led to no latitudinal decrease in genetic diversity. PMID:27346642

  20. Genetic diversity and expanding nonindigenous range of the rhizocephalan Loxothylacus panopaei parasitizing mud crabs in the western north Atlantic.

    PubMed

    Kruse, Inken; Hare, Matthew P

    2007-06-01

    Nonindigenous parasite introductions and range expansions have become a major concern because of their potential to restructure communities and impact fisheries. Molecular markers provide an important tool for reconstructing the pattern of introduction. The parasitic castrator Loxothylacus panopaei, a rhizocephalan barnacle, infects estuarine mud crabs in the Gulf of Mexico and southeastern Florida. A similar parasite introduced into Chesapeake Bay before 1964, presumably via infected crabs associated with oysters from the Gulf of Mexico, was identified as L. panopaei. Our samples of this species during 2004 and 2005 show that the introduced range has expanded as far south as Edgewater, Florida, just north of the northern endemic range limit. The nonindigenous range expanded southward at a rate of up to 165 km/yr with relatively high prevalence, ranging from 30 to 93%. Mitochondrial DNA sequences from the cytochrome oxidase I gene showed that these nonindigenous L. panopaei are genetically distinct from the endemic parasites in southeastern Florida and the eastern Gulf of Mexico. The genetic difference was also associated with distinct host spectra. These results are incompatible with an eastern Gulf source population, but suggest that unrecognized genetic and phenotypic population structure may occur among Gulf of Mexico populations of Loxothvlacus.

  1. Do-or-die life cycles and diverse post-infection resistance mechanisms limit the evolution of parasite host ranges.

    PubMed

    Sieber, Michael; Gudelj, Ivana

    2014-04-01

    In light of the dynamic nature of parasite host ranges and documented potential for rapid host shifts, the observed high host specificity of most parasites remains an ecological paradox. Different variants of host-use trade-offs have become a mainstay of theoretical explanations of the prevalence of host specialism, but empirical evidence for such trade-offs is rare. We propose an alternative theory based on basic features of the parasite life cycle: host selection and subsequent intrahost replication. We introduce a new concept of effective burst size that accounts for the fact that successful host selection does not guarantee intrahost replication. Our theory makes a general prediction that a parasite will expand its host range if its effective burst size is positive. An in silico model of bacteria-phage coevolution verifies our predictions and demonstrates that the tendency for relatively narrow host ranges in parasites can be explained even in the absence of trade-offs. PMID:24495077

  2. Distinct and Diverse: Range-Wide Phylogeography Reveals Ancient Lineages and High Genetic Variation in the Endangered Okapi (Okapia johnstoni)

    PubMed Central

    Stanton, David W. G.; Hart, John; Galbusera, Peter; Helsen, Philippe; Shephard, Jill; Kümpel, Noëlle F.; Wang, Jinliang; Ewen, John G.; Bruford, Michael W.

    2014-01-01

    The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River. PMID:25007188

  3. Distinct and diverse: range-wide phylogeography reveals ancient lineages and high genetic variation in the endangered okapi (Okapia johnstoni).

    PubMed

    Stanton, David W G; Hart, John; Galbusera, Peter; Helsen, Philippe; Shephard, Jill; Kümpel, Noëlle F; Wang, Jinliang; Ewen, John G; Bruford, Michael W

    2014-01-01

    The okapi is an endangered, evolutionarily distinctive even-toed ungulate classified within the giraffidae family that is endemic to the Democratic Republic of Congo. The okapi is currently under major anthropogenic threat, yet to date nothing is known about its genetic structure and evolutionary history, information important for conservation management given the species' current plight. The distribution of the okapi, being confined to the Congo Basin and yet spanning the Congo River, also makes it an important species for testing general biogeographic hypotheses for Congo Basin fauna, a currently understudied area of research. Here we describe the evolutionary history and genetic structure of okapi, in the context of other African ungulates including the giraffe, and use this information to shed light on the biogeographic history of Congo Basin fauna in general. Using nuclear and mitochondrial DNA sequence analysis of mainly non-invasively collected samples, we show that the okapi is both highly genetically distinct and highly genetically diverse, an unusual combination of genetic traits for an endangered species, and feature a complex evolutionary history. Genetic data are consistent with repeated climatic cycles leading to multiple Plio-Pleistocene refugia in isolated forests in the Congo catchment but also imply historic gene flow across the Congo River. PMID:25007188

  4. Divergent pattern of nuclear genetic diversity across the range of the Afromontane Prunus africana mirrors variable climate of African highlands

    PubMed Central

    Kadu, Caroline A. C.; Konrad, Heino; Schueler, Silvio; Muluvi, Geoffrey M.; Eyog-Matig, Oscar; Muchugi, Alice; Williams, Vivienne L.; Ramamonjisoa, Lolona; Kapinga, Consolatha; Foahom, Bernard; Katsvanga, Cuthbert; Hafashimana, David; Obama, Crisantos; Geburek, Thomas

    2013-01-01

    Background and Aims Afromontane forest ecosystems share a high similarity of plant and animal biodiversity, although they occur mainly on isolated mountain massifs throughout the continent. This resemblance has long provoked questions on former wider distribution of Afromontane forests. In this study Prunus africana (one of the character trees of Afromontane forests) is used as a model for understanding the biogeography of this vegetation zone. Methods Thirty natural populations from nine African countries covering a large part of Afromontane regions were analysed using six nuclear microsatellites. Standard population genetic analysis as well as Bayesian and maximum likelihood models were used to infer genetic diversity, population differentiation, barriers to gene flow, and recent and all migration among populations. Key Results Prunus africana exhibits strong divergence among five main Afromontane regions: West Africa, East Africa west of the Eastern Rift Valley (ERV), East Africa east of the ERV, southern Africa and Madagascar. The strongest divergence was evident between Madagascar and continental Africa. Populations from West Africa showed high similarity with East African populations west of the ERV, whereas populations east of the ERV are closely related to populations of southern Africa, respectively. Conclusions The observed patterns indicate divergent population history across the continent most likely associated to Pleistocene changes in climatic conditions. The high genetic similarity between populations of West Africa with population of East Africa west of the ERV is in agreement with faunistic and floristic patterns and provides further evidence for a historical migration route. Contrasting estimates of recent and historical gene flow indicate a shift of the main barrier to gene flow from the Lake Victoria basin to the ERV, highlighting the dynamic environmental and evolutionary history of the region. PMID:23250908

  5. Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China.

    PubMed

    Chen, Liang-Jun; Lin, Xian-Dan; Guo, Wen-Ping; Tian, Jun-Hua; Wang, Wen; Ying, Xu-Hua; Wang, Miao-Ruo; Yu, Bin; Yang, Zhan-Qiu; Shi, Mang; Holmes, Edward C; Zhang, Yong-Zhen

    2016-04-01

    The wide circulation of novel avian influenza viruses (AIVs) highlights the risk of pandemic influenza emergence in China. To investigate the prevalence and genetic diversity of AIVs in different ecological contexts, we surveyed AIVs in live poultry markets (LPMs), free-range poultry and the wetland habitats of wild birds in Zhejiang and Hubei provinces. Notably, LPMs contained the highest frequency of AIV infection, and the greatest number of subtypes (n = 9) and subtype co-infections (n = 14), as well as frequent reassortment, suggesting that they play an active role in fuelling AIV transmission. AIV-positive samples were also identified in wild birds in both provinces and free-range poultry in one sampling site close to a wetland region in Hubei. H9N2, H7N9 and H5N1 were the most commonly sampled subtypes in the LPMs from Zhejiang, whilst H5N6 and H9N2 were the dominant subtypes in the LPMs from Hubei. Phylogenetic analyses of the whole-genome sequences of 43 AIVs revealed that three reassortant H5 subtypes were circulating in LMPs in both geographical regions. Notably, the viruses sampled from the wetland regions and free-range poultry contained complex reassortants, for which the origins of some segments were unclear. Overall, our study highlights the extent of AIV genetic diversity in two highly populated parts of central and south-eastern China, particularly in LPMs, and emphasizes the need for continual surveillance. PMID:26758561

  6. Diversity and evolution of avian influenza viruses in live poultry markets, free-range poultry and wild wetland birds in China.

    PubMed

    Chen, Liang-Jun; Lin, Xian-Dan; Guo, Wen-Ping; Tian, Jun-Hua; Wang, Wen; Ying, Xu-Hua; Wang, Miao-Ruo; Yu, Bin; Yang, Zhan-Qiu; Shi, Mang; Holmes, Edward C; Zhang, Yong-Zhen

    2016-04-01

    The wide circulation of novel avian influenza viruses (AIVs) highlights the risk of pandemic influenza emergence in China. To investigate the prevalence and genetic diversity of AIVs in different ecological contexts, we surveyed AIVs in live poultry markets (LPMs), free-range poultry and the wetland habitats of wild birds in Zhejiang and Hubei provinces. Notably, LPMs contained the highest frequency of AIV infection, and the greatest number of subtypes (n = 9) and subtype co-infections (n = 14), as well as frequent reassortment, suggesting that they play an active role in fuelling AIV transmission. AIV-positive samples were also identified in wild birds in both provinces and free-range poultry in one sampling site close to a wetland region in Hubei. H9N2, H7N9 and H5N1 were the most commonly sampled subtypes in the LPMs from Zhejiang, whilst H5N6 and H9N2 were the dominant subtypes in the LPMs from Hubei. Phylogenetic analyses of the whole-genome sequences of 43 AIVs revealed that three reassortant H5 subtypes were circulating in LMPs in both geographical regions. Notably, the viruses sampled from the wetland regions and free-range poultry contained complex reassortants, for which the origins of some segments were unclear. Overall, our study highlights the extent of AIV genetic diversity in two highly populated parts of central and south-eastern China, particularly in LPMs, and emphasizes the need for continual surveillance.

  7. The genetic diversity of the noble scallop (Chlamys nobilis, Reeve 1852) in China assessed using five microsatellite markers.

    PubMed

    Wang, Yanhong; Fu, Dingkun; Xia, Jianjun

    2013-03-01

    Five highly variable microsatellite loci were used to investigate the genetic diversity and population structure of the noble scallop Chlamys nobilis, in the South China Sea. A total of 200 individual scallops from 4 populations were genotyped. All of the 5 microsatellite loci screened in this study showed polymorphism. A total of 32 different alleles were observed over all loci. The number of alleles per locus ranged from 3 to 12. The average allelic number of these polymorphic markers was 6.4. The averages of observed (Ho) and expected heterozygosity (He) ranged from 0.07 to 0.32 and from 0.119 to 0.459, respectively. A highly significant deviation from the Hardy-Weinberg Law, owing primarily to heterozygote deficiency, was found in all populations studied. The Nanao population exhibited more genetic diversity than the other three populations in terms of allele richness and observed and expected heterozygosity.

  8. Geographic range and structure of cryptic genetic diversity among Pacific North American populations of the non-native amphipod Grandidierella japonica

    USGS Publications Warehouse

    Pilgrim, Erik M.; Blum, Michael J.; Reusser, Deborah A.; Lee, Henry; Darling, John A.

    2013-01-01

    Reconstructing the invasion history of aquatic invasive species can enhance understanding of invasion risks by recognizing areas most susceptible to invasion and forecasting future spread based on past patterns of population expansion. Here we reconstruct the invasion history of the Japanese amphipod Grandidierella japonica Stephensen 1938 combining information from historical collection data with molecular genetic data to better understand post-invasion range expansion and anthropogenic connectivity across the Pacific coast of North America. Compilation of collection data from bays and estuaries of the Pacific North American coast show many new localities have been colonized in the last two decades, moving outward from harbors and bays with high commercial traffic into smaller coastal locations dominated by local recreational traffic. DNA barcode sequence data for G. japonica reveals two distinct clades: one found in San Francisco Bay and sites to the north, and one also found in San Francisco Bay and sites to the south. The two clades differ by an average 7.28 % genetic distance, large enough to consider these invasive amphipods two separate species. Both northern and southern clades exhibit low levels of genetic diversity, suggesting a single introduction event for each. The presence of cryptic diversity within this invasive amphipod highlights the need for more extensive study of the invasive and native populations of aquatic invasive invertebrates to address questions of taxonomy, diversity, and invasion history.

  9. DQB1*06:02 allele specific expression varies by allelic dosage, not narcolepsy status

    PubMed Central

    lachmi, Karin Weiner; Lin, Ling; Kornum, Birgitte Rahbek; Rico, Tom; Lo, Betty; Aran, Adi; Mignot, Emmanuel

    2012-01-01

    The association of narcolepsy-cataplexy, a sleep disorder caused by the loss of hypocretin/orexin neurons in the hypothalamus, with DQA1*01:02-DQB1*06:02 is one of the tightest known single allele HLA associations. In this study, we explored genome wide expression in peripheral white blood cells of 50 narcolepsy versus 47 controls (half of whom were DQB1*06:02 positive) and found the largest differences between the groups to be in the signal from HLA probes. Further studies of HLA-DQ expression (mRNA and protein in a subset) in 125 controls and 147 narcolepsy cases did not reveal any difference, a result we explain by the lack of proper control of allelic diversity in Affymetrix HLA probes. Rather, a clear effect of DQB1*06:02 allelic dosage on DQB1*06:02 mRNA levels (1.65 fold) and protein (1.59 fold) could be demonstrated independent of the disease status. These results indicate that allelic dosage is transmitted into changes in heterodimer availability, a phenomenon that may explain increased risk for narcolepsy in DQB1*06:02 homozygotes versus heterozygotes. PMID:22326585

  10. DQB1*06:02 allele-specific expression varies by allelic dosage, not narcolepsy status.

    PubMed

    Weiner Lachmi, Karin; Lin, Ling; Kornum, Birgitte Rahbek; Rico, Tom; Lo, Betty; Aran, Adi; Mignot, Emmanuel

    2012-04-01

    The association of narcolepsy-cataplexy, a sleep disorder caused by the loss of hypocretin/orexin neurons in the hypothalamus, with DQA1*01:02-DQB1*06:02 is one of the tightest known single-allele human leukocyte antigen (HLA) associations. In this study, we explored genome-wide expression in peripheral white blood cells of 50 narcolepsy versus 47 controls (half of whom were DQB1*06:02 positive) and observed the largest differences between the groups in the signal from HLA probes. Further studies of HLA-DQ expression (mRNA and protein in a subset) in 125 controls and 147 narcolepsy cases did not reveal any difference, a result we explain by the lack of proper control of allelic diversity in Affymetrix HLA probes. Rather, a clear effect of DQB1*06:02 allelic dosage on DQB1*06:02 mRNA levels (1.65-fold) and protein (1.59-fold) could be demonstrated independent of disease status. These results indicate that allelic dosage is transmitted into changes in heterodimer availability, a phenomenon that may explain the increased risk for narcolepsy in DQB1*06:02 homozygotes versus heterozygotes.

  11. CYP2D6: novel genomic structures and alleles

    PubMed Central

    Kramer, Whitney E.; Walker, Denise L.; O’Kane, Dennis J.; Mrazek, David A.; Fisher, Pamela K.; Dukek, Brian A.; Bruflat, Jamie K.; Black, John L.

    2010-01-01

    Objective CYP2D6 is a polymorphic gene. It has been observed to be deleted, to be duplicated and to undergo recombination events involving the CYP2D7 pseudogene and surrounding sequences. The objective of this study was to discover the genomic structure of CYP2D6 recombinants that interfere with clinical genotyping platforms that are available today. Methods Clinical samples containing rare homozygous CYP2D6 alleles, ambiguous readouts, and those with duplication signals and two different alleles were analyzed by long-range PCR amplification of individual genes, PCR fragment analysis, allele-specific primer extension assay, and DNA sequencing to characterize alleles and genomic structure. Results Novel alleles, genomic structures, and the DNA sequence of these structures are described. Interestingly, in 49 of 50 DNA samples that had CYP2D6 gene duplications or multiplications where two alleles were detected, the chromosome containing the duplication or multiplication had identical tandem alleles. Conclusion Several new CYP2D6 alleles and genomic structures are described which will be useful for CYP2D6 genotyping. The findings suggest that the recombination events responsible for CYP2D6 duplications and multiplications are because of mechanisms other than interchromosomal crossover during meiosis. PMID:19741566

  12. Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?

    PubMed Central

    Ralph, Peter; Coop, Graham

    2010-01-01

    Models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new environment by multiple mutations of similar phenotypic effect that arise in parallel, at the same locus or different loci. These mutations can each quickly reach intermediate frequency, preventing any single one from rapidly sweeping to fixation globally, leading to a “soft” sweep in the population. Here we study various models of parallel mutation in a continuous, geographically spread population adapting to a global selection pressure. The slow geographic spread of a selected allele due to limited dispersal can allow other selected alleles to arise and start to spread elsewhere in the species range. When these different selected alleles meet, their spread can slow dramatically and so initially form a geographic patchwork, a random tessellation, which could be mistaken for a signal of local adaptation. This spatial tessellation will dissipate over time due to mixing by migration, leaving a set of partial sweeps within the global population. We show that the spatial tessellation initially formed by mutational types is closely connected to Poisson process models of crystallization, which we extend. We find that the probability of parallel mutation and the spatial scale on which parallel mutation occurs are captured by a single compound parameter, a characteristic length, which reflects the expected distance a spreading allele travels before it encounters a different spreading allele. This characteristic length depends on the mutation rate, the dispersal parameter, the effective local density of individuals, and to a much lesser extent the strength of selection. While our knowledge of these parameters is poor, we argue that even in widely dispersing species, such parallel geographic sweeps may be surprisingly common. Thus, we predict that as more data

  13. Elucidating the native sources of an invasive tree species, Acacia pycnantha, reveals unexpected native range diversity and structure

    PubMed Central

    Ndlovu, Joice; Richardson, David M.; Wilson, John R. U.; O'Leary, Martin; Le Roux, Johannes J.

    2013-01-01

    Background and Aims Understanding the introduction history of invasive plant species is important for their management and identifying effective host-specific biological control agents. However, uncertain taxonomy, intra- and interspecific hybridization, and cryptic speciation may obscure introduction histories, making it difficult to identify native regions to explore for host-specific agents. The overall aim of this study was to identify the native source populations of Acacia pycnantha, a tree native to south-eastern Australia and invasive in South Africa, Western Australia and Portugal. Using a phylogeographical approach also allowed an exploration of the historical processes that have shaped the genetic structure of A. pycnantha in its native range. Methods Nuclear (nDNA) and plastid DNA sequence data were used in network and tree-building analyses to reconstruct phylogeographical relationships between native and invasive A. pycnantha populations. In addition, mismatch distributions, relative rates and Bayesian analyses were used to infer recent demographic processes and timing of events in Australia that led to population structure and diversification. Key Results The plastid network indicated that Australian populations of A. pycnantha are geographically structured into two informally recognized lineages, the wetland and dryland forms, whereas the nuclear phylogeny showed little geographical structure between these two forms. Moreover, the dryland form of A. pycnantha showed close genetic similarity to the wetland form based on nDNA sequence data. Hybrid zones may explain these findings, supported here by incongruent phylogenetic placement of some of these taxa between nuclear and plastid genealogies. Conclusions It is hypothesized that habitat fragmentation due to cycles of aridity inter-dispersed with periods of abundant rainfall during the Pleistocene (approx. 100 kya) probably gave rise to native dryland and wetland forms of A. pycnantha. Although the

  14. Statistical Studies on Protein Polymorphism in Natural Populations. III. Distribution of Allele Frequencies and the Number of Alleles per Locus

    PubMed Central

    Chakraborty, Ranajit; Fuerst, Paul A.; Nei, Masatoshi

    1980-01-01

    With the aim of understanding the mechanism of maintenance of protein polymorphism, we have studied the properties of allele frequency distribution and the number of alleles per locus, using gene-frequency data from a wide range of organisms (mammals, birds, reptiles, amphibians, Drosophila and non-Drosophila invertebrates) in which 20 or more loci with at least 100 genes were sampled. The observed distribution of allele frequencies was U-shaped in all of the 138 populations (mostly species or subspecies) examined and generally agreed with the theoretical distribution expected under the mutation-drift hypothesis, though there was a significant excess of rare alleles (gene frequency, 0 ∼ 0.05) in about a quarter of the populations. The agreement between the mutation-drift theory and observed data was quite satisfactory for the numbers of polymorphic (gene frequency, 0.05 ∼ 0.95) and monomorphic (0.95 ∼ 1.0) alleles.—The observed pattern of allele-frequency distribution was incompatible with the prediction from the overdominance hypothesis. The observed correlations of the numbers of rare alleles, polymorphic alleles and monomorphic alleles with heterozygosity were of the order of magnitude that was expected under the mutation-drift hypothesis. Our results did not support the view that intracistronic recombination is an important source of genetic variation. The total number of alleles per locus was positively correlated with molecular weight in most of the species examined, and the magnitude of the correlation was consistent with the theoretical prediction from mutation-drift hypothesis. The correlation between molecular weight and the number of alleles was generally higher than the correlation between molecular weight and heterozygosity, as expected. PMID:17249018

  15. Population structure and genetic diversity of greater sage-grouse (Centrocercus urophasianus) in fragmented landscapes at the northern edge of their range

    USGS Publications Warehouse

    Bush, K.L.; Dyte, C.K.; Moynahan, B.J.; Aldridge, C.L.; Sauls, H.S.; Battazzo, A.M.; Walker, B.L.; Doherty, K.E.; Tack, J.; Carlson, J.; Eslinger, D.; Nicholson, J.; Boyce, M.S.; Naugle, D.E.; Paszkowski, C.A.; Coltman, D.W.

    2011-01-01

    Range-edge dynamics and anthropogenic fragmentation are expected to impact patterns of genetic diversity, and understanding the influence of both factors is important for effective conservation of threatened wildlife species. To examine these factors, we sampled greater sage-grouse (Centrocercus urophasianus) from a declining, fragmented region at the northern periphery of the species' range and from a stable, contiguous core region. We genotyped 2,519 individuals at 13 microsatellite loci from 104 leks in Alberta, Saskatchewan, Montana, and Wyoming. Birds from northern Montana, Alberta, and Saskatchewan were identified as a single population that exhibited significant isolation by distance, with the Milk River demarcating two subpopulations. Both subpopulations exhibited high genetic diversity with no evidence that peripheral regions were genetically depauperate or highly structured. However, river valleys and a large agricultural region were significant barriers to dispersal. Leks were also composed primarily of non-kin, rejecting the idea that leks form because of male kin association. Northern Montana sage-grouse are maintaining genetic connectivity in fragmented and northern peripheral habitats via dispersal through and around various forms of fragmentation. ?? 2010 Springer Science+Business Media B.V.

  16. Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes

    PubMed Central

    Delwart, Eric; Li, Linlin

    2011-01-01

    The genomes of numerous circoviruses and distantly related circular DNA viruses encoding a rolling circle replication initiator protein (Rep) have been characterized from the tissues of mammals, fish, insects, and plants (geminivirus and nanovirus), human and animal feces, in an algae cell, and in diverse environmental samples. We review the genome organization, phylogenetic relationships and initial prevalence studies of cycloviruses, a proposed new genus in the Circoviridae family. Viral fossil rep sequences were also identified integrated on the chromosomes of mammals, frogs, lancelets, crustaceans, mites, gastropods, roundworms, placozoans, hydrozoans, protozoans, land plants, fungi, algae, and phytoplasma bacterias and their plasmids, reflecting their past host range. An ancient origin for viruses with rep-encoding single stranded small circular genomes, predating the diversification of eukaryotes, is discussed. The cellular hosts and pathogenicity of many recently described rep-containing circular genomes remain to be determined. Future studies of the virome of single cell and multi-cellular eukaryotes are likely to further extend the known diversity and host-range of small rep-containing circular viral genomes. PMID:22155583

  17. Allele Mining Strategies: Principles and Utilisation for Blast Resistance Genes in Rice (Oryza sativa L.).

    PubMed

    Ashkani, Sadegh; Yusop, Mohd Rafii; Shabanimofrad, Mahmoodreza; Azady, Amin; Ghasemzadeh, Ali; Azizi, Parisa; Latif, Mohammad Abdul

    2015-01-01

    Allele mining is a promising way to dissect naturally occurring allelic variants of candidate genes with essential agronomic qualities. With the identification, isolation and characterisation of blast resistance genes in rice, it is now possible to dissect the actual allelic variants of these genes within an array of rice cultivars via allele mining. Multiple alleles from the complex locus serve as a reservoir of variation to generate functional genes. The routine sequence exchange is one of the main mechanisms of R gene evolution and development. Allele mining for resistance genes can be an important method to identify additional resistance alleles and new haplotypes along with the development of allele-specific markers for use in marker-assisted selection. Allele mining can be visualised as a vital link between effective utilisation of genetic and genomic resources in genomics-driven modern plant breeding. This review studies the actual concepts and potential of mining approaches for the discovery of alleles and their utilisation for blast resistance genes in rice. The details provided here will be important to provide the rice breeder with a worthwhile introduction to allele mining and its methodology for breakthrough discovery of fresh alleles hidden in hereditary diversity, which is vital for crop improvement.

  18. Allelic association between marker loci.

    PubMed

    Lonjou, C; Collins, A; Morton, N E

    1999-02-16

    Allelic association has proven useful to refine the location of major genes prior to positional cloning, but it is of uncertain value for genome scans in complex inheritance. We have extended kinship theory to give information content for linkage and allelic association. Application to pairs of closely linked markers as a surrogate for marker x oligogene pairs indicates that association is largely determined by regional founders, with little effect of subsequent demography. Sub-Saharan Africa has the least allelic association, consistent with settlement of other regions by small numbers of founders. Recent speculation about substantial advantages of isolates over large populations, of constant size over expansion, and of F1 hybrids over incrosses is not supported by theory or data. On the contrary, fewer affected cases, less opportunity for replication, and more stochastic variation tend to make isolates less informative for allelic association, as they are for linkage.

  19. What Is a Recessive Allele?

    ERIC Educational Resources Information Center

    American Biology Teacher, 1991

    1991-01-01

    Presents four misconceptions students have concerning the concepts of recessive and dominant alleles. Discusses the spectrum of dominant-recessive relationships, different levels of analysis between phenotype and genotype, possible causes of dominance, and an example involving wrinkled peas. (MDH)

  20. A computer simulation study of VNTR population genetics: Constrained recombination rules out the infinite alleles model

    SciTech Connect

    Harding, R.M.; Martinson, J.J.; Flint, J.; Clegg, J.B.; Boyce, A.J. )

    1993-11-01

    Extensive allelic diversity in variable numbers of tandem repeats (VNTRs) has been discovered in the human genome. For population genetic studies of VNTRs, such as forensic applications, it is important to know whether a neutral mutation-drift balance of VNTR polymorphism can be represented by the infinite alleles model. The assumption of the infinite alleles model that each new mutant is unique is very likely to be violated by unequal sister chromatid exchange (USCE), the primary process believed to generate VNTR mutants. The authors show that increasing both mutation rates and misalignment constraint for intrachromosomal recombination in a computer simulation model reduces simulated VNTR diversity below the expectations of the infinite alleles model. Maximal constraint, represented as slippage of single repeats, reduces simulated VNTR diversity to levels expected from the stepwise mutation model. Although misalignment rule is the more important variable, mutation rate also has an effect. At moderate rates of USCE, simulated VNTR diversity fluctuates around infinite alleles expectation. However, if rates of USCE are high, as for hypervariable VNTRs, simulated VNTR diversity is consistently lower than predicted by the infinite alleles model. This has been observed for many VNTRs and accounted for by technical problems in distinguishing alleles of neighboring size classes. The authors use sampling theory to confirm the intrinsically poor fit to the infinite model of both simulated VNTR diversity and observed VNTR polymorphisms sampled from two Papua New Guinean populations. 25 refs., 20 figs., 4 tabs.

  1. Deciphering diversity in populations of various linguistic and ethnic affiliations of different geographical regions of India: analysis based on 15 microsatellite markers.

    PubMed

    Kashyap, V K; Ashma, Richa; Gaikwad, Sonali; Sarkar, B N; Trivedi, R

    2004-04-01

    The extent of genetic polymorphism at fifteen autosomal microsatellite markers in 54 ethnically, linguistically and geographically diverse human populations of India was studied to decipher intrapopulation diversity. The parameters used to quantify intrapopulation diversity were average allele diversity, average heterozygosity, allele range (base pairs), and number of alleles. Multilocus genotype frequencies calculated for selected populations were utilized for testing conformity with the assumption of Hardy-Weinberg equilibrium. The exact test values, after Bonferroni correction, showed significant deviation amongst Gowda (vWA, Penta E); Dhangar, Satnami and Gounder (D8S1179); Hmar (FGA); Kuki and Balti (vWA) groups. Relatively low number of alleles and allelic diversity (base-pairs size) had been observed in populations of central India as compared with southern and northern regions of the country. The communities of Indo-Caucasoid ethnic origin and Indo-European linguistic family (Kshatriya of Uttar Pradesh) showed highest allelic diversity, as well as rare alleles, not reported in any other Indian populations. Analysis based on average heterozygosity was also found to be lowest among the populations of central India (0.729) and highest among the populations from north (0.777) and west (0.784) regions of the country, having Indo-Caucasoid ethnic origin and Austro-Asiatic linguistic affiliation. The maximum power of discrimination (85%-89%) had been observed at loci FGA, Penta E, D18S51 and D21S11, suggested high intrapopulation diversity in India. Genetic diversity revealed by STR markers was consistent with the known demographic histories of populations. Thus, the present study clearly demonstrated that the intrapopulation diversity is not only present at the national level, but also within smaller geographical regions of the country. This is the first attempt to understand the extent of diversity within populations of India at such a large scale at genomic

  2. Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient

    NASA Astrophysics Data System (ADS)

    Jablonski, David; Belanger, Christina L.; Berke, Sarah K.; Huang, Shan; Krug, Andrew Z.; Roy, Kaustuv; Tomasovych, Adam; Valentine, James W.

    2013-06-01

    Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species. Range expansion of clades may occur via "bridge species," which violate climate-niche conservatism to bridge the tropical-temperate boundary in most OTT genera. Substantial time lags (∼5 Myr) between the origins of tropical clades and their entry into the temperate zone suggest that OTT events are rare on a per-clade basis. Clades with higher diversification rates within the tropics are the most likely to expand OTT and the most likely to produce multiple bridge species, suggesting that high speciation rates promote the OTT dynamic. Although expansion of thermal tolerances is key to the OTT dynamic, most latitudinally widespread species instead achieve their broad ranges by tracking widespread, spatially-uniform temperatures within the tropics (yielding, via the nonlinear relation between temperature and latitude, a pattern opposite to Rapoport's rule). This decoupling of range size and temperature tolerance may also explain the differing roles of species and clade ranges in buffering species from background and mass extinctions.

  3. Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient.

    PubMed

    Jablonski, David; Belanger, Christina L; Berke, Sarah K; Huang, Shan; Krug, Andrew Z; Roy, Kaustuv; Tomasovych, Adam; Valentine, James W

    2013-06-25

    Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species. Range expansion of clades may occur via "bridge species," which violate climate-niche conservatism to bridge the tropical-temperate boundary in most OTT genera. Substantial time lags (∼5 Myr) between the origins of tropical clades and their entry into the temperate zone suggest that OTT events are rare on a per-clade basis. Clades with higher diversification rates within the tropics are the most likely to expand OTT and the most likely to produce multiple bridge species, suggesting that high speciation rates promote the OTT dynamic. Although expansion of thermal tolerances is key to the OTT dynamic, most latitudinally widespread species instead achieve their broad ranges by tracking widespread, spatially-uniform temperatures within the tropics (yielding, via the nonlinear relation between temperature and latitude, a pattern opposite to Rapoport's rule). This decoupling of range size and temperature tolerance may also explain the differing roles of species and clade ranges in buffering species from background and mass extinctions. PMID:23759748

  4. Flexible long-range loops in the VH gene region of the Igh locus facilitate the generation of a diverse antibody repertoire.

    PubMed

    Medvedovic, Jasna; Ebert, Anja; Tagoh, Hiromi; Tamir, Ido M; Schwickert, Tanja A; Novatchkova, Maria; Sun, Qiong; Huis In 't Veld, Pim J; Guo, Chunguang; Yoon, Hye Suk; Denizot, Yves; Holwerda, Sjoerd J B; de Laat, Wouter; Cogné, Michel; Shi, Yang; Alt, Frederick W; Busslinger, Meinrad

    2013-08-22

    The immunoglobulin heavy-chain (Igh) locus undergoes large-scale contraction in pro-B cells, which facilitates VH-DJH recombination by juxtaposing distal VH genes next to the DJH-rearranged gene segment in the 3' proximal Igh domain. By using high-resolution mapping of long-range interactions, we demonstrate that local interaction domains established the three-dimensional structure of the extended Igh locus in lymphoid progenitors. In pro-B cells, these local domains engaged in long-range interactions across the Igh locus, which depend on the regulators Pax5, YY1, and CTCF. The large VH gene cluster underwent flexible long-range interactions with the more rigidly structured proximal domain, which probably ensures similar participation of all VH genes in VH-DJH recombination to generate a diverse antibody repertoire. These long-range interactions appear to be an intrinsic feature of the VH gene cluster, because they are still generated upon mutation of the Eμ enhancer, IGCR1 insulator, or 3' regulatory region in the proximal Igh domain.

  5. Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient.

    PubMed

    Jablonski, David; Belanger, Christina L; Berke, Sarah K; Huang, Shan; Krug, Andrew Z; Roy, Kaustuv; Tomasovych, Adam; Valentine, James W

    2013-06-25

    Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species. Range expansion of clades may occur via "bridge species," which violate climate-niche conservatism to bridge the tropical-temperate boundary in most OTT genera. Substantial time lags (∼5 Myr) between the origins of tropical clades and their entry into the temperate zone suggest that OTT events are rare on a per-clade basis. Clades with higher diversification rates within the tropics are the most likely to expand OTT and the most likely to produce multiple bridge species, suggesting that high speciation rates promote the OTT dynamic. Although expansion of thermal tolerances is key to the OTT dynamic, most latitudinally widespread species instead achieve their broad ranges by tracking widespread, spatially-uniform temperatures within the tropics (yielding, via the nonlinear relation between temperature and latitude, a pattern opposite to Rapoport's rule). This decoupling of range size and temperature tolerance may also explain the differing roles of species and clade ranges in buffering species from background and mass extinctions.

  6. Genetic Diversity and Host Range of Rhizobia Nodulating Lotus tenuis in Typical Soils of the Salado River Basin (Argentina)▿ †

    PubMed Central

    Estrella, María Julia; Muñoz, Socorro; Soto, María José; Ruiz, Oscar; Sanjuán, Juan

    2009-01-01

    A total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating Lotus tenuis in typical soils of the Salado River Basin. A high level of genetic diversity was revealed by repetitive extragenic palindromic PCR, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters A and B, after 16S rRNA restriction fragment length polymorphism analysis. Cluster A strains appeared to be related to the genus Mesorhizobium, whereas cluster B was related to the genus Rhizobium. 16S rRNA sequence and phylogenetic analysis further supported the distribution of most of the symbiotic isolates in either Rhizobium or Mesorhizobium: the only exception was isolate BA135, whose 16S rRNA gene was closely related to the 16S rRNA gene of the genus Aminobacter. Most Mesorhizobium-like isolates were closely related to Mesorhizobium amorphae, Mesorhizobium mediterraneum, Mesorhizobium tianshanense, or the broad-host-range strain NZP2037, but surprisingly few isolates grouped with Mesorhizobium loti type strain NZP2213. Rhizobium-like strains were related to Rhizobium gallicum, Rhizobium etli, or Rhizobium tropici, for which Phaseolus vulgaris is a common host. However, no nodC or nifH genes could be amplified from the L. tenuis isolates, suggesting that they have rather divergent symbiosis genes. In contrast, nodC genes from the Mesorhizobium and Aminobacter strains were closely related to nodC genes from narrow-host-range M. loti strains. Likewise, nifH gene sequences were very highly conserved among the Argentinian isolates and reference Lotus rhizobia. The high levels of conservation of the nodC and nifH genes suggest that there was a common origin of the symbiosis genes in narrow-host-range Lotus symbionts, supporting the hypothesis that both intrageneric horizontal gene transfer and intergeneric horizontal gene transfer are important mechanisms for the spread of symbiotic capacity in the Salado River Basin. PMID

  7. SSR allelic variation in almond (Prunus dulcis Mill.).

    PubMed

    Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

    2006-01-01

    Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

  8. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China*

    PubMed Central

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-01-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population’s genetic background, for individual identification, and for paternity testing in forensic practice. PMID:23733431

  9. The Length Distribution of Class I-Restricted T Cell Epitopes Is Determined by Both Peptide Supply and MHC Allele-Specific Binding Preference.

    PubMed

    Trolle, Thomas; McMurtrey, Curtis P; Sidney, John; Bardet, Wilfried; Osborn, Sean C; Kaever, Thomas; Sette, Alessandro; Hildebrand, William H; Nielsen, Morten; Peters, Bjoern

    2016-02-15

    HLA class I-binding predictions are widely used to identify candidate peptide targets of human CD8(+) T cell responses. Many such approaches focus exclusively on a limited range of peptide lengths, typically 9 aa and sometimes 9-10 aa, despite multiple examples of dominant epitopes of other lengths. In this study, we examined whether epitope predictions can be improved by incorporating the natural length distribution of HLA class I ligands. We found that, although different HLA alleles have diverse length-binding preferences, the length profiles of ligands that are naturally presented by these alleles are much more homogeneous. We hypothesized that this is due to a defined length profile of peptides available for HLA binding in the endoplasmic reticulum. Based on this, we created a model of HLA allele-specific ligand length profiles and demonstrate how this model, in combination with HLA-binding predictions, greatly improves comprehensive identification of CD8(+) T cell epitopes. PMID:26783342

  10. Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China.

    PubMed

    Wang, Hong-dan; Shen, Chun-mei; Liu, Wen-juan; Zhang, Yu-dang; Yang, Guang; Yan, Jiang-wei; Qin, Hai-xia; Zhu, Bo-feng

    2013-06-01

    We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.

  11. Broad-Range Survey of Tick-Borne Pathogens in Southern Germany Reveals a High Prevalence of Babesia microti and a Diversity of Other Tick-Borne Pathogens

    PubMed Central

    Crowder, Chris D.; Carolan, Heather E.; Rounds, Megan A.; Ecker, David J.; Haag, Heike; Mothes, Benedikt; Nolte, Oliver

    2014-01-01

    Abstract Ticks harbor numerous pathogens of significance to human and animal health. A better understanding of the pathogens carried by ticks in a given geographic area can alert health care providers of specific health risks leading to better diagnosis and treatments. In this study, we tested 226 Ixodes ricinis ticks from Southern Germany using a broad-range PCR and electrospray ionization mass spectrometry assay (PCR/ESI-MS) designed to identify tick-borne bacterial and protozoan pathogens in a single test. We found 21.2% of the ticks tested carried Borrelia burgdorferi sensu lato consisting of diverse genospecies; a surprisingly high percentage of ticks were infected with Babesia microti (3.5%). Other organisms found included Borrelia miyamotoi, Rickettsia helvetica, Rickettsia monacensis, and Anaplasma phagocytophilum. Of further significance was our finding that more than 7% of ticks were infected with more than one pathogen or putative pathogen. PMID:25072989

  12. Delimiting Allelic Imbalance of TYMS by Allele-Specific Analysis

    PubMed Central

    Balboa-Beltrán, Emilia; Cruz, Raquel; Carracedo, Angel; Barros, Francisco

    2015-01-01

    Abstract Allelic imbalance of thymidylate synthase (TYMS) is attributed to polymorphisms in the 5′- and 3′-untranslated region (UTR). These polymorphisms have been related to the risk of suffering different cancers, for example leukemia, breast or gastric cancer, and response to different drugs, among which are methotrexate glutamates, stavudine, and specifically 5-fluorouracil (5-FU), as TYMS is its direct target. A vast literature has been published in relation to 5-FU, even suggesting the sole use of these polymorphisms to effectively manage 5-FU dosage. Estimates of the extent to which these polymorphisms influence in TYMS expression have in the past been based on functional analysis by luciferase assays and quantification of TYMS mRNA, but both these studies, as the association studies with cancer risk or with toxicity or response to 5-FU, are very contradictory. Regarding functional assays, the artificial genetic environment created in luciferase assay and the problems derived from quantitative polymerase chain reactions (qPCRs), for example the use of a reference gene, may have distorted the results. To avoid these sources of interference, we have analyzed the allelic imbalance of TYMS by allelic-specific analysis in peripheral blood mononuclear cells (PBMCs) from patients. Allelic imbalance in PBMCs, taken from 40 patients with suspected myeloproliferative haematological diseases, was determined by fluorescent fragment analysis (for the 3′-UTR polymorphism), Sanger sequencing and allelic-specific qPCR in multiplex (for the 5′-UTR polymorphisms). For neither the 3′- nor the 5′-UTR polymorphisms did the observed allelic imbalance exceed 1.5 fold. None of the TYMS polymorphisms is statistically associated with allelic imbalance. The results acquired allow us to deny the previously established assertion of an influence of 2 to 4 fold of the rs45445694 and rs2853542 polymorphisms in the expression of TYMS and narrow its allelic imbalance to 1.5 fold

  13. Robust identification of local adaptation from allele frequencies.

    PubMed

    Günther, Torsten; Coop, Graham

    2013-09-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of "standardized allele frequencies" that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools-a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  14. Robust Identification of Local Adaptation from Allele Frequencies

    PubMed Central

    Günther, Torsten; Coop, Graham

    2013-01-01

    Comparing allele frequencies among populations that differ in environment has long been a tool for detecting loci involved in local adaptation. However, such analyses are complicated by an imperfect knowledge of population allele frequencies and neutral correlations of allele frequencies among populations due to shared population history and gene flow. Here we develop a set of methods to robustly test for unusual allele frequency patterns and correlations between environmental variables and allele frequencies while accounting for these complications based on a Bayesian model previously implemented in the software Bayenv. Using this model, we calculate a set of “standardized allele frequencies” that allows investigators to apply tests of their choice to multiple populations while accounting for sampling and covariance due to population history. We illustrate this first by showing that these standardized frequencies can be used to detect nonparametric correlations with environmental variables; these correlations are also less prone to spurious results due to outlier populations. We then demonstrate how these standardized allele frequencies can be used to construct a test to detect SNPs that deviate strongly from neutral population structure. This test is conceptually related to FST and is shown to be more powerful, as we account for population history. We also extend the model to next-generation sequencing of population pools—a cost-efficient way to estimate population allele frequencies, but one that introduces an additional level of sampling noise. The utility of these methods is demonstrated in simulations and by reanalyzing human SNP data from the Human Genome Diversity Panel populations and pooled next-generation sequencing data from Atlantic herring. An implementation of our method is available from http://gcbias.org. PMID:23821598

  15. Common alleles contribute to schizophrenia in CNV carriers

    PubMed Central

    Tansey, K E; Rees, E; Linden, D E; Ripke, S; Chambert, K D; Moran, J L; McCarroll, S A; Holmans, P; Kirov, G; Walters, J; Owen, M J; O'Donovan, M C

    2016-01-01

    The genetic architecture of schizophrenia is complex, involving risk alleles ranging from common alleles of weak effect to rare alleles of large effect, the best exemplar of the latter being large copy number variants (CNVs). It is currently unknown whether pathophysiology in those with defined rare mutations overlaps with that in other individuals with the disorder who do not share the same rare mutation. Under an extreme heterogeneity model, carriers of specific high-penetrance mutations form distinct subgroups. In contrast, under a polygenic threshold model, high-penetrance rare allele carriers possess many risk factors, of which the rare allele is the only one, albeit an important, factor. Under the latter model, cases with rare mutations can be expected to share some common risk alleles, and therefore pathophysiological mechanisms, with cases without the same mutation. Here we show that, compared with controls, individuals with schizophrenia who have known pathogenic CNVs carry an excess burden of common risk alleles (P=2.25 × 10−17) defined from a genome-wide association study largely based on individuals without known CNVs. Our finding is not consistent with an extreme heterogeneity model for CNV carriers, but does offer support for the polygenic threshold model of schizophrenia. That this is so provides support for the notion that studies aiming to model the effects of rare variation may uncover pathophysiological mechanisms of relevance to those with the disorder more widely. PMID:26390827

  16. Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding*

    PubMed Central

    Wang, Jun-mei; Yang, Jian-ming; Zhu, Jing-huan; Jia, Qiao-jun; Tao, Yue-zhi

    2010-01-01

    The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the barley accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 barley accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China. PMID:20872987

  17. Assessment of genetic diversity by simple sequence repeat markers among forty elite varieties in the germplasm for malting barley breeding.

    PubMed

    Wang, Jun-mei; Yang, Jian-ming; Zhu, Jing-huan; Jia, Qiao-jun; Tao, Yue-zhi

    2010-10-01

    The genetic diversity and relationship among 40 elite barley varieties were analyzed based on simple sequence repeat (SSR) genotyping data. The amplified fragments from SSR primers were highly polymorphic in the barley accessions investigated. A total of 85 alleles were detected at 35 SSR loci, and allelic variations existed at 29 SSR loci. The allele number per locus ranged from 1 to 5 with an average of 2.4 alleles per locus detected from the 40 barley accessions. A cluster analysis based on the genetic similarity coefficients was conducted and the 40 varieties were classified into two groups. Seven malting barley varieties from China fell into the same subgroup. It was found that the genetic diversity within the Chinese malting barley varieties was narrower than that in other barley germplasm sources, suggesting the importance and feasibility of introducing elite genotypes from different origins for malting barley breeding in China. PMID:20872987

  18. Out of the tropics, but how? Fossils, bridge species, and thermal ranges in the dynamics of the marine latitudinal diversity gradient

    PubMed Central

    Jablonski, David; Belanger, Christina L.; Berke, Sarah K.; Huang, Shan; Krug, Andrew Z.; Roy, Kaustuv; Tomasovych, Adam; Valentine, James W.

    2013-01-01

    Latitudinal diversity gradients are underlain by complex combinations of origination, extinction, and shifts in geographic distribution and therefore are best analyzed by integrating paleontological and neontological data. The fossil record of marine bivalves shows, in three successive late Cenozoic time slices, that most clades (operationally here, genera) tend to originate in the tropics and then expand out of the tropics (OTT) to higher latitudes while retaining their tropical presence. This OTT pattern is robust both to assumptions on the preservation potential of taxa and to taxonomic revisions of extant and fossil species. Range expansion of clades may occur via “bridge species,” which violate climate-niche conservatism to bridge the tropical-temperate boundary in most OTT genera. Substantial time lags (∼5 Myr) between the origins of tropical clades and their entry into the temperate zone suggest that OTT events are rare on a per-clade basis. Clades with higher diversification rates within the tropics are the most likely to expand OTT and the most likely to produce multiple bridge species, suggesting that high speciation rates promote the OTT dynamic. Although expansion of thermal tolerances is key to the OTT dynamic, most latitudinally widespread species instead achieve their broad ranges by tracking widespread, spatially-uniform temperatures within the tropics (yielding, via the nonlinear relation between temperature and latitude, a pattern opposite to Rapoport’s rule). This decoupling of range size and temperature tolerance may also explain the differing roles of species and clade ranges in buffering species from background and mass extinctions. PMID:23759748

  19. Diversity of bees and their floral resources at altitudinal areas in the Southern Espinhaço Range, Minas Gerais, Brazil.

    PubMed

    Araújo, Vinícius A; Antonini, Yasmine; Araújo, Ana P A

    2006-01-01

    The Southern Espinhaço Range consists of large areas covered by quartzitic or metaliferous tropical altitudinal fields. The Espinhaço Range ecosystems are endangered by anthropic high impacts, particularly due to mining and urbanization. We conducted a one-year inventory of the bee flora and fauna at the quartzitic Ouro Branco Mountains and a two-year survey of the metaliferous Ouro Preto fields. The samples were collected twice a month, from 8:00 am to 5:00 pm. The bees (677) belonged to 91 species, five families. The family Apidae was the richest and most abundant, followed by the Halictidae and Megachilidae. The bees visited 46 flowering plant species; the most visited plants were the Asteraceae (n = 220), the Malpighiaceae (n = 95), the Melastomataceae (n = 94), the Fabaceae (n = 78), and the Solanaceae (n = 63). Diversity was higher in Ouro Branco (H = 1.47) than in Ouro Preto (H = 1.17). The low richness and abundance of bees in our research site when compared to other Brazilian "Cerrado" areas can be due to the high altitude, low temperature, and low availability of flowers we found. "Canga" and rupestrian areas house fauna and flora species that are rare and threatened by extinction. The southern Espinhaço areas can, therefore, be given the status of permanent biodiversity preservation area.

  20. Effect of cattle on Salmonella carriage, diversity and antimicrobial resistance in free-ranging wild boar (Sus scrofa) in northeastern Spain.

    PubMed

    Navarro-Gonzalez, Nora; Mentaberre, Gregorio; Porrero, Concepción M; Serrano, Emmanuel; Mateos, Ana; López-Martín, José M; Lavín, Santiago; Domínguez, Lucas

    2012-01-01

    Salmonella is distributed worldwide and is a pathogen of economic and public health importance. As a multi-host pathogen with a long environmental persistence, it is a suitable model for the study of wildlife-livestock interactions. In this work, we aim to explore the spill-over of Salmonella between free-ranging wild boar and livestock in a protected natural area in NE Spain and the presence of antimicrobial resistance. Salmonella prevalence, serotypes and diversity were compared between wild boars, sympatric cattle and wild boars from cattle-free areas. The effect of age, sex, cattle presence and cattle herd size on Salmonella probability of infection in wild boars was explored by means of Generalized Linear Models and a model selection based on the Akaike's Information Criterion. Prevalence was higher in wild boars co-habiting with cattle (35.67%, CI 95% 28.19-43.70) than in wild boar from cattle-free areas (17.54%, CI 95% 8.74-29.91). Probability of a wild boar being a Salmonella carrier increased with cattle herd size but decreased with the host age. Serotypes Meleagridis, Anatum and Othmarschen were isolated concurrently from cattle and sympatric wild boars. Apart from serotypes shared with cattle, wild boars appear to have their own serotypes, which are also found in wild boars from cattle-free areas (Enteritidis, Mikawasima, 4:b:- and 35:r:z35). Serotype richness (diversity) was higher in wild boars co-habiting with cattle, but evenness was not altered by the introduction of serotypes from cattle. The finding of a S. Mbandaka strain resistant to sulfamethoxazole, streptomycin and chloramphenicol and a S. Enteritidis strain resistant to ciprofloxacin and nalidixic acid in wild boars is cause for public health concern.

  1. Effect of Cattle on Salmonella Carriage, Diversity and Antimicrobial Resistance in Free-Ranging Wild Boar (Sus scrofa) in Northeastern Spain

    PubMed Central

    Navarro-Gonzalez, Nora; Mentaberre, Gregorio; Porrero, Concepción M.; Serrano, Emmanuel; Mateos, Ana; López-Martín, José M.; Lavín, Santiago; Domínguez, Lucas

    2012-01-01

    Salmonella is distributed worldwide and is a pathogen of economic and public health importance. As a multi-host pathogen with a long environmental persistence, it is a suitable model for the study of wildlife-livestock interactions. In this work, we aim to explore the spill-over of Salmonella between free-ranging wild boar and livestock in a protected natural area in NE Spain and the presence of antimicrobial resistance. Salmonella prevalence, serotypes and diversity were compared between wild boars, sympatric cattle and wild boars from cattle-free areas. The effect of age, sex, cattle presence and cattle herd size on Salmonella probability of infection in wild boars was explored by means of Generalized Linear Models and a model selection based on the Akaike’s Information Criterion. Prevalence was higher in wild boars co-habiting with cattle (35.67%, CI 95% 28.19–43.70) than in wild boar from cattle-free areas (17.54%, CI 95% 8.74–29.91). Probability of a wild boar being a Salmonella carrier increased with cattle herd size but decreased with the host age. Serotypes Meleagridis, Anatum and Othmarschen were isolated concurrently from cattle and sympatric wild boars. Apart from serotypes shared with cattle, wild boars appear to have their own serotypes, which are also found in wild boars from cattle-free areas (Enteritidis, Mikawasima, 4:b:- and 35:r:z35). Serotype richness (diversity) was higher in wild boars co-habiting with cattle, but evenness was not altered by the introduction of serotypes from cattle. The finding of a S. Mbandaka strain resistant to sulfamethoxazole, streptomycin and chloramphenicol and a S. Enteritidis strain resistant to ciprofloxacin and nalidixic acid in wild boars is cause for public health concern. PMID:23284725

  2. Analysis of the genetic diversity of the nematode parasite Baylisascaris schroederi from wild giant pandas in different mountain ranges in China

    PubMed Central

    2013-01-01

    Background Baylisascaris schroederi is one of the most common nematodes of the giant panda, and can cause severe baylisascarosis in both wild and captive giant pandas. Previous studies of the giant pandas indicated that this population is genetically distinct, implying the presence of a new subspecies. Based on the co-evolution between the parasite and the host, the aim of this study was to investigate the genetic differentiation in the B. schroederi population collected from giant pandas inhabiting different mountain ranges, and further to identify whether the evolution of this parasite correlates with the evolution of giant pandas. Methods In this study, 48 B. schroederi were collected from 28 wild giant pandas inhabiting the Qinling, Minshan and Qionglai mountain ranges in China. The complete sequence of the mitochondrial cytochrome b (mtCytb) gene was amplified by PCR, and the corresponding population genetic diversity of the three mountain populations was determined. In addition, we discussed the evolutionary relationship between B. schroederi and its host giant panda. Results For the DNA dataset, insignificant Fst values and a significant, high level of gene flow were detected among the three mountain populations of B. schroederi, and high genetic variation within populations and a low genetic distance were observed. Both phylogenetic analyses and network mapping of the 16 haplotypes revealed a dispersed pattern and an absence of branches strictly corresponding to the three mountain range sampling sites. Neutrality tests and mismatch analysis indicated that B. schroederi experienced a population expansion in the past. Conclusions Taken together, the dispersed haplotype map, extremely high gene flow among the three populations of B. schroederi, low genetic structure and rapid evolutionary rate suggest that the B. schroederi populations did not follow a pattern of isolation by distance, indicating the existence of physical connections before these populations

  3. Identification of 2127 new HLA class I alleles in potential stem cell donors from Germany, the United States and Poland.

    PubMed

    Hernández-Frederick, C J; Giani, A S; Cereb, N; Sauter, J; Silva-González, R; Pingel, J; Schmidt, A H; Ehninger, G; Yang, S Y

    2014-03-01

    We describe 2127 new human leukocyte antigen (HLA) class I alleles found in registered stem cell donors. These alleles represent 28.9% of the currently known class I alleles. Comparing new allele sequences to homologous sequences, we found 68.1% nonsynonymous nucleotide substitutions, 28.9% silent mutations and 3.0% nonsense mutations. Many substitutions occurred at positions that have not been known to be polymorphic before. A large number of HLA alleles and nucleotide variations underline the extreme diversity of the HLA system. Strikingly, 156 new alleles were found not only multiple times, but also in carriers of various parentage, suggesting that some new alleles are not necessarily rare. Moreover, new alleles were found especially often in minority donors. This emphasizes the benefits of specifically recruiting such groups of individuals.

  4. Allele surfing promotes microbial adaptation from standing variation.

    PubMed

    Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartlomiej; Hallatschek, Oskar

    2016-08-01

    The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from 'soft' selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges. PMID:27307400

  5. Ecological-genomic diversity of microsatellites in wild barley, Hordeum spontaneum, populations in Jordan.

    PubMed

    Baek, H J; Beharav, A; Nevo, E

    2003-02-01

    We analyzed the ecological-genomic diversity of microsatellites of wild barley, Hordeum spontaneum (C. Koch) Thell., at 18 loci in 306 individuals of 16 populations from Jordan across a southward transect of increasing aridity. The 18 microsatellites revealed a total of 249 alleles, with an average of 13.8 alleles per locus (range 3-29), with nonrandom distribution. The proportion of polymorphic loci per population averaged 0.91 (range 0.83-1.00); gene diversity, He, averaged 0.512 (range 0.38-0.651). We compared the number of alleles of the 18 loci to those found in Israel populations by Turpeinen et al. Out of the 280 alleles, 138 (49.3%) were unique (i.e. occurred in only one of the countries). The percentage of unique alleles in Jordan and Israel populations was 43.0% and 17.9%, respectively, suggesting that Jordan is an important center of origin and diversity of wild barley. Estimates of mean gene diversity were highest in the populations collected near the Golan Heights, such as Shuni North, Shuni South and Jarash. Sixty nine percent of the microsatellite variation was partitioned within populations and 31% between populations. Associations between ecogeographical values and gene diversity were established for eight microsatellite loci. The cluster produced by simple sequence repeat (SSR) data is mostly coincidence with the result of the dendrogram of the Spalax ehrenbergi superspecies of subterranean mole rats in Jordan based on allozyme gene loci. The major soil type in the wild barley habitat of each ecological group was different. Stepwise multiple regression analysis indicated that the variance of gene diversity was explained by altitude (R(2) = 0.362**). These observations suggest that microsatellites are at least partly adaptive and subject to natural selection. PMID:12589539

  6. Allele-dependent barley grain beta-amylase activity.

    PubMed

    Erkkilä, M J; Leah, R; Ahokas, H; Cameron-Mills, V

    1998-06-01

    The wild ancestor of cultivated barley, Hordeum vulgare subsp. spontaneum (K. Koch) A. & Gr. (H. spontaneum), is a source of wide genetic diversity, including traits that are important for malting quality. A high beta-amylase trait was previously identified in H. spontaneum strains from Israel, and transferred into the backcross progeny of a cross with the domesticated barley cv Adorra. We have used Southern-blot analysis and beta-amy1 gene characterization to demonstrate that the high beta-amylase trait in the backcross line is co-inherited with the beta-amy1 gene from the H. spontaneum parent. We have analyzed the beta-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct beta-amy1 alleles. Two of these beta-amy1 alleles were present in modern barley, one of which was specifically found in good malting barley cultivars. The third allele, linked with high grain beta-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated beta-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of beta-amylase activity in barley grain is proposed.

  7. Allele-Dependent Barley Grain β-Amylase Activity1

    PubMed Central

    Erkkilä, Maria J.; Leah, Robert; Ahokas, Hannu; Cameron-Mills, Verena

    1998-01-01

    The wild ancestor of cultivated barley, Hordeum vulgare subsp. spontaneum (K. Koch) A. & Gr. (H. spontaneum), is a source of wide genetic diversity, including traits that are important for malting quality. A high β-amylase trait was previously identified in H. spontaneum strains from Israel, and transferred into the backcross progeny of a cross with the domesticated barley cv Adorra. We have used Southern-blot analysis and β-amy1 gene characterization to demonstrate that the high β-amylase trait in the backcross line is co-inherited with the β-amy1 gene from the H. spontaneum parent. We have analyzed the β-amy1 gene organization in various domesticated and wild-type barley strains and identified three distinct β-amy1 alleles. Two of these β-amy1 alleles were present in modern barley, one of which was specifically found in good malting barley cultivars. The third allele, linked with high grain β-amylase activity, was found only in a H. spontaneum strain from the Judean foothills in Israel. The sequences of three isolated β-amy1 alleles are compared. The involvement of specific intron III sequences, in particular a 126-bp palindromic insertion, in the allele-dependent expression of β-amylase activity in barley grain is proposed. PMID:9625721

  8. The effects of organic matter-mineral interactions and organic matter chemistry on diuron sorption across a diverse range of soils.

    PubMed

    Smernik, Ronald J; Kookana, Rai S

    2015-01-01

    Sorption of non-ionic organic compounds to soil is usually expressed as the carbon-normalized partition coefficient (KOC), because it is assumed that the main factor that influences the amount sorbed is the organic carbon content of the soil. However, KOC can vary by a factor of at least ten across a range of soils. We investigated two potential causes of variation in diuron KOC - organic matter-mineral interactions and organic matter chemistry - for a diverse set of 34 soils from Sri Lanka, representing a wide range of soil types. Treatment with hydrofluoric acid (HF-treatment) was used to concentrate soil organic matter. HF-treatment increased KOC for the majority of soils (average factor 2.4). We attribute this increase to the blocking of organic matter sorption sites in the whole soils by minerals. There was no significant correlation between KOC for the whole soils and KOC for the HF-treated soils, indicating that the importance of organic matter-mineral interactions varied greatly amongst these soils. There was as much variation in KOC across the HF-treated soils as there was across the whole soils, indicating that the nature of soil organic matter is also an important contributor to KOC variability. Organic matter chemistry, determined by solid-state (13)C nuclear magnetic resonance (NMR) spectroscopy, was correlated with KOC for the HF-treated soils. In particular, KOC increased with the aromatic C content (R=0.64, p=1×10(-6)), and decreased with O-alkyl C (R=-0.32, p=0.03) and alkyl C (R=-0.41, p=0.004) content.

  9. The effects of organic matter-mineral interactions and organic matter chemistry on diuron sorption across a diverse range of soils.

    PubMed

    Smernik, Ronald J; Kookana, Rai S

    2015-01-01

    Sorption of non-ionic organic compounds to soil is usually expressed as the carbon-normalized partition coefficient (KOC), because it is assumed that the main factor that influences the amount sorbed is the organic carbon content of the soil. However, KOC can vary by a factor of at least ten across a range of soils. We investigated two potential causes of variation in diuron KOC - organic matter-mineral interactions and organic matter chemistry - for a diverse set of 34 soils from Sri Lanka, representing a wide range of soil types. Treatment with hydrofluoric acid (HF-treatment) was used to concentrate soil organic matter. HF-treatment increased KOC for the majority of soils (average factor 2.4). We attribute this increase to the blocking of organic matter sorption sites in the whole soils by minerals. There was no significant correlation between KOC for the whole soils and KOC for the HF-treated soils, indicating that the importance of organic matter-mineral interactions varied greatly amongst these soils. There was as much variation in KOC across the HF-treated soils as there was across the whole soils, indicating that the nature of soil organic matter is also an important contributor to KOC variability. Organic matter chemistry, determined by solid-state (13)C nuclear magnetic resonance (NMR) spectroscopy, was correlated with KOC for the HF-treated soils. In particular, KOC increased with the aromatic C content (R=0.64, p=1×10(-6)), and decreased with O-alkyl C (R=-0.32, p=0.03) and alkyl C (R=-0.41, p=0.004) content. PMID:24972176

  10. Pinworm diversity in free-ranging howler monkeys (Alouatta spp.) in Mexico: Morphological and molecular evidence for two new Trypanoxyuris species (Nematoda: Oxyuridae).

    PubMed

    Solórzano-García, Brenda; Nadler, Steven A; Pérez-Ponce de León, Gerardo

    2016-10-01

    Two new species of Trypanoxyuris are described from the intestine of free-ranging howler monkeys in Mexico, Trypanoxyuris multilabiatus n. sp. from the mantled howler Alouatta palliata, and Trypanoxyuris pigrae n. sp. from the black howler Alouatta pigra. An integrative taxonomic approach is followed, where conspicuous morphological traits and phylogenetic trees based on DNA sequences are used to test the validity of the two new species. The mitochondrial cytochrome oxidase subunit 1 gene, and the nuclear ribosomal 18S and 28S rRNA genes were used for evolutionary analyses, with the concatenated dataset of all three genes used for maximum likelihood and Bayesian phylogenetic analyses. The two new species of pinworms from howler monkeys were morphologically distinct and formed reciprocally monophyletic lineages in molecular phylogenetic trees. The three species from howler monkeys, T. multilabiatus n. sp., T. pigrae n. sp., and Trypanoxyuris minutus, formed a monophyletic group with high bootstrap and posterior probability support values. Phylogenetic patterns inferred from sequence data support the hypothesis of a close evolutionary association between these primate hosts and their pinworm parasites. The results suggest that the diversity of pinworm parasites from Neotropical primates might be underestimated.

  11. Allele mining and enhanced genetic recombination for rice breeding.

    PubMed

    Leung, Hei; Raghavan, Chitra; Zhou, Bo; Oliva, Ricardo; Choi, Il Ryong; Lacorte, Vanica; Jubay, Mona Liza; Cruz, Casiana Vera; Gregorio, Glenn; Singh, Rakesh Kumar; Ulat, Victor Jun; Borja, Frances Nikki; Mauleon, Ramil; Alexandrov, Nickolai N; McNally, Kenneth L; Sackville Hamilton, Ruaraidh

    2015-12-01

    Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.

  12. Power of IRT in GWAS: successful QTL mapping of sum score phenotypes depends on interplay between risk allele frequency, variance explained by the risk allele, and test characteristics.

    PubMed

    van den Berg, Stéphanie M; Service, Susan K

    2012-12-01

    As data from sequencing studies in humans accumulate, rare genetic variants influencing liability to disease and disorders are expected to be identified. Three simulation studies show that characteristics and properties of diagnostic instruments interact with risk allele frequency to affect the power to detect a quantitative trait locus (QTL) based on a test score derived from symptom counts or questionnaire items. Clinical tests, that is, tests that show a positively skewed phenotypic sum score distribution in the general population, are optimal to find rare risk alleles of large effect. Tests that show a negatively skewed sum score distribution are optimal to find rare protective alleles of large effect. For alleles of small effect, tests with normally distributed item parameters give best power for a wide range of allele frequencies. The item-response theory framework can help understand why an existing measurement instrument has more power to detect risk alleles with either low or high frequency, or both kinds.

  13. A Polarization-Diversity Homodyne Image-Reject Optical Tranceiver Architecture for Improved Range and Signal Detection in Coherent Doppler Lidars

    NASA Astrophysics Data System (ADS)

    Abari, C. F.; Chu, X.; Mann, J.

    2014-12-01

    Doppler light detection and ranging (lidar) has been used for a few decades for the characterization of wind fields and turbulence structures in the atmosphere. More recently, due to the advances in fiber optic communications, all-fiber coherent Doppler lidars (CDL) have been developed and widely used as a primary instrument for probing the atmospheric boundary layer wind fields. Due to a variety of reasons, all-fiber CDLs have gradually replaced their counterparts benefiting from technologies other than fiber optics. Most CDLs suffer from a number of drawbacks inherent to their principle of operation. For instance, one of the main challenges in CDLs is extracting the signal information from noisy observations, which is common to most opto-electronic systems. Moreover, it is sometimes challenging to extract the sign of the measured radial velocity. Conventionally, CDLs have benefitted from an intermediate frequency (IF) heterodyne receiver architecture for the determination of the radial velocity. In such systems, either the transmitted or the local oscillator (LO) signal is shifted in frequency. Such architectures may suffer from increased noise and spurious effects due to the employment of additional active components, e.g., acousto-optic modulator (AOM), limited measurement bandwidth (BW), and a more sophisticated electronic front-end for signal detection. On the other hand, one of the main challenges in long-range (pulsed) CDLs is the limitations imposed on the pulse repetition rate (PRR) as well as the available transmit power. These restrictions are more significant in all-fiber pulsed CDLs in which Erbium doped fiber amplifiers (EDFA) are employed for the amplification of the optical pulses. In this study, we propose an alternative reconfigurable opto-electronic front-end transceiver architecture in all-fiber CDLs where there is no compromise in the detection BW. Additionally, by benefiting from a polarization diversity architecture we show that both the PRR

  14. Glacial refugia and modern genetic diversity of 22 western North American tree species.

    PubMed

    Roberts, David R; Hamann, Andreas

    2015-04-01

    North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r(2) = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711

  15. Glacial refugia and modern genetic diversity of 22 western North American tree species

    PubMed Central

    Roberts, David R.; Hamann, Andreas

    2015-01-01

    North American tree species, subspecies and genetic varieties have primarily evolved in a landscape of extensive continental ice and restricted temperate climate environments. Here, we reconstruct the refugial history of western North American trees since the last glacial maximum using species distribution models, validated against 3571 palaeoecological records. We investigate how modern subspecies structure and genetic diversity corresponds to modelled glacial refugia, based on a meta-analysis of allelic richness and expected heterozygosity for 473 populations of 22 tree species. We find that species with strong genetic differentiation into subspecies had widespread and large glacial refugia, whereas species with restricted refugia show no differentiation among populations and little genetic diversity, despite being common over a wide range of environments today. In addition, a strong relationship between allelic richness and the size of modelled glacial refugia (r2 = 0.55) suggest that population bottlenecks during glacial periods had a pronounced effect on the presence of rare alleles. PMID:25761711

  16. Linkage disequilibrium between a 5q13 microsatellite null allele and SMA indicates complex but stable deletions/duplications

    SciTech Connect

    Surhk, L.C.; Aubry, H.L.; MacKenzie, A.E.

    1994-09-01

    SMA is a recessively inherited degeneration of alpha motor neurons presenting in three distinct types with diverse onsets ranging from infancy (type I) to childhood (types II and III). All forms have been mapped to chromosome 5q13.1. We have developed PCR primers for two distinct microsatellite repeats (MSR), CATT-40G1 and CATT-192F7. These subloci are constituents of a previously reported 5q13.1 complex CA dinucleotide MSR, CATT-1, with four or more copies per chromosome. Type 1 SMA families (n=35) were examined because stricter clinical criteria permitted greater diagnostic accuracy and, possibly, greater mutational homogeneity. One allele per chromosome is amplified with the 40G1 and 192F7 subloci-specific primers out of a total of 3 and 7 possible alleles, respectively. Significant linkage disequilibrium was observed between the disease phenotype and the 40G1 null allele ({chi}{sup 2}=38.23) and 192F7 allele with 19 CA repeats ({chi}{sup 2}=6.62) in contrast to two markers D5S435 ({chi}{sup 2}=.42) and D5S351 ({chi}{sup 2}=.16), which have been shown to flank the SMA locus at less than 1% recombination. The null alleles present in both subloci appeared to be due to stable deletions rather than isolated DNA sequence polymorphisms. In contrast to recent reports, no evidence of de novo rearrangements were observed. Furthermore, duplications of these subloci have been observed in three normal chromosomes. Our data are consistent with unequal cross-overs generating deletions/duplications which not only account for the complexity being observed in the genomic walk within the critical SMA region, but could also be causally related SMA mutations. Results of similar linkage disequilibrium analyses employing 3 additional 5q13.1 microsatellites will also be presented.

  17. Invasive Allele Spread under Preemptive Competition

    NASA Astrophysics Data System (ADS)

    Yasi, J. A.; Korniss, G.; Caraco, T.

    We study a discrete spatial model for invasive allele spread in which two alleles compete preemptively, initially only the "residents" (weaker competitors) being present. We find that the spread of the advantageous mutation is well described by homogeneous nucleation; in particular, in large systems the time-dependent global density of the resident allele is well approximated by Avrami's law.

  18. Genetic comparison of lake sturgeon populations: Differentiation based on allelic frequencies at seven microsatellite loci

    USGS Publications Warehouse

    McQuown, E.; Krueger, C.C.; Kincaid, H.L.; Gall, G.A.E.; May, B.

    2003-01-01

    The lake sturgeon (Acipenser fulvescens) has recently become a high priority for restoration management because of the near extinction of the species from many areas of North America. The identification of the level of population differentiation that naturally exists among lake sturgeon populations will be useful in the development of management plans to conserve and restore diversity, and in the choice of donor populations to use for re-introduction. Genetic variation among and within 210 lake sturgeon collected from seven locations (St. Lawrence River, Des Prairies River (tributary to the St. Lawrence River), Mattagami River (Hudson Bay drainage), Menominee River (Lake Michigan drainage), Wolf River (Lake Michigan drainage), Niagara River, and Lake Erie) was examined based on allelic variation at seven microsatellite loci (four disomic and three putative tetrasomic). High levels of variability were detected at these loci. Analyses revealed an average of 8.6 alleles per locus (range 5 to 12 alleles per locus) and heterozygosity values at the four disomic loci ranging from 0.46 to 0.66. Multivariate factor analysis of Nei's genetic distance values produced three distinct population groups that were organized by geography: 1) Mattagami (northern Quebec), 2) Menominee/ Wolf (Lake Michigan - Wisconsin), and 3) St. Lawrence/ Des Prairies/ Niagara/ Erie (lower Great Lakes). Differences based on G-tests summed over all loci occurred between all possible paired comparisons of the collections (P < 0.01). These analyses indicated that lake sturgeon populations are differentiated within the Great Lakes basin. Managers of this species will need to identify individual populations in their jurisdictions and provide separate consideration for their conservation and rehabilitation.

  19. Adaptive evolution during an ongoing range expansion: the invasive bank vole (Myodes glareolus) in Ireland.

    PubMed

    White, Thomas A; Perkins, Sarah E; Heckel, Gerald; Searle, Jeremy B

    2013-06-01

    Range expansions are extremely common, but have only recently begun to attract attention in terms of their genetic consequences. As populations expand, demes at the wave front experience strong genetic drift, which is expected to reduce genetic diversity and potentially cause 'allele surfing', where alleles may become fixed over a wide geographical area even if their effects are deleterious. Previous simulation models show that range expansions can generate very strong selective gradients on dispersal, reproduction, competition and immunity. To investigate the effects of range expansion on genetic diversity and adaptation, we studied the population genomics of the bank vole (Myodes glareolus) in Ireland. The bank vole was likely introduced in the late 1920s and is expanding its range at a rate of ~2.5 km/year. Using genotyping-by-sequencing, we genotyped 281 bank voles at 5979 SNP loci. Fourteen sample sites were arranged in three transects running from the introduction site to the wave front of the expansion. We found significant declines in genetic diversity along all three transects. However, there was no evidence that sites at the wave front had accumulated more deleterious mutations. We looked for outlier loci with strong correlations between allele frequency and distance from the introduction site, where the direction of correlation was the same in all three transects. Amongst these outliers, we found significant enrichment for genic SNPs, suggesting the action of selection. Candidates for selection included several genes with immunological functions and several genes that could influence behaviour.

  20. Allelic Spectra of Risk SNPs Are Different for Environment/Lifestyle Dependent versus Independent Diseases

    PubMed Central

    Amos, Christopher I.

    2015-01-01

    Genome-wide association studies (GWAS) have generated sufficient data to assess the role of selection in shaping allelic diversity of disease-associated SNPs. Negative selection against disease risk variants is expected to reduce their frequencies making them overrepresented in the group of minor (<50%) alleles. Indeed, we found that the overall proportion of risk alleles was higher among alleles with frequency <50% (minor alleles) compared to that in the group of major alleles. We hypothesized that negative selection may have different effects on environment (or lifestyle)-dependent versus environment (or lifestyle)-independent diseases. We used an environment/lifestyle index (ELI) to assess influence of environmental/lifestyle factors on disease etiology. ELI was defined as the number of publications mentioning “environment” or “lifestyle” AND disease per 1,000 disease-mentioning publications. We found that the frequency distributions of the risk alleles for the diseases with strong environmental/lifestyle components follow the distribution expected under a selectively neutral model, while frequency distributions of the risk alleles for the diseases with weak environmental/lifestyle influences is shifted to the lower values indicating effects of negative selection. We hypothesized that previously selectively neutral variants become risk alleles when environment changes. The hypothesis of ancestrally neutral, currently disadvantageous risk-associated alleles predicts that the distribution of risk alleles for the environment/lifestyle dependent diseases will follow a neutral model since natural selection has not had enough time to influence allele frequencies. The results of our analysis suggest that prediction of SNP functionality based on the level of evolutionary conservation may not be useful for SNPs associated with environment/lifestyle dependent diseases. PMID:26201053

  1. Genetic diversity of wild Prunus cerasifera Ehrhart (wild cherry plum) in China revealed by simple-sequence repeat markers.

    PubMed

    Zhao, Y; Li, Y; Liu, Y; Yang, Y F

    2015-07-28

    Simple-sequence repeat (SSR) markers were employed to assess the genetic diversity of wild Prunus cerasifera Ehrhart (wild cherry plum) in China. Fourteen SSR primer pairs generated a total of 94 alleles (90 were polymorphic, accounting for 95.74%), with a mean of 6.71 alleles per locus. The number of alleles detected at each locus ranged from 2 at BPPCT 028 to 13 at BPPCT 002, with an average of 6.71 alleles per locus. Nei's genetic diversity ranged from 0.0938 to 0.4951 and Shannon's information index ranged from 0.1706 to 0.6882, with averages of 0.3295 and 0.4899, respectively. The SSR data indicated moderate genetic diversity of P. cerasifera in China. In the unweighted pair group method with arithmetic mean phylogenetic tree, the 40 forms of P. cerasifera were divided into 3 genetic clusters. However, the 3 clades determined using SSR data were not consistent with the classification based on morphological characters, such as fruit color. Because of the endangered status and the moderate genetic diversity of P. cerasifera in China, both in situ and ex situ conservation strategies should be adopted.

  2. Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers.

    PubMed Central

    Schoen, D J; Brown, A H

    1993-01-01

    Wild crop relatives are an important source of genetic variation for improving domesticated species. Given limited resources, methods for maximizing the genetic diversity of collections of wild relatives are needed to help spread protection over a larger number of populations and species. Simulations were conducted to investigate the optimal strategy of sampling materials from populations of wild relatives, with the objective of maximizing the number of alleles (allelic richness) in collections of fixed size. Two methods, based on assessing populations for variation at marker loci (e.g., allozymes, restriction fragment length polymorphisms), were developed and compared with several methods that are not dependent on markers. Marker-assisted methods yielded higher overall allelic richness in the simulated collections, and they were particularly effective in conserving geographically localized alleles, the class of alleles that is most subject to loss. PMID:8248153

  3. Adapting populations in space: clonal interference and genetic diversity

    NASA Astrophysics Data System (ADS)

    Weissman, Daniel; Barton, Nick

    Most species inhabit ranges much larger than the scales over which individuals interact. How does this spatial structure interact with adaptive evolution? We consider a simple model of a spatially-extended, adapting population and show that, while clonal interference severely limits the adaptation of purely asexual populations, even rare recombination is enough to allow adaptation at rates approaching those of well-mixed populations. We also find that the genetic hitchhiking produced by the adaptive alleles sweeping through the population has strange effects on the patterns of genetic diversity. In large spatial ranges, even low rates of adaptation cause all individuals in the population to rapidly trace their ancestry back to individuals living in a small region in the center of the range. The probability of fixation of an allele is thus strongly dependent on the allele's spatial location, with alleles from the center favored. Surprisingly, these effects are seen genome-wide (instead of being localized to the regions of the genome undergoing the sweeps). The spatial concentration of ancestry produces a power-law dependence of relatedness on distance, so that even individuals sampled far apart are likely to be fairly closely related, masking the underlying spatial structure.

  4. Identification and characterization of variant alleles at CODIS STR loci.

    PubMed

    Allor, Catherine; Einum, David D; Scarpetta, Marco

    2005-09-01

    Short tandem repeat (STR) profiles from 32,671 individuals generated by the ABI Profiler Plus and Cofiler systems were screened for variant alleles not represented within manufacturer-provided allelic ladders. A total of 85 distinct variants were identified at 12 of the 13 CODIS loci, most of which involve a truncated tetranucleotide repeat unit. Twelve novel alleles, identified at D3S1358, FGA, D18S51, D5S818, D7S820 and TPOX, were confirmed by nucleotide sequence analysis and include both insertions and deletions involving the repeat units themselves as well as DNA flanking the repeat regions. Population genetic data were collected for all variants and frequencies range from 0.0003 (many single observations) to 0.0042 (D7S820 '10.3' in North American Hispanics). In total, the variant alleles identified in this study are carried by 1.6% of the estimated 1 million individuals tested annually in the U.S. for the purposes of parentage resolution. A paternity case involving a recombination event of paternal origin is presented and demonstrates how variant alleles can significantly strengthen the genetic evidence in troublesome cases. In such instances, increased costs and turnaround time associated with additional testing may be eliminated.

  5. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

    PubMed Central

    2012-01-01

    Background Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Results Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Conclusion Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive

  6. Frequency of HLA-A alleles in the Syrian population genotyped by sequence-based typing.

    PubMed

    Madania, A; Ghoury, I; Al-Ashkar, W; Nweder, S; Zarzour, H

    2014-10-01

    HLA-A molecules are highly polymorphic. Their accurate typing at a high-resolution level is crucial for successful organ, bone marrow and cord blood transplantation. Furthermore, several HLA alleles have been involved in susceptibility to autoimmune diseases, allergies, cancers and inflammations. In order to determine common HLA-A alleles in Syria and their frequencies, sequence-based typing (SBT) was used to genotype HLA-A alleles at high resolution (four digit level) among one hundred and thirty randomly selected Syrian individuals. Exons 2, 3 and 4 of the HLA-A gene were amplified by PCR and sequenced. The sbt-engine software was used for allele assignment. Ambiguities were solved using group-specific sequencing primers (GSSPs). We could identify 32 different HLA-A alleles which were divided into 3 groups: high frequency (approximately 10%, A*01:01; A*24:02; A*03:01; A*02:01), moderate frequency (approximately 3%, such as A*02:05, A*31:01 and A*33:01), and low frequency (approximately 1%, such as A*02:11, A*29:01, A*02:02 and A*36:01). Homozygosity rate was higher than expected (11.5% vs. 7.15%). For high frequency alleles, our results show similarity to neighbouring countries. However, 15 alleles (such as A*02:04, A*02:06, A*02:11 and A*02:17) found in our cohort in low frequencies were never reported in some or all neighbouring countries. This is the first report on HLA-A allele frequencies in Syria. In spite of the relatively low number of tested subjects, our results revealed a high degree of diversity, with 32 different alleles, reflecting the high ethnic heterogeneity of the Syrian population. The identification of alleles rarely or never reported in neighbouring countries indicates a higher genetic diversity in Syria.

  7. Distribution of a pseudodeficiency allele among Tay-Sachs carriers

    SciTech Connect

    Tomczak, J.; Grebner, E.E. ); Boogen, C. )

    1993-08-01

    Recently Triggs-Raine et al. (1992) identified a new mutation in the gene coding for the [alpha]-subunit of [beta]-hexosaminidase A (hex A), the enzyme whose deficiency causes Tay-Sachs disease. This mutation, a C[sub 739]-to-T transition in exon 7, results in an altered enzyme that is active (albeit at reduced levels) in cells but that has essentially no activity in serum. This so-called pseudodeficient allele was first detected in compound heterozygotes who also carried a Tay-Sachs disease allele and therefore had no detectable hex A in their serum but who were in good health. Carriers of this apparently benign mutation are generally indistinguishable from carriers of a lethal mutation by means of routine enzyme-based screening tests, because the product of the pseudodeficient allele is not detectable in serum and has decreased activity in cells. This suggests that some individuals who have been classified as Tay-Sachs carriers are actually carriers of the pseudodeficient allele and are not at risk to have a child affected with Tay-Sachs disease. The pseudodeficient allele may also be responsible for some inconclusive diagnoses, where leukocyte values fall below the normal range but are still above the carrier range. The fact that there are now two mutant alleles (the psuedodeficient and the adult) that are indistinguishable from the lethal infantile mutations by means of enzyme assay yet that are phenotypically very different and that together may account for as much as 12% of enzyme-defined carriers on the basis of the data here suggests that DNA analysis should be part of a comprehensive screening program. It will be particularly useful to identify the mutations in couples at risk, before they undergo prenatal diagnosis. DNA analysis will also resolve some inconclusive diagnoses.

  8. The Chief Diversity Officer

    ERIC Educational Resources Information Center

    Williams, Damon; Wade-Golden, Katrina

    2007-01-01

    Numerous institutions are moving toward the chief diversity officer model of leading and managing diversity in higher education. These officers carry formal administrative titles and ranks that range from vice president for institutional diversity to associate vice chancellor for diversity and climate and dean of diversity and academic engagement.…

  9. RHD allele distribution in Africans of Mali

    PubMed Central

    Wagner, Franz F; Moulds, Joann M; Tounkara, Anatole; Kouriba, Bourema; Flegel, Willy A

    2003-01-01

    Background Aberrant and non-functional RHD alleles are much more frequent in Africans than in Europeans. The DAU cluster of RHD alleles exemplifies that the alleles frequent in Africans have evaded recognition until recently. A comprehensive survey of RHD alleles in any African population was lacking. Results We surveyed the molecular structure and frequency of RHD alleles in Mali (West Africa) by evaluating 116 haplotypes. Only 69% could be attributed to standard RHD (55%) or the RHD deletion (14%). The aberrant RHD allele DAU-0 was predicted for 19%, RHDΨ for 7% and Ccdes for 4% of all haplotypes. DAU-3 and the new RHD allele RHD(L207F), dubbed DMA, were found in one haplotype each. A PCR-RFLP for the detection of the hybrid Rhesus box diagnostic for the RHD deletion in Europeans was false positive in 9 individuals, including all carriers of RHDΨ . Including two silent mutations and the RHD deletion, a total of 9 alleles could be differentiated. Conclusion Besides standard RHD and the RHD deletion, DAU-0, RHDΨ and Ccdes are major alleles in Mali. Our survey proved that the most frequent alleles of West Africans have been recognized allowing to devise reliable genotyping and phenotyping strategies. PMID:14505497

  10. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    NASA Astrophysics Data System (ADS)

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-03-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation.

  11. KIR2DL2/2DL3-E35 alleles are functionally stronger than -Q35 alleles

    PubMed Central

    Bari, Rafijul; Thapa, Rajoo; Bao, Ju; Li, Ying; Zheng, Jie; Leung, Wing

    2016-01-01

    KIR2DL2 and KIR2DL3 segregate as alleles of a single locus in the centromeric motif of the killer cell immunoglobulin-like receptor (KIR) gene family. Although KIR2DL2/L3 polymorphism is known to be associated with many human diseases and is an important factor for donor selection in allogeneic hematopoietic stem cell transplantation, the molecular determinant of functional diversity among various alleles is unclear. In this study we found that KIR2DL2/L3 with glutamic acid at position 35 (E35) are functionally stronger than those with glutamine at the same position (Q35). Cytotoxicity assay showed that NK cells from HLA-C1 positive donors with KIR2DL2/L3-E35 could kill more target cells lacking their ligands than NK cells with the weaker -Q35 alleles, indicating better licensing of KIR2DL2/L3+ NK cells with the stronger alleles. Molecular modeling analysis reveals that the glutamic acid, which is negatively charged, interacts with positively charged histidine located at position 55, thereby stabilizing KIR2DL2/L3 dimer and reducing entropy loss when KIR2DL2/3 binds to HLA-C ligand. The results of this study will be important for future studies of KIR2DL2/L3-associated diseases as well as for donor selection in allogeneic stem cell transplantation. PMID:27030405

  12. Identification of novel alleles of the rice blast resistance gene Pi54

    NASA Astrophysics Data System (ADS)

    Vasudevan, Kumar; Gruissem, Wilhelm; Bhullar, Navreet K.

    2015-10-01

    Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.

  13. [Prevalence of VRN1 Locus Alleles among Spring Common Wheat Cultivars Cultivated in Western Siberia].

    PubMed

    Efremova, T T; Chumanova, E V; Trubacheeva, N V; Arbuzova, V S; Belan, I A; Pershina, L A

    2016-02-01

    With the use of allele-specific primers developed for the VRN1 loci, the allelic diversity of the VRN-A1, VRN-B1, and VRN-D1 genes was studied in 148 spring common wheat cultivars cultivated under the conditions of Western Siberia. It was demonstrated that modern Western Siberian cultivars have the VRN-A1a allele, which is widely distributed in the world (alone or in combination with the VRN-B1a and VRN-B1c alleles). It was established that the main contribution in acceleration of the.seedling-heading time is determined by a dominant VRN-A1a allele, while the VRN-A1b allele, on the contrary, determines later plant heading. Cultivars that have the VRN-A1b allele in the genotype are found with a frequency of 8%. It was shown that cultivars with different allele combinations of two dominant genes (VRN-A1a + VRN-B1c and VRN-A1a + VRN-B1a) are characterized by earlier heading and maturing.

  14. Origin of the diversity in DNA recognition domains in phasevarion associated modA genes of pathogenic Neisseria and Haemophilus influenzae.

    PubMed

    Gawthorne, Jayde A; Beatson, Scott A; Srikhanta, Yogitha N; Fox, Kate L; Jennings, Michael P

    2012-01-01

    Phase variable restriction-modification (R-M) systems have been identified in a range of pathogenic bacteria. In some it has been demonstrated that the random switching of the mod (DNA methyltransferase) gene mediates the coordinated expression of multiple genes and constitutes a phasevarion (phase variable regulon). ModA of Neisseria and Haemophilus influenzae contain a highly variable, DNA recognition domain (DRD) that defines the target sequence that is modified by methylation and is used to define modA alleles. 18 distinct modA alleles have been identified in H. influenzae and the pathogenic Neisseria. To determine the origin of DRD variability, the 18 modA DRDs were used to search the available databases for similar sequences. Significant matches were identified between several modA alleles and mod gene from distinct bacterial species, indicating one source of the DRD variability was via horizontal gene transfer. Comparison of DRD sequences revealed significant mosaicism, indicating exchange between the Neisseria and H. influenzae modA alleles. Regions of high inter- and intra-allele similarity indicate that some modA alleles had undergone recombination more frequently than others, generating further diversity. Furthermore, the DRD from some modA alleles, such as modA12, have been transferred en bloc to replace the DRD from different modA alleles.

  15. Generation of humoral immune responses to multi-allele PfAMA1 vaccines; effect of adjuvant and number of component alleles on the breadth of response.

    PubMed

    Kusi, Kwadwo A; Faber, Bart W; Riasat, Vanessa; Thomas, Alan W; Kocken, Clemens H M; Remarque, Edmond J

    2010-11-03

    There is increasing interest in multi-allele vaccines to overcome strain-specificity against polymorphic vaccine targets such as Apical Membrane Antigen 1 (AMA1). These have been shown to induce broad inhibitory antibodies in vitro and formed the basis for the design of three Diversity-Covering (DiCo) proteins with similar immunological effects. The antibodies produced are to epitopes that are shared between vaccine alleles and theoretically, increasing the number of component AMA1 alleles is expected to broaden the antibody response. A plateau effect could however impose a limit on the number of alleles needed to achieve the broadest specificity. Moreover, production cost and the vaccine formulation process would limit the number of component alleles. In this paper, we compare rabbit antibody responses elicited with multi-allele vaccines incorporating seven (three DiCos and four natural AMA1 alleles) and three (DiCo mix) antigens for gains in broadened specificity. We also investigate the effect of three adjuvant platforms on antigen specificity and antibody functionality. Our data confirms a broadened response after immunisation with DiCo mix in all three adjuvants. Higher antibody titres were elicited with either CoVaccine HT™ or Montanide ISA 51, resulting in similar in vitro inhibition (65-82%) of five out of six culture-adapted P. falciparum strains. The antigen binding specificities of elicited antibodies were also similar and independent of the adjuvant used or the number of vaccine component alleles. Thus neither the four extra antigens nor adjuvant had any observable benefits with respect to specificity broadening, although adjuvant choice influenced the absolute antibody levels and thus the extent of parasite inhibition. Our data confirms the feasibility and potential of multi-allele PfAMA1 formulations, and highlights the need for adjuvants with improved antibody potentiation properties for AMA1-based vaccines.

  16. Global distribution of allele frequencies at the human dopamine D4 receptor locus

    SciTech Connect

    Chang, F.M.; Kidd, J.R.; Livak, K.J.

    1994-09-01

    The dopamine D4 receptor (DRD4) is a candidate gene for schizophrenia because the dopaminergic system has been implicated in this neuropsychiatric disorder. Several research groups have reported an association between allelic variants at DRD4 and schizophrenia, while others have been unable to replicate that finding. Knowledge of the appropriate gene frequencies in the underlying populations may resolve these inconsistencies. We have determined the frequencies of 8 different alleles of the 48 bp imperfect tandem repeat of exon 3 at the DRD4 locus in samples from 33 populations around the world. The frequencies vary considerably in the different populations with the most common allele ranging from 16% to 95%. Frequencies and Fst values will be presented for the 3 most common alleles (4-, 7-, and 2- repeat) by continental groupings, but the individual populations vary significantly around the averages. The populations averaged 4.3 alleles (range 2 to 7).

  17. Cytomorphological and molecular diversity in backcross-derived inbred lines of sunflower (Helianthus annuus L.).

    PubMed

    Sujatha, M; Prabakaran, A J; Dwivedi, Sangam L; Chandra, S

    2008-04-01

    A set of 250 distinct, stable, and uniform backcross-derived inbred lines were developed in sunflower through 5 interspecific cross combinations involving 4 wild diploid annual species (Helianthus argophyllus, H. petiolaris, H. annuus, and H. debilis). The presence of the wild-species genome in these inbred lines was confirmed through higher chromosome associations (tri- and quadrivalents) at diakinesis. Maximum structural rearrangements of chromosomes were observed in lines derived from H. petiolaris. Forty morphologically diverse inbred lines along with 2 controls were subjected to measurements of phenotypic and genetic distance using 118 simple sequence repeat (SSR) markers of known map location. A total of 204 alleles were identified and the number of alleles per locus varied between 2 and 5. There were 46 unique alleles and the number of unique alleles was highest in the lines derived from the cross involving H. petiolaris. The polymorphism information content (PIC) values ranged from 0.05 to 0.575. The pair-wise comparison values based on genetic dissimilarity estimates computed using molecular marker data varied between 0.143 and 0.486 among the 42 lines. The results indicate that the sunflower gene pool could benefit from introgression of novel alleles from the latent genetic diversity present in the wild species and particularly through exploitation of the diploid annual H. petiolaris.

  18. A novel measurement of allele discrimination for assessment of allele-specific silencing by RNA interference.

    PubMed

    Takahashi, Masaki; Hohjoh, Hirohiko

    2014-11-01

    Allele-specific silencing by RNA interference (ASP-RNAi) is an atypical RNAi that is capable of discriminating target alleles from non-target alleles, and may be therapeutically useful for specific inhibition of disease-causing alleles without affecting their corresponding normal alleles. However, it is difficult to design and select small interfering RNA (siRNAs) that confer ASP-RNAi. A major problem is that there are few appropriate measures in determining optimal allele-specific siRNAs. Here we show two novel formulas for calculating a new measure of allele-discrimination, named "ASP-score". The formulas and ASP-score allow for an unbiased determination of optimal siRNAs, and may contribute to characterizing such allele-specific siRNAs.

  19. Diversity of potato genetic resources

    PubMed Central

    Machida-Hirano, Ryoko

    2015-01-01

    A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection. PMID:25931978

  20. Efficient genotype elimination via adaptive allele consolidation.

    PubMed

    De Francesco, Nicoletta; Lettieri, Giuseppe; Martini, Luca

    2012-01-01

    We propose the technique of Adaptive Allele Consolidation, that greatly improves the performance of the Lange-Goradia algorithm for genotype elimination in pedigrees, while still producing equivalent output. Genotype elimination consists in removing from a pedigree those genotypes that are impossible according to the Mendelian law of inheritance. This is used to find errors in genetic data and is useful as a preprocessing step in other analyses (such as linkage analysis or haplotype imputation). The problem of genotype elimination is intrinsically combinatorial, and Allele Consolidation is an existing technique where several alleles are replaced by a single “lumped” allele in order to reduce the number of combinations of genotypes that have to be considered, possibly at the expense of precision. In existing Allele Consolidation techniques, alleles are lumped once and for all before performing genotype elimination. The idea of Adaptive Allele Consolidation is to dynamically change the set of alleles that are lumped together during the execution of the Lange-Goradia algorithm, so that both high performance and precision are achieved. We have implemented the technique in a tool called Celer and evaluated it on a large set of scenarios, with good results.

  1. Shared genetic diversity across the global invasive range of the monk parakeet suggests a common restricted geographic origin and the possibility of convergent selection.

    PubMed

    Edelaar, Pim; Roques, Severine; Hobson, Elizabeth A; Gonçalves da Silva, Anders; Avery, Michael L; Russello, Michael A; Senar, Juan C; Wright, Timothy F; Carrete, Martina; Tella, José L

    2015-05-01

    While genetic diversity is hypothesized to be an important factor explaining invasion success, there is no consensus yet on how variation in source populations or demographic processes affects invasiveness. We used mitochondrial DNA haplotypic and microsatellite genotypic data to investigate levels of genetic variation and reconstruct the history of replicate invasions on three continents in a globally invasive bird, the monk parakeet (Myiopsitta monachus). We evaluated whether genetic diversity at invasive sites could be explained by (i) the native source populations from which they were derived and (ii) demographic bottlenecks during introduction. Genetic data indicated a localized source area for most sampled invasive populations, with limited evidence for admixing of native source populations. This pattern largely coincides with historical data on pet trade exports. However, the invasive populations are genetically more similar than predicted from the export data alone. The extent of bottleneck effects varied among invasive populations. The observed low genetic diversity, evidence of demographic contraction and restricted source area do not support the hypothesis that invasion is favoured by the mixing and recombining of genetic variation from multiple source populations. Instead, they suggest that reduced genetic variation through random processes may not inhibit successful establishment and invasion in this species. However, convergent selection across invasive sites could also explain the observed patterns of reduction and similarity in genetic variation and/or the restricted source area. In general, the alternative explanation of intraspecific variation in invasive potential among genotypes or geographic areas is neglected, but warrants more attention as it could inform comparative studies and management of biological invaders.

  2. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences.

    PubMed

    Bhatia, Shipra; Kleinjan, Dirk A

    2014-07-01

    The precise control of gene expression programs is crucial for the establishment of the diverse gene activity patterns required for the correct development, patterning and differentiation of the myriad of cell types within an organism. The crucial importance of non-coding regions of the genome in the control of gene regulation is well established and depends on a diverse group of sequence fragments called cis-regulatory elements that reside in these regions. Advances in novel genome-wide techniques have greatly increased the ability to identify potential regulatory elements. In contrast, their functional characterisation and the determination of their diverse modes of action remain a major bottleneck. Greater knowledge of gene expression control is of major importance for human health as disruption of gene regulation has become recognised as a significant cause of human disease. Appreciation of the role of cis-regulatory polymorphism in natural variation and susceptibility to common disease is also growing. While novel techniques such as GWAS and NGS provide the ability to collect large genomic datasets, the challenge for the twenty-first century will be to extract the relevant sequences and how to investigate the functional consequences of disease-associated changes. Here, we review how studies of transcriptional control at selected paradigm disease gene loci have revealed general principles of cis-regulatory logic and regulatory genome organisation, yet also demonstrate how the variety of mechanisms can combine to result in unique phenotypic outcomes. Integration of these principles with the emerging wealth of genome-wide data will provide enhanced insight into the workings of our regulatory genome.

  3. Association of the HLA-B*52 allele with non-progression to AIDS in Brazilian HIV-1-infected individuals.

    PubMed

    Teixeira, S L M; de Sá, N B R; Campos, D P; Coelho, A B; Guimarães, M L; Leite, T C N F; Veloso, V G; Morgado, M G

    2014-04-01

    Several human leukocyte antigen (HLA) class I alleles are associated with the susceptibility to human immunodeficiency virus-1 (HIV-1) infection and/or AIDS progression. Of these, the HLA-B alleles are considered the strongest genetic determinant of disease outcome. We evaluated the influence of the HLA-B alleles on AIDS progression among HIV-1-positive individuals from Rio de Janeiro, Brazil, who were categorized as rapid progressors (RPs), typical progressors (TPs) or long-term non-progressors (LTNPs). In this study, significant differences in HLA-B allele frequencies were observed among the three progression groups for the B*48, B*49 and B*52 alleles. After controlling for other factors associated with AIDS progression, the presence of the B*52 allele was shown to be a significant protective factor (hazard ratio (HR) 0.49 (95% confidence interval (CI) 0.27-0.90) P<0.03). Although no direct association was observed between the presence of the B*27 or B*57 allele and the LTNP profile compared with the TP or RP groups, the adjusted model confirmed that these alleles are protective factors against AIDS progression (HR 0.62 (95% CI 0.38-0.99) P<0.05), as previously described. These data corroborate the existence of significant differences in HLA-B allele frequencies among the distinct AIDS progression profiles and further elucidate the role of HLA alleles in the outcome of HIV infections in diverse populations.

  4. Distribution of forensic marker allelic frequencies in Pernambuco, Northestern Brazil.

    PubMed

    Santos, S M; Souza, C A; Rabelo, K C N; Souza, P R E; Moura, R R; Oliveira, T C; Crovella, S

    2015-04-30

    Pernambuco is one of the 27 federal units of Brazil, ranking seventh in the number of inhabitants. We examined the allele frequencies of 13 short tandem repeat loci (CFS1PO, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D21S11, FGA, TH01, vWA, and TPOX), the minimum recommended by the Federal Bureau of Investigation and commonly used in forensic genetics laboratories in Brazil, in a sample of 609 unrelated individuals from all geographic regions of Pernambuco. The allele frequencies ranged from 5 to 47.2%. No significant differences for any loci analyzed were observed compared with other publications in other various regions of Brazil. Most of the markers observed were in Hardy-Weinberg equilibrium. The occurrence of the allele 47.2 (locus FGA) and alleles 35.1 and 39 (locus D21S11), also described in a single study of the Brazilian population, was observed. The other forensic parameters analyzed (matching probability, power of discrimination, polymorphic information content, paternity exclusion, complement factor I, observed heterozygosity, expected heterozygosity) indicated that the studied markers are very informative for human forensic identification purposes in the Pernambuco population.

  5. Inactive alleles of cytochrome P450 2C19 may be positively selected in human evolution

    PubMed Central

    2014-01-01

    Background Cytochrome P450 CYP2C19 metabolizes a wide range of pharmacologically active substances and a relatively small number of naturally occurring environmental toxins. Poor activity alleles of CYP2C19 are very frequent worldwide, particularly in Asia, raising the possibility that reduced metabolism could be advantageous in some circumstances. The evolutionary selective forces acting on this gene have not previously been investigated. We analyzed CYP2C19 genetic markers from 127 Gambians and on 120 chromosomes from Yoruba, Europeans and Asians (Japanese + Han Chinese) in the Hapmap database. Haplotype breakdown was explored using bifurcation plots and relative extended haplotype homozygosity (REHH). Allele frequency differentiation across populations was estimated using the fixation index (FST) and haplotype diversity with coalescent models. Results Bifurcation plots suggested conservation of alleles conferring slow metabolism (CYP2C19*2 and *3). REHH was high around CYP2C19*2 in Yoruba (REHH 8.3, at 133.3 kb from the core) and to a lesser extent in Europeans (3.5, at 37.7 kb) and Asians (2.8, at −29.7 kb). FST at the CYP2C19 locus was low overall (0.098). CYP2C19*3 was an FST outlier in Asians (0.293), CYP2C19 haplotype diversity < = 0.037, p <0.001. Conclusions We found some evidence that the slow metabolizing allele CYP2C19*2 is subject to positive selective forces worldwide. Similar evidence was also found for CYP2C19*3 which is frequent only in Asia. FST is low at the CYP2C19 locus, suggesting balancing selection overall. The biological factors responsible for these selective pressures are currently unknown. One possible explanation is that early humans were exposed to a ubiquitous novel toxin activated by CYP2C19. The genetic adaptation took place within the last 10,000 years which coincides with the development of systematic agricultural practices. PMID:24690327

  6. Ethical guideposts for allelic variation databases.

    PubMed

    Knoppers, B M; Laberge, C M

    2000-01-01

    Basically, a mutation database (MDB) is a repository where allelic variations are described and assigned within a specific gene locus. The purposes of an MDB may vary greatly and have different content and structure. The curator of an electronic and computer-based MDB will provide expert feedback (clinical and research). This requires ethical guideposts. Going to direct on-line public access for the content of an MDB or to interactive communication also raises other considerations. Currently, HUGO's MDI (Mutation Database Initiative) is the only integrated effort supporting and guiding the coordinated deployment of MDBs devoted to genetic diversity. Thus, HUGO's ethical "Statements" are applicable. Among the ethical principles, the obligation of preserving the confidentiality of information transferred by a collaborator to the curator is particularly important. Thus, anonymization of such data prior to transmission is essential. The 1997 Universal Declaration on the Human Genome and Human Rights of UNESCO addresses the participation of vulnerable persons. Researchers in charge of MDBs should ensure that information received on the testing of children or incompetent adults is subject to ethical review and approval in the country of origin. Caution should be taken against the involuntary consequences of public disclosure of results without complete explanation. Clear and enforceable regulations must be developed to protect the public against misuse of genetic databanks. Interaction with a databank could be seen as creating a "virtual" physician-patient relationship. However, interactive public MDBs should not give medical advice. We have identified new social ethical principles to govern different levels of complexity of genetic information. They are: reciprocity, mutuality, solidarity, and universality. Finally, precaution and prudence at this early stage of the MDI may not only avoid ethically inextricable conundrums but also provide for the respect for the rights

  7. Diploid male dynamics under different numbers of sexual alleles and male dispersal abilities.

    PubMed

    Faria, Luiz R R; Soares, Elaine Della Giustina; Carmo, Eduardo do; Oliveira, Paulo Murilo Castro de

    2016-09-01

    Insects in the order Hymenoptera (bees, wasps and ants) present an haplodiploid system of sexual determination in which fertilized eggs become females and unfertilized eggs males. Under single locus complementary sex-determination (sl-CSD) system, the sex of a specimen depends on the alleles at a single locus: when diploid, an individual will be a female if heterozygous and male if homozygous. Significant diploid male (DM) production may drive a population to an extinction scenario called "diploid male vortex". We aimed at studying the dynamics of populations of a sl-CSD organism under several combinations of two parameters: male flight abilities and number of sexual alleles. In these simulations, we evaluated the frequency of DM and a genetic diversity measure over 10,000 generations. The number of sexual alleles varied from 10 to 100 and, at each generation, a male offspring might fly to another random site within a varying radius R. Two main results emerge from our simulations: (i) the number of DM depends more on male flight radius than on the number of alleles; (ii) in large geographic regions, the effect of males flight radius on the allelic diversity turns out much less pronounced than in small regions. In other words, small regions where inbreeding normally appears recover genetic diversity due to large flight radii. These results may be particularly relevant when considering the population dynamics of species with increasingly limited dispersal ability (e.g., forest-dependent species of euglossine bees in fragmented landscapes). PMID:27067711

  8. Spatial sorting and range shifts: consequences for evolutionary potential and genetic signature of a dispersal trait.

    PubMed

    Cobben, M M P; Verboom, J; Opdam, P F M; Hoekstra, R F; Jochem, R; Smulders, M J M

    2015-05-21

    Species are shifting their ranges under climate change, with genetic and evolutionary consequences. As a result, the spatial distribution of genetic diversity in a species' range can show a signature of range expansion. This genetic signature takes time to decay after the range stops expanding and it is important to take that lag time into account when interpreting contemporary spatial patterns of genetic diversity. In addition, the return to spatial equilibrium on an ecologically relevant timescale will depend on migration of genetic diversity across the species' range. However, during a range shift alleles may go extinct at the retracting range margin due to spatial sorting. Here we studied the spatial pattern of genotypes that differ in dispersal rate across the species range before, during and after a range shift, assessed the effect of range retraction on this pattern, and quantified the duration of the ephemeral genetic signature of range expansion for this trait. We performed simulation experiments with an individual-based metapopulation model under several contemporary climate change scenarios. The results show an increase of the number of individuals with high dispersal rate. If the temperature increased long enough the allele coding for low dispersal rate would go extinct. The duration of the genetic signature of range expansion after stabilisation of the species' distribution lasted up to 1200 generations after a temperature increase for 60 years at the contemporary rate. This depended on the total displacement of the climate optimum, as the product of the rate of temperature increase and its duration. So genetic data collected in the field do not necessarily reflect current selection pressures but can be affected by historic changes in species distribution, long after the establishment of the current species' range. Return to equilibrium patterns may be hampered by loss of evolutionary potential during range shift. PMID:25817038

  9. Spatial sorting and range shifts: consequences for evolutionary potential and genetic signature of a dispersal trait.

    PubMed

    Cobben, M M P; Verboom, J; Opdam, P F M; Hoekstra, R F; Jochem, R; Smulders, M J M

    2015-05-21

    Species are shifting their ranges under climate change, with genetic and evolutionary consequences. As a result, the spatial distribution of genetic diversity in a species' range can show a signature of range expansion. This genetic signature takes time to decay after the range stops expanding and it is important to take that lag time into account when interpreting contemporary spatial patterns of genetic diversity. In addition, the return to spatial equilibrium on an ecologically relevant timescale will depend on migration of genetic diversity across the species' range. However, during a range shift alleles may go extinct at the retracting range margin due to spatial sorting. Here we studied the spatial pattern of genotypes that differ in dispersal rate across the species range before, during and after a range shift, assessed the effect of range retraction on this pattern, and quantified the duration of the ephemeral genetic signature of range expansion for this trait. We performed simulation experiments with an individual-based metapopulation model under several contemporary climate change scenarios. The results show an increase of the number of individuals with high dispersal rate. If the temperature increased long enough the allele coding for low dispersal rate would go extinct. The duration of the genetic signature of range expansion after stabilisation of the species' distribution lasted up to 1200 generations after a temperature increase for 60 years at the contemporary rate. This depended on the total displacement of the climate optimum, as the product of the rate of temperature increase and its duration. So genetic data collected in the field do not necessarily reflect current selection pressures but can be affected by historic changes in species distribution, long after the establishment of the current species' range. Return to equilibrium patterns may be hampered by loss of evolutionary potential during range shift.

  10. Genetic Diversity of the Two Commercial Tetraploid Cotton Species in the Gossypium Diversity Reference Set.

    PubMed

    Hinze, Lori L; Gazave, Elodie; Gore, Michael A; Fang, David D; Scheffler, Brian E; Yu, John Z; Jones, Don C; Frelichowski, James; Percy, Richard G

    2016-05-01

    A diversity reference set has been constructed for the Gossypium accessions in the US National Cotton Germplasm Collection to facilitate more extensive evaluation and utilization of accessions held in the Collection. A set of 105 mapped simple sequence repeat markers was used to study the allelic diversity of 1933 tetraploid Gossypium accessions representative of the range of diversity of the improved and wild accessions of G. hirsutum and G. barbadense. The reference set contained 410 G. barbadense accessions and 1523 G. hirsutum accessions. Observed numbers of polymorphic and private bands indicated a greater diversity in G. hirsutum as compared to G. barbadense as well as in wild-type accessions as compared to improved accessions in both species. The markers clearly differentiated the 2 species. Patterns of diversity within species were observed but not clearly delineated, with much overlap occurring between races and regions of origin for wild accessions and between historical and geographic breeding pools for cultivated accessions. Although the percentage of accessions showing introgression was higher among wild accessions than cultivars in both species, the average level of introgression within individual accessions, as indicated by species-specific bands, was much higher in wild accessions of G. hirsutum than in wild accessions of G. barbadense. The average level of introgression within individual accessions was higher in improved G. barbadense cultivars than in G. hirsutum cultivars. This molecular characterization reveals the levels and distributions of genetic diversity that will allow for better exploration and utilization of cotton genetic resources.

  11. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib

    PubMed Central

    Vasudevan, Kumar; Vera Cruz, Casiana M.; Gruissem, Wilhelm; Bhullar, Navreet K.

    2016-01-01

    Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level. PMID:27446145

  12. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib.

    PubMed

    Vasudevan, Kumar; Vera Cruz, Casiana M; Gruissem, Wilhelm; Bhullar, Navreet K

    2016-01-01

    Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level. PMID:27446145

  13. VNTR allele frequency distributions under the stepwise mutation model: A computer simulation approach

    SciTech Connect

    Shriver, M.D.; Jin, L.; Chakraborty, R.; Boerwinkle, E. )

    1993-07-01

    Variable numbers of tandem repeats (VNTRs) are a class of highly informative and widely dispersed genetic markers. Despite their wide application in biological science, little is known about their mutational mechanisms or population dynamics. The objective of this work was to investigate four summary measures of VNTR allele frequency distributions: number of alleles, number of modes, range in allele size, and heterozygosity, using computer simulations of the one-step stepwise mutation model (SMM). The authors estimated these measures and their probability distributions for a wide range of mutation rates and compared the simulation results with predictions from analytical formulations of the one-step SMM. The average heterozygosity from the simulations agreed with the analytical expectation under the SMM. The average number of alleles, however, was larger in the simulations than the analytical expectation of the SMM. The authors then compared simulation expectations with actual data reported in the literature. They used the sample size and observed heterozygosity to determine the expected value, 5th and 95th percentiles for the other three summary measures, allelic size range, number of modes and number of alleles. The loci analyzed were classified into three groups based on the size of the repeat unit: microsatellites (1-2 base pair (bp) repeat unit), short tandem repeats [(STR) 3-5 bp repeat unit], and minisatellites (15-70 bp repeat unit). In general, STR loci were most similar to the simulation results under the SMM for the three summary measures (number of alleles, number of modes and range in allele size), followed by the microsatellite loci and then by the minisatellite loci, which showed deviations in the direction of the infinite allele model (IAM). Based on these differences, it is hypothesized that these three classes of loci are subject to different mutational forces.

  14. Characterization of the treefrog null allele, 1991

    SciTech Connect

    Guttman, S.I.

    1992-04-01

    Spring peeper (Hyla crucifer) tadpoles collected from the waste storage area during the Biological and Ecological Site Characterization of the Feed Materials Production Center (FEMP) in 1986 and 1987 appeared to be unique. A null (inactive) allele was found at the glucose phosphate isomerase enzyme locus in significant frequencies (approximately 20%) each year; this allele did not appear to occur in the offsite sample collected approximately 15km from the FEMP. Null alleles at this locus have not been reported in other amphibian populations; when they have been found in other organisms they have invariably been lethal in the homozygous condition.

  15. Characterization of the treefrog null allele

    SciTech Connect

    Guttman, S.I. . Dept. of Zoology)

    1990-12-01

    As part of the authors intensive year-long baseline ecological study, they characterized the degree of genetic polymorphism and heterozygosity in selected Feed Materials Production Center (FMPC) populations using electrophoretic techniques. These data are being used as an indicator of stress by comparing populations on and off the FMPC site. The current study was initiated to determine whether this GPI null allele is lethal, when homozygous, in spring peepers. Also, a sampling protocol was implemented to determine whether a linear effect occurs relative to the frequency of the null allele offsite and to determine the origination site of the null allele. 18 refs., 2 figs., 4 tabs.

  16. Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing response gene.

    PubMed

    Salmon, Jemma; Ward, Sally P; Hanley, Steven J; Leyser, Ottoline; Karp, Angela

    2014-05-01

    Willows (Salix spp.) are important biomass crops due to their ability to grow rapidly with low fertilizer inputs and ease of cultivation in short-rotation coppice cycles. They are relatively undomesticated and highly diverse, but functional testing to identify useful allelic variation is time-consuming in trees and transformation is not yet possible in willow. Arabidopsis is heralded as a model plant from which knowledge can be transferred to advance the improvement of less tractable species. Here, knowledge and methodologies from Arabidopsis were successfully used to identify a gene influencing stem number in coppiced willows, a complex trait of key biological and industrial relevance. The strigolactone-related More AXillary growth (MAX) genes were considered candidates due to their role in shoot branching. We previously demonstrated that willow and Arabidopsis show similar response to strigolactone and that transformation rescue of Arabidopsis max mutants with willow genes could be used to detect allelic differences. Here, this approach was used to screen 45 SxMAX1, SxMAX2, SxMAX3 and SxMAX4 alleles cloned from 15 parents of 11 mapping populations varying in shoot-branching traits. Single-nucleotide polymorphism (SNP) frequencies were locus dependent, ranging from 29.2 to 74.3 polymorphic sites per kb. SxMAX alleles were 98%-99% conserved at the amino acid level, but different protein products varying in their ability to rescue Arabidopsis max mutants were identified. One poor rescuing allele, SxMAX4D, segregated in a willow mapping population where its presence was associated with increased shoot resprouting after coppicing and colocated with a QTL for this trait.

  17. Suppression of Seedling Damping-Off Caused by Pythium ultimum, P. irregulare, and Rhizoctonia solani in Container Media Amended with a Diverse Range of Pacific Northwest Compost Sources.

    PubMed

    Scheuerell, Steven J; Sullivan, Dan M; Mahaffee, Walter F

    2005-03-01

    ABSTRACT Suppression of seedling damping-off disease caused by Pythium spp. and Rhizoctonia solani is a potential benefit of formulating soilless container media with compost. Thirty-six compost samples from Pacific Northwest commercial composting facilities were analyzed for a number of physical, chemical, and biological properties, including suppression of damping-off caused by Pythium ultimum, P. irregulare, and R. solani. The samples were produced from diverse feedstocks and composting technol ogies; this was reflected in a large degree of variability in the measured properties. When mixed with sphagnum peat moss and inorganic aggregates, 67% of the compost samples significantly suppressed P. irregulare damping-off of cucumber, 64% suppressed P. ultimum damping-off of cucumber, and 17% suppressed damping-off of cabbage caused by R. solani. Suppression of Pythium damping-off was related to the potential of compost to support microbial activity and a qualitative index of ammonia volatilization. Suppression of Rhizoctonia damping-off was not related to any one compost factor. Currently available compost products potentially could provide commercially acceptable control of damping-off caused by Pythium spp., but it is necessary to fortify composts with microbial antagonists for the control of R. solani.

  18. Multiple origins of Plasmodium falciparum dihydropteroate synthetase mutant alleles associated with sulfadoxine resistance in India.

    PubMed

    Lumb, Vanshika; Das, Manoj K; Singh, Neeru; Dev, Vas; Khan, Wajihullah; Sharma, Yagya D

    2011-06-01

    With the spread of chloroquine (CQ)-resistant malaria in India, sulfadoxine-pyrimethamine (SP) alone or in combination with artesunate is used as an alternative antimalarial drug. Due to continuous drug pressure, the Plasmodium falciparum parasite is exhibiting resistance to antifolates because of mutations in candidate genes dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps). Our earlier study on flanking microsatellite markers of dhfr mutant alleles from India had shown a single origin of the pyrimethamine resistance and some minor haplotypes which shared haplotypes with Southeast Asian (Thailand) strains. In the present study, we have analyzed 193 of these Indian P. falciparum isolates for 15 microsatellite loci around dhps to investigate the genetic lineages of the mutant dhps alleles in different parts of the country. Eighty-one of these samples had mutant dhps alleles, of which 62 were from Andaman and Nicobar Islands and the remaining 19 were from mainland India. Of 112 isolates with a wild-type dhps allele, 109 were from mainland India and only 3 were from Andaman and Nicobar Islands. Consistent with the model of selection, the mean expected heterozygosity (H(e)) around mutant dhps alleles (H(e) = 0.55; n = 81) associated with sulfadoxine resistance was lower (P ≤ 0.05) than the mean H(e) around the wild-type dhps allele (H(e) = 0.80; n = 112). There was more genetic diversity in flanking microsatellites of dhps than dhfr among these isolates, which confirms the assertion that dhps mutations are at a very early stage of fixation in the parasite population. Microsatellite haplotypes around various mutant dhps alleles suggest that the resistant dhps alleles have multiple independent origins in India, especially in Andaman and Nicobar Islands. Determining the genetic lineages of the resistant dhps alleles on Andaman and Nicobar Islands and mainland India is significant, given the role of Asia in the intercontinental spread of chloroquine

  19. [Genetic diversity of microsatellite loci in captive Amur tigers].

    PubMed

    Zhang, Yu-Gaung; Li, Di-Qiang; Xiao, Qi-Ming; Rao, Li-Qun; Zhang, Xue-Wen

    2004-09-01

    The tiger is one of the most threatened wildlife species since the abundance and distribution of tiger have decreased dramatically in the last century. The wild Amur tiger (Panthera tigris altaica) only distributed in northeast China, the far east area of Russia and the north Korea and its size of wild population is about 450 in the world and 20 in China. Several hundred captive populations of Amur tigers are the main source to protect gene library of tiger and the source of recovering the wild populations. The Breeding Center for Felidae at Hengdaohezi and Haoerbin Tiger Park in Heilongjiang Province is the biggest captive breeding base in China. How to make clear the genetic pedigree and establish reasonable breeding system is the urgent issues. So we use the microsatellite DNA markers and non-invasive technology to research on the genetic diversity of captive Amur tiger in this study. Ten microsatellite loci (Fca005, Fca075, Fca094, Fca152, Fca161, Fca294, Pti002, Pti003, Pti007 and Pti010), highly variable nuclear markers, were studied their genetic diversity in 113 captive Amur tigers. The PCR amplified products of microsatellite loci were detected by non-denatured polyacrylamide gel electrophoresis. Allele numbers, allelic frequency, gene heterozygosity(H(e)), polymorphism information content(PIC) and effective number of allele(N(e)) were calculated. 41 alleles were found and their size were ranged from 110bp to 250bp in ten microsatellite loci, Fca152 had 6 alleles, Fca075, Fca094 and Fca294 had 5 alleles, Fca005 and Pti002 had 4 alleles and the others had 3 alleles in all tiger samples, respectively. The allelic frequencies were from 0.009 to 0.767; The He ranged from 0.385 to 0.707, and Fca294 and Pti010 locus had the highest and lowest value; the PIC were from 0.353 to 0.658, Fca294 and Pti010 locus had the highest and lowest value; and N(e) were from 1.626 to 3.409, Fca294 and Pti010 locus had the highest and lowest value, which showed the ten

  20. Alleles conferring improved fiber quality from EMS mutagenesis of elite cotton genotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The elite gene pool of cotton (Gossypium spp.) has less diversity than those of most other major crops, making identification of novel alleles important to ongoing crop improvement. A total of 3,164 M5 lines resulting from ethyl methanesulfonate mutagenesis of two G. hirsutum breeding lines, TAM 94L...

  1. Host range and genetic diversity of croton yellow vein mosaic virus, a weed-infecting monopartite begomovirus causing leaf curl disease in tomato.

    PubMed

    Pramesh, D; Mandal, Bikash; Phaneendra, Chigurupati; Muniyappa, V

    2013-03-01

    Croton yellow vein mosaic virus (CYVMV) is a widely occurring begomovirus in Croton bonplandianum, a common weed in the Indian subcontinent. In this study, CYVMV (genus Begomovirus, family Geminiviridae) was transmitted by whiteflies (Bemisia tabaci) to as many as 35 plant species belonging to 11 families, including many vegetables, tobacco varieties, ornamentals and weeds. CYVMV produced bright yellow vein symptoms in croton, whereas in all the other host species, the virus produced leaf curl symptoms. CYVMV produced leaf curl in 13 tobacco species and 22 cultivars of Nicotiana tabacum and resembled tobacco leaf curl virus (TobLCV) in host reactions. However, CYVMV was distinguished from TobLCV in four differential hosts, Ageratum conyzoides, C. bonplandianum, Euphorbia geniculata and Sonchus bracyotis. The complete genome sequences of four isolates originating from northern, eastern and southern India revealed that a single species of DNA-A and a betasatellite, croton yellow vein mosaic betasatellite (CroYVMB) were associated with the yellow vein mosaic disease of croton. The sequence identity among the isolates of CYVMV DNA-A and CroYVMB occurring in diverse plant species was 91.8-97.9 % and 83.3-100 %, respectively. The CYVMV DNA-A and CroYVMB generated through rolling-circle amplification of the cloned DNAs produced typical symptoms of yellow vein mosaic and leaf curling in croton and tomato, respectively. The progeny virus from both the croton and tomato plants was transmitted successfully by B. tabaci. The present study establishes the etiology of yellow vein mosaic disease of C. bonplandianum and provides molecular evidence that a weed-infecting monopartite begomovirus causes leaf curl in tomato.

  2. Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates.

    PubMed

    García-Verdugo, C; Sajeva, M; La Mantia, T; Harrouni, C; Msanda, F; Caujapé-Castells, J

    2015-02-01

    Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats; and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N = 66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.

  3. The T-box transcription factor 3 is a promising biomarker and a key regulator of the oncogenic phenotype of a diverse range of sarcoma subtypes.

    PubMed

    Willmer, T; Cooper, A; Sims, D; Govender, D; Prince, S

    2016-01-01

    Sarcomas represent a complex group of malignant neoplasms of mesenchymal origin and their heterogeneity poses a serious diagnostic and therapeutic challenge. There is therefore a need to elucidate the molecular mechanisms underpinning the pathogenesis of the more than 70 distinguishable sarcoma subtypes. The transcription factor TBX3, a critical developmental regulator, is overexpressed in several cancers of epithelial origin where it contributes to tumorigenesis by different molecular mechanisms. However, the status and role of TBX3 in sarcomas have not been reported. Here we show that a diverse subset of soft tissue and bone sarcoma cell lines and patient-derived sarcoma tissues express high levels of TBX3. We further explore the significance of this overexpression using a small interferring RNA approach and demonstrate that TBX3 promotes the migratory ability of chondrosarcoma, rhabdomyosarcoma and liposarcoma cells but inhibits fibrosarcoma cell migration. This suggested that TBX3 may play a key role in the development of different sarcoma subtypes by functioning as either an oncoprotein or as a brake to prevent tumour progression. To further explore this, TBX3 knockdown and overexpression cell culture models were established using chondrosarcoma and fibrosarcoma cells as representatives of each scenario, and the resulting cells were characterized with regard to key features of tumorigenesis. Results from in vitro and in vivo assays reveal that, while TBX3 promotes substrate-dependent and -independent cell proliferation, migration and tumour formation in chondrosarcoma cells, it discourages fibrosarcoma formation. Our findings provide novel evidence linking TBX3 to cancers of mesenchymal origin. Furthermore, we show that TBX3 may be a biomarker for the diagnosis of histologically dynamic sarcoma subtypes and that it impacts directly on their oncogenic phenotype. Indeed, we reveal that TBX3 may exhibit oncogene or tumour suppressor activity in sarcomas, which

  4. Allelic variation in the squirrel monkey x-linked color vision gene: biogeographical and behavioral correlates.

    PubMed

    Cropp, Susan; Boinski, Sue; Li, Wen-Hsiung

    2002-06-01

    Most Neotropical primate species possess a polymorphic X-linked and a monomorphic autosomal color vision gene. Consequently, populations are composed of both dichromatics and trichromatics. Most theories on the maintenance of this genetic system revolve around possible advantages for foraging ecology. To examine the issue from a different angle, we compared the numbers and relative frequencies of alleles at the X-linked locus among three species of Saimiri representing a wide range of geographical and behavioral variation in the genus. Exons 3, 4, and 5 of the X-linked opsin gene were sequenced for a large number of X chromosomes for all three species. Several synonymous mutations were detected in exons 4 and 5 for the originally reported alleles but only a single nonsynonymous change was detected. Two alleles were found that appeared to be the result of recombination events. The low occurrence of recombinant alleles and absence of mutations in the amino acids critical for spectral tuning indicates that stabilizing selection acts to maintain the combinations of critical sites specific to each allele. Allele frequencies were approximately the same for all Saimiri species, with a slight but significant difference between S. boliviensis and S. oerstedii. No apparent correlation exists between allele frequencies and behavioral or biogeographical differences between species, casting doubt on the speculation that the spectral sensitivities of the alleles have been maintained because they are specifically well-tuned to Saimiri visual ecology. Rather, the spectral tuning peaks might have been maintained because they are as widely spaced as possible within the limited range of middlewave to longwave spectra useful to all primates. This arrangement creates a balance between maximizing the distance between spectral tuning peaks (allowing the color opponency of the visual system to distinguish between peaks) and maximizing the number of alleles within a limited range (yielding

  5. High genetic diversity in gametophyte clones of Undaria pinnatifida from Vladivostok, Dalian and Qingdao revealed using microsatellite analysis

    NASA Astrophysics Data System (ADS)

    Shan, Tifeng; Pang, Shaojun; Liu, Feng; Xu, Na; Zhao, Xiaobo; Gao, Suqin

    2012-03-01

    Breeding practice for Undaria pinnatifida (Harvey) Suringar requires the screening of a large number of offspring from gametophyte crossings to obtain an elite variety for large-scale cultivation. To better understand the genetic relationships of different gametophyte cultures isolated from different sources, 20 microsatellite loci were screened and 53 gametophyte clone cultures analyzed for U. pinnatifida isolated from wild sporophytes in Vladivostok, Russia and from cultivated sporophytes from Dalian and Qingdao, China. One locus was abandoned because of poor amplification. At the sex-linked locus of Up-AC-2A8, 3 alleles were detected in 25 female gametophyte clones, with sizes ranging from 307 to 316 bp. At other loci, 3 to 7 alleles were detected with an average of 4.5 alleles per locus. The average number of alleles at each locus was 1.3 and 3.7 for Russian and Chinese gametophyte clones, respectively. The average gene diversity for Russian, Chinese, and for the combined total of gametophyte clones was 0.1, 0.4, and 0.5, respectively. Russian gametophyte clones had unique alleles at 7 out of the 19 loci. In cluster analysis, Russian and Chinese gametophyte clones were separated into two different groups according to genetic distance. Overall, high genetic diversity was detected in gametophyte clones isolated from the two countries. These gametophyte cultures were believed to be appropriate parental materials for conducting breeding programs in the future.

  6. Allele Workbench: transcriptome pipeline and interactive graphics for allele-specific expression.

    PubMed

    Soderlund, Carol A; Nelson, William M; Goff, Stephen A

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  7. Abnormal segregation of alleles in CEPH pedigree DNAs arising from allele loss in lymphoblastoid DNA

    SciTech Connect

    Royle, N.J.; Armour, J.A.L.; Crosier, M.; Jeffreys, A.J. )

    1993-01-01

    Somatic events that result in the reduction to hemior homozygosity at all loci affected by the event have been identified in lymphoblastoid DNA from mothers of two CEPH families. Using suitably informative probes, the allele deficiencies were detected by the abnormal transmission of alleles from grandparents to grandchildren, with the apparent absence of the alleles from the parent. Undetected somatic deficiencies in family DNAs could result in misscoring of recombination events and consequently introduce errors into linkage analysis. 15 refs., 2 figs.

  8. Allele Workbench: Transcriptome Pipeline and Interactive Graphics for Allele-Specific Expression

    PubMed Central

    Soderlund, Carol A.; Nelson, William M.; Goff, Stephen A.

    2014-01-01

    Sequencing the transcriptome can answer various questions such as determining the transcripts expressed in a given species for a specific tissue or condition, evaluating differential expression, discovering variants, and evaluating allele-specific expression. Differential expression evaluates the expression differences between different strains, tissues, and conditions. Allele-specific expression evaluates expression differences between parental alleles. Both differential expression and allele-specific expression have been studied for heterosis (hybrid vigor), where the hybrid has improved performance over the parents for one or more traits. The Allele Workbench software was developed for a heterosis study that evaluated allele-specific expression for a mouse F1 hybrid using libraries from multiple tissues with biological replicates. This software has been made into a distributable package, which includes a pipeline, a Java interface to build the database, and a Java interface for query and display of the results. The required input is a reference genome, annotation file, and one or more RNA-Seq libraries with optional replicates. It evaluates allelic imbalance at the SNP and transcript level and flags transcripts with significant opposite directional allele-specific expression. The Java interface allows the user to view data from libraries, replicates, genes, transcripts, exons, and variants, including queries on allele imbalance for selected libraries. To determine the impact of allele-specific SNPs on protein folding, variants are annotated with their effect (e.g., missense), and the parental protein sequences may be exported for protein folding analysis. The Allele Workbench processing results in transcript files and read counts that can be used as input to the previously published Transcriptome Computational Workbench, which has a new algorithm for determining a trimmed set of gene ontology terms. The software with demo files is available from https://code.google.com/p/allele

  9. Center of Origin and Centers of Diversity in an Ancient Crop, Brassica rapa (Turnip Rape).

    PubMed

    Guo, Yiming; Chen, Sheng; Li, Zaiyun; Cowling, Wallace A

    2014-04-01

    Brassica rapa is the most widely distributed and has the longest history of domestication of the agricultural Brassica species. Molecular genetic diversity, based on 51 simple sequence repeat primer pairs and 715 alleles at polymorphic loci, was used to predict the center of origin and centers of diversity in a global collection of 173 B. rapa accessions. The accessions were separated into 3 molecular genetic groups based on STRUCTURE analysis-group 1 from the classical Old World (Europe and west Asia-north Africa), group 2 from east Asia, and group 3 from east, central, south, and southeast Asia. Accessions classified as "wild" (B. rapa var. sylvestris) were found only in group 1 and this group had the highest number and richness of private alleles. Each group included a diverse range of agricultural morphotypes (oilseed, root, or leafy vegetable types), flowering habit (winter, semi-winter, or spring type), self-compatibility or incompatibility, and seed color. The Old World and east, south, and central Asia were distinct subpopulations based on analysis of shared unique alleles. This study supports the theory that the classical Old World is the center of origin of B. rapa, with centers of diversity in east Asia and along ancient trade routes in Asia, with recent migration to the New World.

  10. Evolution in karst massifs: Cryptic diversity among bent-toed geckos along the Truong Son Range with descriptions of three new species and one new country record from Laos.

    PubMed

    Luu, Vinh Quang; Bonkowski, Michael; Nguyen, Truong Quang; Le, Minh Duc; Schneider, Nicole; Ngo, Hanh Thi; Ziegler, Thomas

    2016-01-01

    Species designated as 'cryptic' share a similar morphotype, and are often only clearly separable by molecular data. Cyrtodactylus, the most diverse gecko genus of the family Gekkonidae, is a prime example, because many morphologically similar taxa have only recently been identified as new species as a result of available genetic evidence. However, while cryptic diversity of Cyrtodactylus is already well documented on the Vietnamese side of the Truong Son range, only scarce data is available from central Laos. In this study, we address this issue by means of an integrative approach, which employs morphological, molecular, and ecological data to distinguish cryptic species of the Cyrtodacylus phongnhakebangensis species group primarily distributed along the northern Truong Son Range. Our analyses based on 12 selected morphological characters, a partial mitochondrial gene (COI), and five ecological parameters revealed three undescribed cryptic Cyrtodactylus species from Hin Nam No National Protected Area, which are described as Cyrtodactylus calamei sp. nov., Cyrtodactylus hinnamnoensis sp. nov., and Cyrtodactylus sommerladi sp. nov. A fourth discovered Cyrtodactylus population in Hin Nam No proved to be the first country record of C. cryptus for Laos. Our results highlight the importance of applying an integrative approach to resolving the taxonomy of complex and cryptic species groups, and the role of the Truong Son Range in maintaining the high level of biodiversity over time. PMID:27394811

  11. Sphaeromyxids form part of a diverse group of myxosporeans infecting the hepatic biliary systems of a wide range of host organisms

    PubMed Central

    2013-01-01

    Background Approximately 40 species of Sphaeromyxa have been described, all of which are coelozoic parasites from gall bladders of marine fish. They are unique amongst the myxosporeans as they have polar filaments that are flat and folded instead of being tubular and spirally wound. This unusual feature was used as a subordinal character to erect the suborder Sphaeromyxina, which contains one family, the Sphaeromyxidae, and a single genus Sphaeromyxa. Methods In the present study, we examine eelpout from the genus Lycodes from Iceland for the presence of myxosporean parasites in the gall bladder and perform morphological and DNA studies. Results A novel myxosporean, Sphaeromyxa lycodi n. sp., was identified in the gall bladders of five of the six species of Lycodes examined, with a prevalence ranging from 29 - 100%. The coelozoic plasmodia are large, polysporous and contain disporic pansporoblasts and mature spores which are arcuate. The pyriform polar capsules encase long and irregularly folded ribbon-like polar filaments. Each spore valve has two distinct ends and an almost 180° twist along the relatively indistinct suture line. The single sporoplasm is granular with two nuclei. Sphaeromyxa lycodi is phylogenetically related to other arcuate sphaeromyxids and is reproducibly placed with all known sphaeromyxids and forms part of a robustly supported clade of numerous myxosporean genera which infect the hepatic biliary systems of a wide range of hosts. Conclusions Sphaeromyxa lycodi is a common gall bladder myxosporean in eelpout of the genus Lycodes from Northern Iceland. It has characteristics typical of the genus and develops arcuate spores. Molecular phylogenetic analyses confirm that sphaeromyxids form a monophyletic group, subdivided into straight and arcuate spore forms, within the hepatic biliary clade that infect a wide range of freshwater associated animals. The ancestral spore form for the hepatic biliary clade was probably a Chloromyxum morphotype

  12. Distribution of repeat unit differences between alleles at tandem repeat microsatellite loci

    SciTech Connect

    Jin, L. |; Zhong, Y.; Chakraborty, R.

    1994-09-01

    PCR-based assays of tandemly repeated microsatellite loci detect genetic variation from which alleles may be scored by their repeat unit lengths. Comparison of allele sizes from such data yields a probability distribution (P{sub k}) of repeat unit differences (k) between alleles segregating in a population. We show that this distribution (P{sub k}; k = 0, 1,2,...) provides insight regarding the mechanism of production of new alleles at such loci and the demographic history of populations, far better than that obtained from other summary measures (e.g., heterozygosity, number of alleles, and the range of allele sizes). The distributions of P{sub k} under multi-step stepwise models of mutation are analytically derived, which show that when a population is at equilibrium under the mutation-drift balance, the distribution of repeat unit differences between alleles is positively skewed with a mode larger than zero. However, when the heterozygosity at a locus is low (say, less than 40%), P{sub k} is a monotonically decreasing function of k. Applications of this theory to data on repeat unit sizes at over 1,240 microsatellite loci from the Caucasians, categorized by the average heterozygosity of loci, indicate that at most microsatellite loci new alleles are produced by stepwise mutations, and this is consistent with the replication slippage mechanism of mutations. The repeat size changes of mutants are probably within one or two units of alleles from which the mutants arise. Distributions of P{sub k} at microsatellite loci located within genes show evidence of allele size constraints. No significant evidence of recent expansion of population sizes in the Caucasians is detected by the distribution of P{sub k}.

  13. Genetic diversity in wild sweet cherries (Prunus avium) in Turkey revealed by SSR markers.

    PubMed

    Ercisli, S; Agar, G; Yildirim, N; Duralija, B; Vokurka, A; Karlidag, H

    2011-06-21

    Wild sweet cherry (Prunus avium) trees are abundant in the northern part of Turkey, including the Coruh Valley. We analyzed 18 wild sweet cherry genotypes collected from diverse environments in the upper Coruh Valley in Turkey to determine genetic variation, using 10 SSR primers. These SSR primers generated 46 alleles; the number of alleles per primer ranged from 3 to 7, with a mean of 4.6. The primer PS12A02 gave the highest number of polymorphic bands (N = 7), while CPSCT010, UDAp-401 and UDAp-404 gave the lowest number (N = 3). Seven groups were separated in the dendrogram, although most of the genotypes did not cluster according to phenological and morphological traits. This level of genetic diversity in these wild sweet cherry genotypes is very high and therefore these trees would be useful as breeders for crosses between cultivated sweet cherry and wild genotypes.

  14. Female sticklebacks count alleles in a strategy of sexual selection explaining MHC polymorphism.

    PubMed

    Reusch, T B; Häberli, M A; Aeschlimann, P B; Milinski, M

    2001-11-15

    The origin and maintenance of polymorphism in major histocompatibility complex (MHC) genes in natural populations is still unresolved. Sexual selection, frequency-dependent selection by parasites and pathogens, and heterozygote advantage have been suggested to explain the maintenance of high allele diversity at MHC genes. Here we argue that there are two (non-exclusive) strategies for MHC-related sexual selection, representing solutions to two different problems: inbreeding avoidance and parasite resistance. In species prone to inadvertent inbreeding, partners should prefer dissimilar MHC genotypes to similar ones. But if the goal is to maximize the resistance of offspring towards potential infections, the choosing sex should prefer mates with a higher diversity of MHC alleles. This latter strategy should apply when there are several MHC loci, as is the case in most vertebrates. We tested the relative importance of an 'allele counting' strategy compared to a disassortative mating strategy using wild-caught three-spined sticklebacks (Gasterosteus aculeatus) from an interconnected system of lakes. Here we show that gravid female fish preferred the odour of males with a large number of MHC class-IIB alleles to that of males with fewer alleles. Females did not prefer male genotypes dissimilar to their own. PMID:11713527

  15. Analysis of genetic diversity and differentiation of seven stocks of Litopenaeus vannamei using microsatellite markers

    NASA Astrophysics Data System (ADS)

    Zhang, Kai; Wang, Weiji; Li, Weiya; Zhang, Quanqi; Kong, Jie

    2014-08-01

    Seven microsatellite markers were used to evaluate the genetic diversity and differentiation of seven stocks of Litopenaeus vannamei, which were introduced from Central and South America to China. All seven microsatellite loci were polymorphic, with polymorphism information content ( PIC) values ranging from 0.593 to 0.952. Totally 92 alleles were identified, and the number of alleles ( Na) and effective alleles ( Ne) varied between 4 and 21 and 2.7 and 14.6, respectively. Observed heterozygosity ( H o) values were lower than the expected heterozygosity ( H e) values (0.526-0.754), which indicated that the seven stocks possessed a rich genetic diversity. Thirty-seven tests were detected for reasonable significant deviation from Hardy-Weinberg equilibrium. F is values were positive at five loci, suggesting that there was a relatively high degree of inbreeding within stocks. Pairwise F st values ranged from 0.0225 to 0.151, and most of the stock pairs were moderately differentiated. Genetic distance and cluster analysis using UPGMA revealed a close genetic relationship of L. vannamei between Pop2 and Pop3. AMOVA indicated that the genetic variation among stocks (11.3%) was much lower than that within stocks (88.7%). Although the seven stocks had a certain degree of genetic differentiation and a rich genetic diversity, there is an increasing risk of decreased performance due to inbreeding in subsequent generations.

  16. A multi-farm assessment of Greek black pig genetic diversity using microsatellite molecular markers.

    PubMed

    Michailidou, S; Kalivas, A; Ganopoulos, I; Stea, E; Michailidis, G; Tsaftaris, A; Argiriou, A

    2014-01-01

    Local breeds are important for the maintenance of genetic diversity and future food security. Nowadays, the worldwide distribution of pigs is dominated by a few breeds, tending towards a severe loss of pig biodiversity. Thus, it is critical to maintain distinct populations of pig breeds. The Greek black pig, a breed raised locally and known for the high quality of its meat for cured products, is the only traditional indigenous pig breed reared in Greece. We investigated the genetic diversity, based on microsatellite analysis, of the Greek black pig and evaluated its genetic uniqueness. One hundred and three pigs from 12 Greek farms were analyzed using 11 microsatellites. The total number of alleles amounted to 135, with a mean number of alleles per locus of 12.27, ranging between 10 and 16 alleles. The observed heterozygosity ranged from 0.363 to 0.825 per locus. The expected heterozygosity ranged from 0.471 to 0.707. The inbreeding coefficient ranged from -0.329 to 0.229. We conclude that the Greek black pig, despite its low population size, has a high degree of genetic variability, which will be useful for breeding programs aimed at maintaining long-term survival of this ancient breed. PMID:24782089

  17. Rapid Microarray-Based Identification of Different mecA Alleles in Staphylococci

    PubMed Central

    Müller, Elke; Schwarz, Stefan; Hotzel, Helmut; Ehricht, Ralf

    2012-01-01

    To screen isolates and to identify mecA alleles, published mecA sequences were analyzed, and a microarray for the rapid discrimination of mecA alleles was designed. A GenBank analysis yielded 135 full-length gene sequences annotated as mecA. These sequences clustered into 32 different alleles corresponding to 28 unique amino acid sequences and to 15 distinct hybridization patterns on this microarray. A collection of 78 clinical and veterinary isolates of Staphylococcus spp. was characterized using this assay. Nine of the 15 expected patterns, as well as one as-yet-unknown pattern, were identified. These patterns were detected in various epidemic methicillin-resistant Staphylococcus aureus strains, in S. pseudintermedius, and in coagulase-negative species such as S. epidermidis, S. fleurettii, or S. haemolyticus. There was no correlation between the different mecA hybridization patterns and the SCCmec type. Determination of MICs showed that mecA alleles corresponding to only four of these nine patterns were associated with β-lactam resistance. The mecA alleles that did not confer β-lactam resistance were largely restricted to coagulase-negative staphylococci of animal origin, such as S. sciuri and S. vitulinus. Because of the diversity of sequences and the different impact on β-lactam susceptibility, the existence of different mecA alleles needs to be taken into account when designing diagnostic assays for the detection of mecA. PMID:22890767

  18. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa. PMID:24990677

  19. Natural selection for the Duffy-null allele in the recently admixed people of Madagascar.

    PubMed

    Hodgson, Jason A; Pickrell, Joseph K; Pearson, Laurel N; Quillen, Ellen E; Prista, António; Rocha, Jorge; Soodyall, Himla; Shriver, Mark D; Perry, George H

    2014-08-22

    While gene flow between distantly related populations is increasingly recognized as a potentially important source of adaptive genetic variation for humans, fully characterized examples are rare. In addition, the role that natural selection for resistance to vivax malaria may have played in the extreme distribution of the protective Duffy-null allele, which is nearly completely fixed in mainland sub-Saharan Africa and absent elsewhere, is controversial. We address both these issues by investigating the evolution of the Duffy-null allele in the Malagasy, a recently admixed population with major ancestry components from both East Asia and mainland sub-Saharan Africa. We used genome-wide genetic data and extensive computer simulations to show that the high frequency of the Duffy-null allele in Madagascar can only be explained in the absence of positive natural selection under extreme demographic scenarios involving high genetic drift. However, the observed genomic single nucleotide polymorphism diversity in the Malagasy is incompatible with such extreme demographic scenarios, indicating that positive selection for the Duffy-null allele best explains the high frequency of the allele in Madagascar. We estimate the selection coefficient to be 0.066. Because vivax malaria is endemic to Madagascar, this result supports the hypothesis that malaria resistance drove fixation of the Duffy-null allele in mainland sub-Saharan Africa.

  20. Rapid microarray-based identification of different mecA alleles in Staphylococci.

    PubMed

    Monecke, Stefan; Müller, Elke; Schwarz, Stefan; Hotzel, Helmut; Ehricht, Ralf

    2012-11-01

    To screen isolates and to identify mecA alleles, published mecA sequences were analyzed, and a microarray for the rapid discrimination of mecA alleles was designed. A GenBank analysis yielded 135 full-length gene sequences annotated as mecA. These sequences clustered into 32 different alleles corresponding to 28 unique amino acid sequences and to 15 distinct hybridization patterns on this microarray. A collection of 78 clinical and veterinary isolates of Staphylococcus spp. was characterized using this assay. Nine of the 15 expected patterns, as well as one as-yet-unknown pattern, were identified. These patterns were detected in various epidemic methicillin-resistant Staphylococcus aureus strains, in S. pseudintermedius, and in coagulase-negative species such as S. epidermidis, S. fleurettii, or S. haemolyticus. There was no correlation between the different mecA hybridization patterns and the SCCmec type. Determination of MICs showed that mecA alleles corresponding to only four of these nine patterns were associated with β-lactam resistance. The mecA alleles that did not confer β-lactam resistance were largely restricted to coagulase-negative staphylococci of animal origin, such as S. sciuri and S. vitulinus. Because of the diversity of sequences and the different impact on β-lactam susceptibility, the existence of different mecA alleles needs to be taken into account when designing diagnostic assays for the detection of mecA.

  1. Pseudomonas genomes: diverse and adaptable.

    PubMed

    Silby, Mark W; Winstanley, Craig; Godfrey, Scott A C; Levy, Stuart B; Jackson, Robert W

    2011-07-01

    Members of the genus Pseudomonas inhabit a wide variety of environments, which is reflected in their versatile metabolic capacity and broad potential for adaptation to fluctuating environmental conditions. Here, we examine and compare the genomes of a range of Pseudomonas spp. encompassing plant, insect and human pathogens, and environmental saprophytes. In addition to a large number of allelic differences of common genes that confer regulatory and metabolic flexibility, genome analysis suggests that many other factors contribute to the diversity and adaptability of Pseudomonas spp. Horizontal gene transfer has impacted the capability of pathogenic Pseudomonas spp. in terms of disease severity (Pseudomonas aeruginosa) and specificity (Pseudomonas syringae). Genome rearrangements likely contribute to adaptation, and a considerable complement of unique genes undoubtedly contributes to strain- and species-specific activities by as yet unknown mechanisms. Because of the lack of conserved phenotypic differences, the classification of the genus has long been contentious. DNA hybridization and genome-based analyses show close relationships among members of P. aeruginosa, but that isolates within the Pseudomonas fluorescens and P. syringae species are less closely related and may constitute different species. Collectively, genome sequences of Pseudomonas spp. have provided insights into pathogenesis and the genetic basis for diversity and adaptation.

  2. Patterns of species range evolution in Indo-Pacific reef assemblages reveal the Coral Triangle as a net source of transoceanic diversity

    PubMed Central

    Evans, Sean M.; McKenna, Caroline; Simpson, Stephen D.; Tournois, Jennifer

    2016-01-01

    The Coral Triangle in the Indo-Pacific is a region renowned for exceptional marine biodiversity. The area could have acted as a ‘centre of origin’ where speciation has been prolific or a ‘centre of survival’ by providing refuge during major environmental shifts such as sea-level changes. The region could also have acted as a ‘centre of accumulation’ for species with origins outside of the Coral Triangle, owing to it being at a central position between the Indian and Pacific oceans. Here, we investigated support for these hypotheses using population-level DNA sequence-based reconstructions of the range evolution of 45 species (314 populations) of Indo-Pacific reef-associated organisms. Our results show that populations undergoing the most ancient establishment were significantly more likely to be closer to the centre of the Coral Triangle than to peripheral locations. The data are consistent with the Coral Triangle being a net source of coral-reef biodiversity for the Indo-Pacific region, suggesting that the region has acted primarily as a centre of survival, a centre of origin or both. These results provide evidence of how a key location can influence the large-scale distributions of biodiversity over evolutionary timescales. PMID:27330168

  3. A new rauisuchid (Archosauria, Pseudosuchia) from the Upper Triassic (Norian) of New Mexico increases the diversity and temporal range of the clade

    PubMed Central

    Smith, Nathan D.; Turner, Alan H.; Irmis, Randall B.; Nesbitt, Sterling J.

    2016-01-01

    Rauisuchids are large (2–6 m in length), carnivorous, and quadrupedal pseudosuchian archosaurs closely related to crocodylomorphs. Though geographically widespread, fossils of this clade are relatively rare in Late Triassic assemblages. The middle Norian (∼212 Ma) Hayden Quarry of northern New Mexico, USA, in the Petrified Forest Member of the Chinle Formation, has yielded isolated postcranial elements and associated skull elements of a new species of rauisuchid. Vivaron haydeni gen. et. sp. nov. is diagnosed by the presence of two posteriorly directed prongs at the posterior end of the maxilla for articulation with the jugal. The holotype maxilla and referred elements are similar to those of the rauisuchid Postosuchus kirkpatricki from the southwestern United States, but V. haydeni shares several maxillary apomorphies (e.g., a distinct dropoff to the antorbital fossa that is not a ridge, a straight ventral margin, and a well defined dental groove) with the rauisuchid Teratosaurus suevicus from the Norian of Germany. Despite their geographic separation, this morphological evidence implies a close phylogenetic relationship between V. haydeni and T. suevicus. The morphology preserved in the new Hayden Quarry rauisuchid V. haydeni supports previously proposed and new synapomorphies for nodes within Rauisuchidae. The discovery of Vivaron haydeni reveals an increased range of morphological disparity for rauisuchids from the low-paleolatitude Chinle Formation and a clear biogeographic connection with high paleolatitude Pangea.

  4. A new rauisuchid (Archosauria, Pseudosuchia) from the Upper Triassic (Norian) of New Mexico increases the diversity and temporal range of the clade

    PubMed Central

    Smith, Nathan D.; Turner, Alan H.; Irmis, Randall B.; Nesbitt, Sterling J.

    2016-01-01

    Rauisuchids are large (2–6 m in length), carnivorous, and quadrupedal pseudosuchian archosaurs closely related to crocodylomorphs. Though geographically widespread, fossils of this clade are relatively rare in Late Triassic assemblages. The middle Norian (∼212 Ma) Hayden Quarry of northern New Mexico, USA, in the Petrified Forest Member of the Chinle Formation, has yielded isolated postcranial elements and associated skull elements of a new species of rauisuchid. Vivaron haydeni gen. et. sp. nov. is diagnosed by the presence of two posteriorly directed prongs at the posterior end of the maxilla for articulation with the jugal. The holotype maxilla and referred elements are similar to those of the rauisuchid Postosuchus kirkpatricki from the southwestern United States, but V. haydeni shares several maxillary apomorphies (e.g., a distinct dropoff to the antorbital fossa that is not a ridge, a straight ventral margin, and a well defined dental groove) with the rauisuchid Teratosaurus suevicus from the Norian of Germany. Despite their geographic separation, this morphological evidence implies a close phylogenetic relationship between V. haydeni and T. suevicus. The morphology preserved in the new Hayden Quarry rauisuchid V. haydeni supports previously proposed and new synapomorphies for nodes within Rauisuchidae. The discovery of Vivaron haydeni reveals an increased range of morphological disparity for rauisuchids from the low-paleolatitude Chinle Formation and a clear biogeographic connection with high paleolatitude Pangea. PMID:27651983

  5. A new rauisuchid (Archosauria, Pseudosuchia) from the Upper Triassic (Norian) of New Mexico increases the diversity and temporal range of the clade.

    PubMed

    Lessner, Emily J; Stocker, Michelle R; Smith, Nathan D; Turner, Alan H; Irmis, Randall B; Nesbitt, Sterling J

    2016-01-01

    Rauisuchids are large (2-6 m in length), carnivorous, and quadrupedal pseudosuchian archosaurs closely related to crocodylomorphs. Though geographically widespread, fossils of this clade are relatively rare in Late Triassic assemblages. The middle Norian (∼212 Ma) Hayden Quarry of northern New Mexico, USA, in the Petrified Forest Member of the Chinle Formation, has yielded isolated postcranial elements and associated skull elements of a new species of rauisuchid. Vivaron haydeni gen. et. sp. nov. is diagnosed by the presence of two posteriorly directed prongs at the posterior end of the maxilla for articulation with the jugal. The holotype maxilla and referred elements are similar to those of the rauisuchid Postosuchus kirkpatricki from the southwestern United States, but V. haydeni shares several maxillary apomorphies (e.g., a distinct dropoff to the antorbital fossa that is not a ridge, a straight ventral margin, and a well defined dental groove) with the rauisuchid Teratosaurus suevicus from the Norian of Germany. Despite their geographic separation, this morphological evidence implies a close phylogenetic relationship between V. haydeni and T. suevicus. The morphology preserved in the new Hayden Quarry rauisuchid V. haydeni supports previously proposed and new synapomorphies for nodes within Rauisuchidae. The discovery of Vivaron haydeni reveals an increased range of morphological disparity for rauisuchids from the low-paleolatitude Chinle Formation and a clear biogeographic connection with high paleolatitude Pangea.

  6. A new rauisuchid (Archosauria, Pseudosuchia) from the Upper Triassic (Norian) of New Mexico increases the diversity and temporal range of the clade.

    PubMed

    Lessner, Emily J; Stocker, Michelle R; Smith, Nathan D; Turner, Alan H; Irmis, Randall B; Nesbitt, Sterling J

    2016-01-01

    Rauisuchids are large (2-6 m in length), carnivorous, and quadrupedal pseudosuchian archosaurs closely related to crocodylomorphs. Though geographically widespread, fossils of this clade are relatively rare in Late Triassic assemblages. The middle Norian (∼212 Ma) Hayden Quarry of northern New Mexico, USA, in the Petrified Forest Member of the Chinle Formation, has yielded isolated postcranial elements and associated skull elements of a new species of rauisuchid. Vivaron haydeni gen. et. sp. nov. is diagnosed by the presence of two posteriorly directed prongs at the posterior end of the maxilla for articulation with the jugal. The holotype maxilla and referred elements are similar to those of the rauisuchid Postosuchus kirkpatricki from the southwestern United States, but V. haydeni shares several maxillary apomorphies (e.g., a distinct dropoff to the antorbital fossa that is not a ridge, a straight ventral margin, and a well defined dental groove) with the rauisuchid Teratosaurus suevicus from the Norian of Germany. Despite their geographic separation, this morphological evidence implies a close phylogenetic relationship between V. haydeni and T. suevicus. The morphology preserved in the new Hayden Quarry rauisuchid V. haydeni supports previously proposed and new synapomorphies for nodes within Rauisuchidae. The discovery of Vivaron haydeni reveals an increased range of morphological disparity for rauisuchids from the low-paleolatitude Chinle Formation and a clear biogeographic connection with high paleolatitude Pangea. PMID:27651983

  7. Assessment of genetic diversity in the sorghum reference set using EST-SSR markers.

    PubMed

    Ramu, P; Billot, C; Rami, J-F; Senthilvel, S; Upadhyaya, H D; Ananda Reddy, L; Hash, C T

    2013-08-01

    Selection and use of genetically diverse genotypes are key factors in any crop breeding program to develop cultivars with a broad genetic base. Molecular markers play a major role in selecting diverse genotypes. In the present study, a reference set representing a wide range of sorghum genetic diversity was screened with 40 EST-SSR markers to validate both the use of these markers for genetic structure analyses and the population structure of this set. Grouping of accessions is identical in distance-based and model-based clustering methods. Genotypes were grouped primarily based on race within the geographic origins. Accessions derived from the African continent contributed 88.6 % of alleles confirming the African origin of sorghum. In total, 360 alleles were detected in the reference set with an average of 9 alleles per marker. The average PIC value was 0.5230 with a range of 0.1379-0.9483. Sub-race, guinea margaritiferum (Gma) from West Africa formed a separate cluster in close proximity to wild accessions suggesting that the Gma group represents an independent domestication event. Guineas from India and Western Africa formed two distinct clusters. Accessions belongs to the kafir race formed the most homogeneous group as observed in earlier studies. This analysis suggests that the EST-SSR markers used in the present study have greater discriminating power than the genomic SSRs. Genetic variance within the subpopulations was very high (71.7 %) suggesting that the germplasm lines included in the set are more diverse. Thus, this reference set representing the global germplasm is an ideal material for the breeding community, serving as a community resource for trait-specific allele mining as well as genome-wide association mapping.

  8. Genetic diversity of four populations of Qualea grandiflora Mart. in fragments of the Brazilian Cerrado.

    PubMed

    Antiqueira, Lia Maris Orth Ritter; Kageyama, Paulo Yoshio

    2014-02-01

    We analyzed the genetic structure and diversity of Qualea grandiflora Mart., the most abundant woody species in the Brazilian Cerrado. Eight microsatellite loci were used to analyze samples from four populations subjected to different types of anthropic pressure, distributed throughout the state of São Paulo in the regions of Assis, Brotas, Itirapina and Pedregulho. Results indicated a mean number of 12 alleles per locus, but only six effective alleles. Alleles private to particular populations and rare alleles were also detected. An excess of homozygotes and moderate levels of inbreeding were observed. No clones were identified. All populations departed from Hardy-Weinberg equilibrium (p < 0.05). Spatial structure was observed in the distribution of specimens in distance classes ranging from 30 to 40 km and three genetic clusters were identified, with genotypes in the Pedregulho population differing from the others by up to 90 %. The influence of the Wahlund effect on the studied populations lies between 8.5 and 53.3 %. Estimates of effective population size were low (<10), and the minimum viable area for conservation in the short-, medium- and long-term was estimated to be between 4 and 184 ha. Gene flow was high enough to counter the effects of genetic drift. The genetic diversity and divergence between the studied populations indicated that the Pedregulho population should be considered an Evolutionary Significant Unit and a Management Unit.

  9. A conditional allele of Rspo3 reveals redundant function of R-spondins during mouse limb development.

    PubMed

    Neufeld, Stanley; Rosin, Jessica M; Ambasta, Anshula; Hui, Kristen; Shaneman, Venessa; Crowder, Ray; Vickerman, Lori; Cobb, John

    2012-10-01

    R-spondins are secreted ligands that bind cell surface receptors and activate Wnt/β-catenin signaling. Human mutations and gene inactivation studies in mice have revealed a role for these four proteins (RSPO1-4) in diverse developmental processes ranging from sex determination to limb development. Among the genes coding for R-spondins, only inactivation of Rspo3 shows early embryonic lethality (E10.5 in mice). Therefore, a conditional allele of this gene is necessary to understand the function of R-spondins throughout murine development. To address this need, we have produced an allele in which loxP sites flank exons 2-4 of Rspo3, allowing tissue-specific deletion of these exons in the presence of Cre recombinase. We used these mice to investigate the role of Rspo3 during limb development and found that limbs ultimately developed normally in the absence of Rspo3 function. However, severe hindlimb truncations resulted when Rspo3 and Rspo2 mutations were combined, demonstrating redundant function of these genes.

  10. Forensic Loci Allele Database (FLAD): Automatically generated, permanent identifiers for sequenced forensic alleles.

    PubMed

    Van Neste, Christophe; Van Criekinge, Wim; Deforce, Dieter; Van Nieuwerburgh, Filip

    2016-01-01

    It is difficult to predict if and when massively parallel sequencing of forensic STR loci will replace capillary electrophoresis as the new standard technology in forensic genetics. The main benefits of sequencing are increased multiplexing scales and SNP detection. There is not yet a consensus on how sequenced profiles should be reported. We present the Forensic Loci Allele Database (FLAD) service, made freely available on http://forensic.ugent.be/FLAD/. It offers permanent identifiers for sequenced forensic alleles (STR or SNP) and their microvariants for use in forensic allele nomenclature. Analogous to Genbank, its aim is to provide permanent identifiers for forensically relevant allele sequences. Researchers that are developing forensic sequencing kits or are performing population studies, can register on http://forensic.ugent.be/FLAD/ and add loci and allele sequences with a short and simple application interface (API).

  11. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

    PubMed

    Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

    2016-01-01

    Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among

  12. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran

    PubMed Central

    Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

    2016-01-01

    Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among

  13. Strong Genetic Differentiation of Submerged Plant Populations across Mountain Ranges: Evidence from Potamogeton pectinatus in Iran.

    PubMed

    Abbasi, Shabnam; Afsharzadeh, Saeed; Saeidi, Hojjatollah; Triest, Ludwig

    2016-01-01

    Biogeographic barriers for freshwater biota can be effective at various spatial scales. At the largest spatial scale, freshwater organisms can become genetically isolated by their high mountain ranges, vast deserts, and inability to cross oceans. Isolation by distance of aquatic plants is expected to be stronger across than alongside mountain ridges whereas the heterogeneity of habitats among populations and temporary droughts may influence connectivity and hamper dispersal. Suitable aquatic plant habitats became reduced, even for the widespread submerged Potamogeton pectinatus L. (also named Stuckenia pectinata) giving structure to various aquatic habitats. We compared the level of genetic diversity in a heterogeneous series of aquatic habitats across Iran and tested their differentiation over distances and across mountain ranges (Alborz and Zagros) and desert zones (Kavir), with values obtained from temperate region populations. The diversity of aquatic ecosystems across and along large geographic barriers provided a unique ecological situation within Iran. P. pectinatus were considered from thirty-six sites across Iran at direct flight distances ranging from 20 to 1,200 km. Nine microsatellite loci revealed a very high number of alleles over all sites. A PCoA, NJT clustering and STRUCTURE analysis revealed a separate grouping of individuals of southeastern Iranian sites and was confirmed by their different nuclear ITS and cpDNA haplotypes thereby indicating an evolutionary significant unit (ESU). At the level of populations, a positive correlation between allelic differentiation Dest with geographic distance was found. Individual-based STRUCTURE analysis over 36 sites showed 7 genetic clusters. FST and RST values for ten populations reached 0.343 and 0.521, respectively thereby indicating that allele length differences are more important and contain evolutionary information. Overall, higher levels of diversity and a stronger differentiation was revealed among

  14. A comparison of type 2 diabetes risk allele load between African Americans and European Americans.

    PubMed

    Keaton, Jacob M; Cooke Bailey, Jessica N; Palmer, Nicholette D; Freedman, Barry I; Langefeld, Carl D; Ng, Maggie C Y; Bowden, Donald W

    2014-12-01

    The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African-derived populations were genotyped in 1,990 African Americans (n = 963 T2D cases, n = 1,027 controls) and 1,644 European Americans (n = 719 T2D cases, n = 925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p < 0.05). African American individuals carried 38-67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p < 0.05). European American individuals carried 38-65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.8 risk alleles (p = 3.97 × 10(-89)) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result

  15. A Comparison of Type 2 Diabetes Risk Allele Load between African Americans and European Americans

    PubMed Central

    Keaton, Jacob M.; Cooke Bailey, Jessica N.; Palmer, Nicholette D.; Freedman, Barry I.; Langefeld, Carl D.; Ng, Maggie C. Y.; Bowden, Donald W.

    2014-01-01

    The prevalence of type 2 diabetes (T2D) is greater in populations of African descent compared to European-descent populations. Genetic risk factors may underlie the disparity in disease prevalence. Genome-wide association studies (GWAS) have identified >60 common genetic variants that contribute to T2D risk in populations of European, Asian, African, and Hispanic descent. These studies have not comprehensively examined population differences in cumulative risk allele load. To investigate the relationship between risk allele load and T2D risk, 46 T2D single nucleotide polymorphisms (SNPs) in 43 loci from GWAS in European, Asian, and African derived populations were genotyped in 1,990 African Americans (n=963 T2D cases, n=1,027 controls) and 1,644 European Americans (n=719 T2D cases, n=925 controls) ascertained and recruited using a common protocol in the southeast United States. A genetic risk score (GRS) was constructed from the cumulative risk alleles for each individual. In African American subjects, risk allele frequencies ranged from 0.024 to 0.964. Risk alleles from 26 SNPs demonstrated directional consistency with previous studies, and 3 SNPs from ADAMTS9, TCF7L2, and ZFAND6 showed nominal evidence of association (p<0.05). African American individuals carried 38–67 (53.7 ± 4.0, mean ± SD) risk alleles. In European American subjects, risk allele frequencies ranged from 0.084 to 0.996. Risk alleles from 36 SNPs demonstrated directional consistency, and 10 SNPs from BCL11A, PSMD6, ADAMTS9, ZFAND3, ANK1, CDKN2A/B, TCF7L2, PRC1, FTO, and BCAR1 showed evidence of association (p<0.05). European American individuals carried 38–65 (50.9 ± 4.4) risk alleles. African Americans have a significantly greater burden of 2.9 risk alleles (p=3.97×10−89) compared to European Americans. However, GRS modeling showed that cumulative risk allele load was associated with risk of T2D in European Americans, but only marginally in African Americans. This result suggests that

  16. Three allele combinations associated with Multiple Sclerosis

    PubMed Central

    Favorova, Olga O; Favorov, Alexander V; Boiko, Alexey N; Andreewski, Timofey V; Sudomoina, Marina A; Alekseenkov, Alexey D; Kulakova, Olga G; Gusev, Eugenyi I; Parmigiani, Giovanni; Ochs, Michael F

    2006-01-01

    Background Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As genotyping methods improve throughput, approaches that can explore multigene interactions appropriately should lead to improved understanding of MS. Methods 286 unrelated patients with definite MS and 362 unrelated healthy controls of Russian descent were genotyped at polymorphic loci (including SNPs, repeat polymorphisms, and an insertion/deletion) of the DRB1, TNF, LT, TGFβ1, CCR5 and CTLA4 genes and TNFa and TNFb microsatellites. Each allele carriership in patients and controls was compared by Fisher's exact test, and disease-associated combinations of alleles in the data set were sought using a Bayesian Markov chain Monte Carlo-based method recently developed by our group. Results We identified two previously unknown MS-associated tri-allelic combinations: -509TGFβ1*C, DRB1*18(3), CTLA4*G and -238TNF*B1,-308TNF*A2, CTLA4*G, which perfectly separate MS cases from controls, at least in the present sample. The previously described DRB1*15(2) allele, the microsatellite TNFa9 allele and the biallelic combination CCR5Δ32, DRB1*04 were also reidentified as MS-associated. Conclusion These results represent an independent validation of MS association with DRB1*15(2) and TNFa9 in Russians and are the first to find the interplay of three loci in conferring susceptibility to MS. They demonstrate the efficacy of our approach for the identification of complex-disease-associated combinations of alleles. PMID:16872485

  17. The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of theta.

    PubMed

    Haasl, Ryan J; Payseur, Bret A

    2010-12-01

    Theoretical work focused on microsatellite variation has produced a number of important results, including the expected distribution of repeat sizes and the expected squared difference in repeat size between two randomly selected samples. However, closed-form expressions for the sampling distribution and frequency spectrum of microsatellite variation have not been identified. Here, we use coalescent simulations of the stepwise mutation model to develop gamma and exponential approximations of the microsatellite allele frequency spectrum, a distribution central to the description of microsatellite variation across the genome. For both approximations, the parameter of biological relevance is the number of alleles at a locus, which we express as a function of θ, the population-scaled mutation rate, based on simulated data. Discovered relationships between θ, the number of alleles, and the frequency spectrum support the development of three new estimators of microsatellite θ. The three estimators exhibit roughly similar mean squared errors (MSEs) and all are biased. However, across a broad range of sample sizes and θ values, the MSEs of these estimators are frequently lower than all other estimators tested. The new estimators are also reasonably robust to mutation that includes step sizes greater than one. Finally, our approximation to the microsatellite allele frequency spectrum provides a null distribution of microsatellite variation. In this context, a preliminary analysis of the effects of demographic change on the frequency spectrum is performed. We suggest that simulations of the microsatellite frequency spectrum under evolutionary scenarios of interest may guide investigators to the use of relevant and sometimes novel summary statistics.

  18. Genomic landscape of human allele-specific DNA methylation.

    PubMed

    Fang, Fang; Hodges, Emily; Molaro, Antoine; Dean, Matthew; Hannon, Gregory J; Smith, Andrew D

    2012-05-01

    DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. Simulation results indicate technical specifications of existing methylome data, such as read length and coverage, are sufficient for full-genome ASM profiling based on our model. We used our model to analyze methylomes for a diverse set of human cell types, including cultured and uncultured differentiated cells, embryonic stem cells and induced pluripotent stem cells. Regions of ASM identified most consistently across methylomes are tightly connected with known imprinted genes and precisely delineate the boundaries of several known imprinting control regions. Predicted regions of ASM common to multiple cell types frequently mark noncoding RNA promoters and represent promising starting points for targeted validation. More generally, our model provides the analytical complement to cutting-edge experimental technologies for surveying ASM in specific cell types and across species. PMID:22523239

  19. Cytochrome allelic variants and clopidogrel metabolism in cardiovascular diseases therapy.

    PubMed

    Jarrar, Mohammed; Behl, Shalini; Manyam, Ganiraju; Ganah, Hany; Nazir, Mohammed; Nasab, Reem; Moustafa, Khaled

    2016-06-01

    Clopidogrel and aspirin are among the most prescribed dual antiplatelet therapies to treat the acute coronary syndrome and heart attacks. However, their potential clinical impacts are a subject of intense debates. The therapeutic efficiency of clopidogrel is controlled by the actions of hepatic cytochrome P450 (CYPs) enzymes and impacted by individual genetic variations. Inter-individual polymorphisms in CYPs enzymes affect the metabolism of clopidogrel into its active metabolites and, therefore, modify its turnover and clinical outcome. So far, clinical trials fail to confirm higher or lower adverse cardiovascular effects in patients treated with combinations of clopidogrel and proton pump inhibitors, compared with clopidogrel alone. Such inconclusive findings may be due to genetic variations in the cytochromes CYP2C19 and CYP3A4/5. To investigate potential interactions/effects of these cytochromes and their allele variants on the treatment of acute coronary syndrome with clopidogrel alone or in combination with proton pump inhibitors, we analyze recent literature and discuss the potential impact of the cytochrome allelic variants on cardiovascular events and stent thrombosis treated with clopidogrel. The diversity of CYP2C19 polymorphisms and prevalence span within various ethnic groups, subpopulations and demographic areas are also debated. PMID:27072373

  20. Genomic landscape of human allele-specific DNA methylation

    PubMed Central

    Fang, Fang; Hodges, Emily; Molaro, Antoine; Dean, Matthew; Hannon, Gregory J.; Smith, Andrew D.

    2012-01-01

    DNA methylation mediates imprinted gene expression by passing an epigenomic state across generations and differentially marking specific regulatory regions on maternal and paternal alleles. Imprinting has been tied to the evolution of the placenta in mammals and defects of imprinting have been associated with human diseases. Although recent advances in genome sequencing have revolutionized the study of DNA methylation, existing methylome data remain largely untapped in the study of imprinting. We present a statistical model to describe allele-specific methylation (ASM) in data from high-throughput short-read bisulfite sequencing. Simulation results indicate technical specifications of existing methylome data, such as read length and coverage, are sufficient for full-genome ASM profiling based on our model. We used our model to analyze methylomes for a diverse set of human cell types, including cultured and uncultured differentiated cells, embryonic stem cells and induced pluripotent stem cells. Regions of ASM identified most consistently across methylomes are tightly connected with known imprinted genes and precisely delineate the boundaries of several known imprinting control regions. Predicted regions of ASM common to multiple cell types frequently mark noncoding RNA promoters and represent promising starting points for targeted validation. More generally, our model provides the analytical complement to cutting-edge experimental technologies for surveying ASM in specific cell types and across species. PMID:22523239

  1. Diverse Thinking about Diversity

    ERIC Educational Resources Information Center

    Kaplan, Sandra N.

    2013-01-01

    This article focuses on the concept of diversity in educational decision making. It is noted that the differences that distinguish the needs, interests and abilities are identified by educators. It lists misconceptions resulting from not attending to within-group diversity, and states that a "loss of self" for individual members of…

  2. Tracking human migrations by the analysis of the distribution of HLA alleles, lineages and haplotypes in closed and open populations

    PubMed Central

    Vina, Marcelo A. Fernandez; Hollenbach, Jill A.; Lyke, Kirsten E.; Sztein, Marcelo B.; Maiers, Martin; Klitz, William; Cano, Pedro; Mack, Steven; Single, Richard; Brautbar, Chaim; Israel, Shosahna; Raimondi, Eduardo; Khoriaty, Evelyne; Inati, Adlette; Andreani, Marco; Testi, Manuela; Moraes, Maria Elisa; Thomson, Glenys; Stastny, Peter; Cao, Kai

    2012-01-01

    The human leucocyte antigen (HLA) system shows extensive variation in the number and function of loci and the number of alleles present at any one locus. Allele distribution has been analysed in many populations through the course of several decades, and the implementation of molecular typing has significantly increased the level of diversity revealing that many serotypes have multiple functional variants. While the degree of diversity in many populations is equivalent and may result from functional polymorphism(s) in peptide presentation, homogeneous and heterogeneous populations present contrasting numbers of alleles and lineages at the loci with high-density expression products. In spite of these differences, the homozygosity levels are comparable in almost all of them. The balanced distribution of HLA alleles is consistent with overdominant selection. The genetic distances between outbred populations correlate with their geographical locations; the formal genetic distance measurements are larger than expected between inbred populations in the same region. The latter present many unique alleles grouped in a few lineages consistent with limited founder polymorphism in which any novel allele may have been positively selected to enlarge the communal peptide-binding repertoire of a given population. On the other hand, it has been observed that some alleles are found in multiple populations with distinctive haplotypic associations suggesting that convergent evolution events may have taken place as well. It appears that the HLA system has been under strong selection, probably owing to its fundamental role in varying immune responses. Therefore, allelic diversity in HLA should be analysed in conjunction with other genetic markers to accurately track the migrations of modern humans. PMID:22312049

  3. Growth behavior of additional offspring with a beneficial reversal allele in the asymmetric sharply-peaked landscape in the coupled discrete-time mutation-selection model

    NASA Astrophysics Data System (ADS)

    Gill, Wonpyong

    2013-01-01

    The probability of additional offspring with a beneficial reversal allele for growing to a size NC for a range of population sizes N, sequence lengths L, selective advantages s, and measuring parameters C was calculated for a haploid, asexual population in the coupled discrete-time mutation-selection model in an asymmetric sharply-peaked landscape with a positive selective advantage of the reversal allele over the optimal allele. The growing probability in the stochastic region was inversely proportional to the measuring parameter when C < 1 /Ns, bent when C ≈ 1/ Ns and saturated when C > 1/ Ns. The crossing time and the time dependence of the increase in relative density of the reversal allele in the coupled discrete-time mutation-selection model was approximated using the Wright-Fisher two-allele model with the same selective advantage and corresponding effective mutation rate. The growth behavior of additional offspring with the reversal allele in the asymmetric sharply-peaked landscape in the coupled discrete-time mutation-selection model was controlled by the selective advantage of the reversal allele compared to the optimal allele and could be described by using the Wright-Fisher two-allele model, in spite of there being many other alleles with lower fitness, and in spite of there being two alleles, the optimal and reversal allele, separated by a low-fitness valley with a tunable depth and width.

  4. Intragenic allele pyramiding combines different specificities of wheat Pm3 resistance alleles.

    PubMed

    Brunner, Susanne; Hurni, Severine; Streckeisen, Philipp; Mayr, Gabriele; Albrecht, Mario; Yahiaoui, Nabila; Keller, Beat

    2010-11-01

    Some plant resistance genes occur as allelic series, with each member conferring specific resistance against a subset of pathogen races. In wheat, there are 17 alleles of the Pm3 gene. They encode nucleotide-binding (NB-ARC) and leucine-rich-repeat (LRR) domain proteins, which mediate resistance to distinct race spectra of powdery mildew. It is not known if specificities from different alleles can be combined to create resistance genes with broader specificity. Here, we used an approach based on avirulence analysis of pathogen populations to characterize the molecular basis of Pm3 recognition spectra. A large survey of mildew races for avirulence on the Pm3 alleles revealed that Pm3a has a resistance spectrum that completely contains that of Pm3f, but also extends towards additional races. The same is true for the Pm3b and Pm3c gene pair. The molecular analysis of these allelic pairs revealed a role of the NB-ARC protein domain in the efficiency of effector-dependent resistance. Analysis of the wild-type and chimeric Pm3 alleles identified single residues in the C-terminal LRR motifs as the main determinant of allele specificity. Variable residues of the N-terminal LRRs are necessary, but not sufficient, to confer resistance specificity. Based on these data, we constructed a chimeric Pm3 gene by intragenic allele pyramiding of Pm3d and Pm3e that showed the combined resistance specificity and, thus, a broader recognition spectrum compared with the parental alleles. Our findings support a model of stepwise evolution of Pm3 recognition specificities.

  5. Allelic background of LEPRE1 mutations that cause recessive forms of osteogenesis imperfecta in different populations

    PubMed Central

    Pepin, Melanie G; Schwarze, Ulrike; Singh, Virendra; Romana, Marc; Jones-LeCointe, Altheia; Byers, Peter H

    2013-01-01

    Biallelic mutations in LEPRE1 result in recessively inherited forms of osteogenesis imperfecta (OI) that are often lethal in the perinatal period. A mutation (c.1080+1G>T, IVS5+1G>T) in African Americans has a carrier frequency of about 1/240. The mutant allele originated in West Africa in tribes of Ghana and Nigeria where the carrier frequencies are 2% and 5%. By examining 200 samples from an African-derived population in Tobago and reviewing hospital neonatal death records, we determined that the carrier frequency of c.1080+1G>T was about one in 200 and did not contribute to the neonatal deaths recorded over a 3-year period of time in Trinidad. In the course of sequence analysis, we found surprisingly high LEPRE1 allelic diversity in the Tobago DNA samples in which there were 11 alleles distinguished by a single basepair variant in or near exon 5. All the alleles found in the Tobago population that were within the sequence analysis region were found in the African American population in the Exome Variant Project. This diversity appeared to reflect the geographic origin of the original population in Tobago. In 44 individuals with biallelic LEPRE1 mutations identified by clinical diagnostic testing, we found the sequence alterations occurred on seven of the 11 variant alleles. All but one of the mutations identified resulted in mRNA or protein instability for the majority of the transcripts from the altered allele. These findings suggest that the milder end of the clinical spectrum could be due to as yet unidentified missense mutations in LEPRE1. PMID:24498616

  6. Molecular and morphological diversity in locally grown non-commercial (heirloom) mango varieties of North India.

    PubMed

    Bajpai, Anju; Muthukumar, M; Ahmad, Israr; Ravishankar, K V; Parthasarthy, V A; Sthapit, Bhuwon; Rao, Ramanatha; Verma, J P; Rajan, S

    2016-03-01

    Mango (Mangifera indica L.) has been cultivated and conserved in different agro-ecologies including Malihabad region in northern part of India, that is well known for housing diverse types (heirloom and commercial varieties). In the present study, 37 mango types comprising of 27 heirloom varieties from Malihabad region and 10 commercial varieties grown in North and Eastern India were assessed for morphological attributes and molecular diversity. The employed SSR markers amplified 2-13 alleles individually, cumulatively amplifying 124 alleles. These were studied for allelic diversity and genetic dissimilarity ranged from 0.035 to 0.892 arranging the varieties in three major clusters. The results revealed that majority of unique heirloom mangoes from Malihabad were different from the eastern part of the country. It is interesting to note Dashehari, a commercial variety from Malihabad was not aligned with heirloom varieties. Commercial varieties like Gulabkhas and Langra were placed in a separate group including Bombay Green, Himsagar, Dashehari, etc., indicating their dissimilarity with heirloom varieties at molecular level and thus, indicating importance for later from conservation point of view. Furthermore, the hierarchical clustering of varieties based on fruit morphology, assembled these into four groups largely influenced by fruit size. The maximum agreement subtree indicated seemingly good fit as thirteen varieties were arrayed in common grouping pattern. Appreciable dissimilarity among the heirloom varieties demonstrated by molecular analysis, underlines the importance for their on-farm conservation. PMID:27097441

  7. Molecular and morphological diversity in locally grown non-commercial (heirloom) mango varieties of North India.

    PubMed

    Bajpai, Anju; Muthukumar, M; Ahmad, Israr; Ravishankar, K V; Parthasarthy, V A; Sthapit, Bhuwon; Rao, Ramanatha; Verma, J P; Rajan, S

    2016-03-01

    Mango (Mangifera indica L.) has been cultivated and conserved in different agro-ecologies including Malihabad region in northern part of India, that is well known for housing diverse types (heirloom and commercial varieties). In the present study, 37 mango types comprising of 27 heirloom varieties from Malihabad region and 10 commercial varieties grown in North and Eastern India were assessed for morphological attributes and molecular diversity. The employed SSR markers amplified 2-13 alleles individually, cumulatively amplifying 124 alleles. These were studied for allelic diversity and genetic dissimilarity ranged from 0.035 to 0.892 arranging the varieties in three major clusters. The results revealed that majority of unique heirloom mangoes from Malihabad were different from the eastern part of the country. It is interesting to note Dashehari, a commercial variety from Malihabad was not aligned with heirloom varieties. Commercial varieties like Gulabkhas and Langra were placed in a separate group including Bombay Green, Himsagar, Dashehari, etc., indicating their dissimilarity with heirloom varieties at molecular level and thus, indicating importance for later from conservation point of view. Furthermore, the hierarchical clustering of varieties based on fruit morphology, assembled these into four groups largely influenced by fruit size. The maximum agreement subtree indicated seemingly good fit as thirteen varieties were arrayed in common grouping pattern. Appreciable dissimilarity among the heirloom varieties demonstrated by molecular analysis, underlines the importance for their on-farm conservation.

  8. Genetic diversity analysis of barley landraces and cultivars in the Shanghai region of China.

    PubMed

    Chen, Z-W; Lu, R-J; Zou, L; Du, Z-Z; Gao, R-H; He, T; Huang, J-H

    2012-01-01

    We analyzed the genetic diversity of 115 barley germplasms, including 112 landraces and three new barley cultivars grown in the Shanghai region, using a set of 11 SSR markers. Sixty-six alleles were observed at the 11 SSR loci, ranged from three to ten, with a mean of six alleles per locus. The polymorphism information content ranged from 0.568 to 0.853, with a mean of 0.732, indicating considerable genetic variation in barley in the Shanghai area. Clustering analysis indicated that these barley accessions could be divided into two categories (A and B). Ninety-seven six-rowed barley cultivars were classified in the A category; sixteen two-rowed and two six-rowed barley cultivars were classified in the B category. This demonstrated genetic differences between two-rowed and six-rowed barley varieties. In addition, we found that the three new barley cultivars are closely related. PMID:22535400

  9. Impact of alternative regeneration methods on genetic diversity in coastal Douglas-fir

    USGS Publications Warehouse

    Adams, W.T.; Zuo, J.; Shimizu, J.Y.; Tappeiner, J.C.

    1998-01-01

    Genetic implications of natural and artificial regeneration following three regeneration methods (group selection, shelterwood, and clearcut) were investigated in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) using genetic markers (17 allozyme loci). In general, harvesting followed by either natural or artificial regeneration resulted in offspring populations little altered from those in the previous generation. Cutting the smallest trees to form shelterwoods, however, resulted in the removal of rare, presumably deleterious, alleles, such that slightly fewer alleles per locus were observed among residual trees (2.76) and natural regeneration (2.75) than found in uncut (control) stands (2.86). Thus, although the shelterwood regime appears quite compatible with gene conservation, it would be best to leave parent trees of a range of sizes in shelterwoods designated as gene conservation reserves, in order to maximize the number of alleles (regardless of current adaptive value) in naturally regenerated offspring. Seedling stocks used for artificial regeneration in clearcut, shelterwood, and group selection stands (7 total) had significantly greater levels of genetic diversity, on average, than found in natural regeneration. This is probably because the seeds used in artificial seedling stocks came from many wild stands and thus, sampled more diversity than found in single populations.Genetic implications of natural and artificial regeneration following three regeneration methods (group selection, shelterwood, and clearcut) were investigated in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii [Mirb.] Franco) using genetic markers (17 allozyme loci). In general, harvesting followed by either natural or artificial regeneration resulted in offspring populations little altered from those in the previous generation. Cutting the smallest trees to form shelterwoods, however, resulted in the removal of rare, presumably deleterious, alleles

  10. Allelic associations of two polymorphic microsatellites in intron 40 of the human von Willebrand factor gene

    SciTech Connect

    Pena, S.D.J.; De Souza, K.T. ); De Andrade, M.; Chakraborty, R. )

    1994-01-18

    At intron 40 of the von Willebrand factor (vWF) gene, two GATA-repeat polymorphic sites exist that are physically separated by 212 bp. At the first site (vWF1 locus), seven segregating repeat alleles were observed in a Brazilian Caucasian population, and at the second (vWF2 locus) there were eight alleles, detected through PCR amplifications of this DNA region. Haplotype analysis of individuals revealed 36 different haplotypes in a sample of 338 chromosomes examined. Allele frequencies between generations and gender at each locus were not significantly different, and the genotype frequencies were consistent with their Hardy-Weinberg expectations. Linkage disequilibrium between loci is highly significant with positive allele size association; that is, large alleles at the loci tend to occur together, and so do the same alleles. Variability at each locus appeared to have arisen in a stepwise fashion, suggesting replication slippage as a possible mechanism of production of new alleles. However, the authors observed an increased number of haplotypes, in contrast with the predictions of a stepwise production of variation in the entire region, suggesting some form of cooperative changes between loci that could be due to either gene conversion, or a common control mechanism of production of new variation at these repeat polymorphism sites. The high degree of polymorphism (gene diversity values of 72% and 78% at vWF1 and vWF2, respectively, and of 93% at the haplotype level) makes these markers informative for paternity testing, genetic counseling, and individual-identification purposes.

  11. Population genetic diversity and fitness in multiple environments

    EPA Science Inventory

    When a large number of alleles are lost from a population, increases in homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of populations t...

  12. Population Genetic Diversity and Fitness in Multiple Environments(BMCEB)

    EPA Science Inventory

    When a large number of alleles are lost from a population, increases in individual homozygosity may reduce individual fitness through inbreeding depression. Modest losses of allelic diversity may also negatively impact long-term population viability by reducing the capacity of p...

  13. Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research.

    PubMed

    Chesler, Elissa J

    2014-02-01

    The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.

  14. Genome destabilizing mutator alleles drive specific mutational trajectories in Saccharomyces cerevisiae.

    PubMed

    Stirling, Peter C; Shen, Yaoqing; Corbett, Richard; Jones, Steven J M; Hieter, Philip

    2014-02-01

    In addition to environmental factors and intrinsic variations in base substitution rates, specific genome-destabilizing mutations can shape the mutational trajectory of genomes. How specific alleles influence the nature and position of accumulated mutations in a genomic context is largely unknown. Understanding the impact of genome-destabilizing alleles is particularly relevant to cancer genomes where biased mutational signatures are identifiable. We first created a more complete picture of cellular pathways that impact mutation rate using a primary screen to identify essential Saccharomyces cerevisiae gene mutations that cause mutator phenotypes. Drawing primarily on new alleles identified in this resource, we measure the impact of diverse mutator alleles on mutation patterns directly by whole-genome sequencing of 68 mutation-accumulation strains derived from wild-type and 11 parental mutator genotypes. The accumulated mutations differ across mutator strains, displaying base-substitution biases, allele-specific mutation hotspots, and break-associated mutation clustering. For example, in mutants of POLα and the Cdc13-Stn1-Ten1 complex, we find a distinct subtelomeric bias for mutations that we show is independent of the target sequence. Together our data suggest that specific genome-instability mutations are sufficient to drive discrete mutational signatures, some of which share properties with mutation patterns seen in tumors. Thus, in a population of cells, genome-instability mutations could influence clonal evolution by establishing discrete mutational trajectories for genomes.

  15. Genome Destabilizing Mutator Alleles Drive Specific Mutational Trajectories in Saccharomyces cerevisiae

    PubMed Central

    Stirling, Peter C.; Shen, Yaoqing; Corbett, Richard; Jones, Steven J. M.; Hieter, Philip

    2014-01-01

    In addition to environmental factors and intrinsic variations in base substitution rates, specific genome-destabilizing mutations can shape the mutational trajectory of genomes. How specific alleles influence the nature and position of accumulated mutations in a genomic context is largely unknown. Understanding the impact of genome-destabilizing alleles is particularly relevant to cancer genomes where biased mutational signatures are identifiable. We first created a more complete picture of cellular pathways that impact mutation rate using a primary screen to identify essential Saccharomyces cerevisiae gene mutations that cause mutator phenotypes. Drawing primarily on new alleles identified in this resource, we measure the impact of diverse mutator alleles on mutation patterns directly by whole-genome sequencing of 68 mutation-accumulation strains derived from wild-type and 11 parental mutator genotypes. The accumulated mutations differ across mutator strains, displaying base-substitution biases, allele-specific mutation hotspots, and break-associated mutation clustering. For example, in mutants of POLα and the Cdc13–Stn1–Ten1 complex, we find a distinct subtelomeric bias for mutations that we show is independent of the target sequence. Together our data suggest that specific genome-instability mutations are sufficient to drive discrete mutational signatures, some of which share properties with mutation patterns seen in tumors. Thus, in a population of cells, genome-instability mutations could influence clonal evolution by establishing discrete mutational trajectories for genomes. PMID:24336748

  16. ADZE: a rarefaction approach for counting alleles private to combinations of populations

    PubMed Central

    Szpiech, Zachary A.; Jakobsson, Mattias; Rosenberg, Noah A.

    2008-01-01

    Motivation: Analysis of the distribution of alleles across populations is a useful tool for examining population diversity and relationships. However, sample sizes often differ across populations, sometimes making it difficult to assess allelic distributions across groups. Results: We introduce a generalized rarefaction approach for counting alleles private to combinations of populations. Our method evaluates the number of alleles found in each of a set of populations but absent in all remaining populations, considering equal-sized subsamples from each population. Applying this method to a worldwide human microsatellite dataset, we observe a high number of alleles private to the combination of African and Oceanian populations. This result supports the possibility of a migration out of Africa into Oceania separate from the migrations responsible for the majority of the ancestry of the modern populations of Asia, and it highlights the utility of our approach to sample size correction in evaluating hypotheses about population history. Availability: We have implemented our method in the computer pro-gram ADZE, which is available for download at http://rosenberglab.bioinformatics.med.umich.edu/adze.html. Contact: szpiechz@umich.edu PMID:18779233

  17. Two prevalent h alleles in para-Bombay haplotypes among 250,000 Taiwanese.

    PubMed

    Chen, Ding-Ping; Tseng, Ching-Ping; Wang, Wei-Ting; Peng, Chien-Ting; Tsao, Kuo-Chien; Wu, Tsu-Lan; Lin, Kuan-Tsou; Sun, Chien-Feng

    2004-01-01

    Alpha(1,2)-fucosyltransferase catalyzes the transfer of fucose to the C-2 position of galactose on type II precursor substrate Gal beta1-4GlcNAc beta1-R. It plays an important biological role in the formation of H antigen, a precursor oligosaccharide for both A and B antigens on red blood cells. Aberration of alpha(1,2)-fucosyltransferase activity by gene mutations results in decreased synthesis of H antigen, leading to the para-Bombay phenotype. In this study, we collected about 250,000 blood samples in Taiwan during 5 yr and identified the subjects with para-Bombay phenotype. Then we analyzed the sequence of the alpha(1,2)-fucosyltransferase gene by direct sequencing and gene cloning methods, using the blood samples of 30 para-Bombay individuals and 30 control subjects who were randomly selected. The goals of this study were to search for new h alleles, to determine the h allele frequencies, and to test whether the sporadic theory is applicable in Taiwan. Six different h alleles (ha, 547-548 AG-del; hb, 880-881 TT-del; hc, R220C; hd, R220H; he, F174L; and hf, N327T) were observed. Two h alleles, he and hf, were newly discovered in Taiwan. The he allele has a nucleotide 522C>A point mutation, predicting the amino acid 174 substitution of Phe to Leu; the hf allele has missense mutation of nucleotide 980A>C, predicting the amino acid 327 substitution of Asn to Thr. Frequencies of the 6 alleles are ha 46.67%, hb 38.33%, hc 5.00%, hd 1.67%, he 3.33%, and hf 5.00%, respectively. These findings in the Taiwanese population confirm previous observations in other populations that the Bombay and para-Bombay phenotypes are due to diverse, sporadic, nonfunctional alleles, predominantly ha and hb, leading to H deficiency of red blood cells. In contrast to previous reports of non-prevalent associations of h alleles with para-Bombay phenotype, our results suggest a regional allele preference associated with para-Bombay individuals in Taiwan.

  18. Capturing the Diversity in Lexical Diversity

    ERIC Educational Resources Information Center

    Jarvis, Scott

    2013-01-01

    The range, variety, or diversity of words found in learners' language use is believed to reflect the complexity of their vocabulary knowledge as well as the level of their language proficiency. Many indices of lexical diversity have been proposed, most of which involve statistical relationships between types and tokens, and which ultimately…

  19. Multiple mating but not recombination causes quantitative increase in offspring genetic diversity for varying genetic architectures.

    PubMed

    Rueppell, Olav; Meier, Stephen; Deutsch, Roland

    2012-01-01

    Explaining the evolution of sex and recombination is particularly intriguing for some species of eusocial insects because they display exceptionally high mating frequencies and genomic recombination rates. Explanations for both phenomena are based on the notion that both increase colony genetic diversity, with demonstrated benefits for colony disease resistance and division of labor. However, the relative contributions of mating number and recombination rate to colony genetic diversity have never been simultaneously assessed. Our study simulates colonies, assuming different mating numbers, recombination rates, and genetic architectures, to assess their worker genotypic diversity. The number of loci has a strong negative effect on genotypic diversity when the allelic effects are inversely scaled to locus number. In contrast, dominance, epistasis, lethal effects, or limiting the allelic diversity at each locus does not significantly affect the model outcomes. Mating number increases colony genotypic variance and lowers variation among colonies with quickly diminishing returns. Genomic recombination rate does not affect intra- and inter-colonial genotypic variance, regardless of mating frequency and genetic architecture. Recombination slightly increases the genotypic range of colonies and more strongly the number of workers with unique allele combinations across all loci. Overall, our study contradicts the argument that the exceptionally high recombination rates cause a quantitative increase in offspring genotypic diversity across one generation. Alternative explanations for the evolution of high recombination rates in social insects are therefore needed. Short-term benefits are central to most explanations of the evolution of multiple mating and high recombination rates in social insects but our results also apply to other species.

  20. Nonfunctional alleles of long‐day suppressor genes independently regulate flowering time

    PubMed Central

    Zheng, Xiao‐Ming; Feng, Li; Wang, Junrui; Qiao, Weihua; Zhang, Lifang; Cheng, Yunlian

    2015-01-01

    Abstract Due to the remarkable adaptability to various environments, rice varieties with diverse flowering times have been domesticated or improved from Oryza rufipogon. Detailed knowledge of the genetic factors controlling flowering time will facilitate understanding the adaptation mechanism in cultivated rice and enable breeders to design appropriate genotypes for distinct preferences. In this study, four genes (Hd1, DTH8, Ghd7 and OsPRR37) in a rice long‐day suppression pathway were collected and sequenced in 154, 74, 69 and 62 varieties of cultivated rice (Oryza sativa) respectively. Under long‐day conditions, varieties with nonfunctional alleles flowered significantly earlier than those with functional alleles. However, the four genes have different genetic effects in the regulation of flowering time: Hd1 and OsPRR37 are major genes that generally regulate rice flowering time for all varieties, while DTH8 and Ghd7 only regulate regional rice varieties. Geographic analysis and network studies suggested that the nonfunctional alleles of these suppression loci with regional adaptability were derived recently and independently. Alleles with regional adaptability should be taken into consideration for genetic improvement. The rich genetic variations in these four genes, which adapt rice to different environments, provide the flexibility needed for breeding rice varieties with diverse flowering times. PMID:26220807

  1. Structural analysis of substitution patterns in alleles of human immunoglobulin VH genes.

    PubMed

    Romo-González, Tania; Vargas-Madrazo, Enrique

    2005-05-01

    The diversity in repertoires of antibodies (Abs) needed in response to the antigen challenge is produced by evolutionary and somatic processes. The mechanisms operating at a somatic level have been studied in great detail. In contrast, neither the mechanisms nor the strategies of diversification at an evolutionary level have yet been understood in similar detail. Particularly, the substitution patterns in alleles of immunoglobulin genes (Igs) have not been systematically studied. Furthermore, there is a scarcity of studies which link the analysis at a genetic level of the diversification of repertoires with the structural consequences at the protein level of the changes in DNA information. For the purpose of systematically characterizing the strategies of evolutionary diversification through sequence variation at alleles, in this work, we built a database for all the alleles of the IGHV locus in humans reported until now. Based on these data, we performed diverse analyses of substitution patterns and linked these results with studies at the protein level. We found that the sequence diversification in different alleles does not operate with equal intensity for all V genes. Our studies, both of the number of substitutions and of the type of amino acid change per sub-segment of the V-REGION evidenced differences in the selective pressure to which these regions are exposed. The implications of these results for understanding the evolutionary diversification strategies, as well as for the somatic generation of antibody repertoires are discussed.

  2. High-precision genetic mapping of behavioral traits in the diversity outbred mouse population

    PubMed Central

    Logan, R W; Robledo, R F; Recla, J M; Philip, V M; Bubier, J A; Jay, J J; Harwood, C; Wilcox, T; Gatti, D M; Bult, C J; Churchill, G A; Chesler, E J

    2013-01-01

    Historically our ability to identify genetic variants underlying complex behavioral traits in mice has been limited by low mapping resolution of conventional mouse crosses. The newly developed Diversity Outbred (DO) population promises to deliver improved resolution that will circumvent costly fine-mapping studies. The DO is derived from the same founder strains as the Collaborative Cross (CC), including three wild-derived strains. Thus the DO provides more allelic diversity and greater potential for discovery compared to crosses involving standard mouse strains. We have characterized 283 male and female DO mice using open-field, light–dark box, tail-suspension and visual-cliff avoidance tests to generate 38 behavioral measures. We identified several quantitative trait loci (QTL) for these traits with support intervals ranging from 1 to 3 Mb in size. These intervals contain relatively few genes (ranging from 5 to 96). For a majority of QTL, using the founder allelic effects together with whole genome sequence data, we could further narrow the positional candidates. Several QTL replicate previously published loci. Novel loci were also identified for anxiety- and activity-related traits. Half of the QTLs are associated with wild-derived alleles, confirming the value to behavioral genetics of added genetic diversity in the DO. In the presence of wild-alleles we sometimes observe behaviors that are qualitatively different from the expected response. Our results demonstrate that high-precision mapping of behavioral traits can be achieved with moderate numbers of DO animals, representing a significant advance in our ability to leverage the mouse as a tool for behavioral genetics PMID:23433259

  3. Allele-Specific Deletions in Mouse Tumors Identify Fbxw7 as Germline Modifier of Tumor Susceptibility

    PubMed Central

    Perez-Losada, Jesus; Wu, Di; DelRosario, Reyno; Balmain, Allan; Mao, Jian-Hua

    2012-01-01

    Genome-wide association studies (GWAS) have been successful in finding associations between specific genetic variants and cancer susceptibility in human populations. These studies have identified a range of highly statistically significant associations between single nucleotide polymorphisms (SNPs) and susceptibility to development of a range of human tumors. However, the effect of each SNP in isolation is very small, and all of the SNPs combined only account for a relatively minor proportion of the total genetic risk (5–10%). There is therefore a major requirement for alternative routes to the discovery of genetic risk factors for cancer. We have previously shown using mouse models that chromosomal regions harboring susceptibility genes identified by linkage analysis frequently exhibit allele-specific genetic alterations in tumors. We demonstrate here that the Fbxw7 gene, a commonly mutated gene in a wide range of mouse and human cancers, shows allele-specific deletions in mouse lymphomas and skin tumors. Lymphomas from three different F1 hybrids show 100% allele-specificity in the patterns of allelic loss. Parental alleles from 129/Sv or Spretus/Gla mice are lost in tumors from F1 hybrids with C57BL/6 animals, due to the presence of a specific non-synonymous coding sequence polymorphism at the N-terminal portion of the gene. A specific genetic test of association between this SNP and lymphoma susceptibility in interspecific backcross mice showed a significant linkage (p = 0.001), but only in animals with a functional p53 gene. These data therefore identify Fbxw7 as a p53-dependent tumor susceptibility gene. Increased p53-dependent tumor susceptibility and allele-specific losses were also seen in a mouse skin model of skin tumor development. We propose that analysis of preferential allelic imbalances in tumors may provide an efficient means of uncovering genetic variants that affect mouse and human tumor susceptibility. PMID:22348067

  4. Grain sorghum proteomics: integrated approach toward characterization of endosperm storage proteins in kafirin allelic variants.

    PubMed

    Cremer, Julia E; Bean, Scott R; Tilley, Michael M; Ioerger, Brian P; Ohm, Jae B; Kaufman, Rhett C; Wilson, Jeff D; Innes, David J; Gilding, Edward K; Godwin, Ian D

    2014-10-01

    Grain protein composition determines quality traits, such as value for food, feedstock, and biomaterials uses. The major storage proteins in sorghum are the prolamins, known as kafirins. Located primarily on the periphery of the protein bodies surrounding starch, cysteine-rich β- and γ-kafirins may limit enzymatic access to internally positioned α-kafirins and starch. An integrated approach was used to characterize sorghum with allelic variation at the kafirin loci to determine the effects of this genetic diversity on protein expression. Reversed-phase high performance liquid chromatography and lab-on-a-chip analysis showed reductions in alcohol-soluble protein in β-kafirin null lines. Gel-based separation and liquid chromatography-tandem mass spectrometry identified a range of redox active proteins affecting storage protein biochemistry. Thioredoxin, involved in the processing of proteins at germination, has reported impacts on grain digestibility and was differentially expressed across genotypes. Thus, redox states of endosperm proteins, of which kafirins are a subset, could affect quality traits in addition to the expression of proteins.

  5. Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Soybean Plants Carrying the Rj4 Allele

    PubMed Central

    Faruque, Omar M.; Miwa, Hiroki; Yasuda, Michiko; Fujii, Yoshiharu; Kaneko, Takakazu; Sato, Shusei

    2015-01-01

    Symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. While these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. The formation of nodules in soybean plants (Glycine max) is controlled by several host genes, which are referred to as Rj genes. The soybean cultivar BARC2 carries the Rj4 gene, which restricts nodulation by specific strains, including Bradyrhizobium elkanii USDA61. Here we employed transposon mutagenesis to identify the genetic locus in USDA61 that determines incompatibility with soybean varieties carrying the Rj4 allele. Introduction of the Tn5 transposon into USDA61 resulted in the formation of nitrogen fixation nodules on the roots of soybean cultivar BARC2 (Rj4 Rj4). Sequencing analysis of the sequence flanking the Tn5 insertion revealed that six genes encoding a putative histidine kinase, transcriptional regulator, DNA-binding transcriptional activator, helix-turn-helix-type transcriptional regulator, phage shock protein, and cysteine protease were disrupted. The cysteine protease mutant had a high degree of similarity with the type 3 effector protein XopD of Xanthomonas campestris. Our findings shed light on the diverse and complicated mechanisms that underlie these highly host-specific interactions and indicate the involvement of a type 3 effector in Rj4 nodulation restriction, suggesting that Rj4 incompatibility is partly mediated by effector-triggered immunity. PMID:26187957

  6. Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Soybean Plants Carrying the Rj4 Allele.

    PubMed

    Faruque, Omar M; Miwa, Hiroki; Yasuda, Michiko; Fujii, Yoshiharu; Kaneko, Takakazu; Sato, Shusei; Okazaki, Shin

    2015-10-01

    Symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. While these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. The formation of nodules in soybean plants (Glycine max) is controlled by several host genes, which are referred to as Rj genes. The soybean cultivar BARC2 carries the Rj4 gene, which restricts nodulation by specific strains, including Bradyrhizobium elkanii USDA61. Here we employed transposon mutagenesis to identify the genetic locus in USDA61 that determines incompatibility with soybean varieties carrying the Rj4 allele. Introduction of the Tn5 transposon into USDA61 resulted in the formation of nitrogen fixation nodules on the roots of soybean cultivar BARC2 (Rj4 Rj4). Sequencing analysis of the sequence flanking the Tn5 insertion revealed that six genes encoding a putative histidine kinase, transcriptional regulator, DNA-binding transcriptional activator, helix-turn-helix-type transcriptional regulator, phage shock protein, and cysteine protease were disrupted. The cysteine protease mutant had a high degree of similarity with the type 3 effector protein XopD of Xanthomonas campestris. Our findings shed light on the diverse and complicated mechanisms that underlie these highly host-specific interactions and indicate the involvement of a type 3 effector in Rj4 nodulation restriction, suggesting that Rj4 incompatibility is partly mediated by effector-triggered immunity. PMID:26187957

  7. Carriage of One or Two FMR1 Premutation Alleles Seems to Have No Effect on Illness Severity in a FXTAS Female with an Autozygous FMR1 Premutation Allele.

    PubMed

    Rodriguez-Revenga, Laia; Pagonabarraga, Javier; Gómez-Anson, Beatriz; López-Mourelo, Olga; Izquierdo, Silvia; Alvarez-Mora, Maria Isabel; Granell, Esther; Madrigal, Irene; Milà, Montserrat

    2016-10-01

    Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder that occurs in FMR1 premutation carriers. The prevalence of FMR1 premutation carriers in the general population is relatively high, and although rare, a premutation in both X chromosomes may occur in females inheriting a premutation allele from each of both parent carriers. Here, we report the first female with an autozygous (homozygous by descendent) FMR1 premutation allele, who fulfills neurological and radiological FXTAS findings/criteria. Molecular characterization included CGG repeat length, AGG interruption pattern, FMR1 messenger RNA (mRNA), fragile X mental retardation protein (FMRP) level quantification, and single-nucleotide polymorphism (SNP) microarray. Neuroradiological assessment of 3-T magnetic resonance imaging and neurological and cognitive/neuropsychological evaluations were performed. Neurological and neuroradiological examination of the female with the same FMR1 allele in the premutation range (77 CGGs) demonstrated FXTAS features. Further familial evaluation showed a similar neuropsychiatric profile, with impairments in cognitive flexibility and visuospatial function, mainly. A unique family with an autozygous FMR1 premutation female is presented. Neurological/cognitive and neuroradiological examinations revealed FXTAS-specific findings in the female with the autozygous FMR1 premutation allele. The consistent molecular and cognitive/psychiatric phenotype in family members suggests that carrying one or two FMR1 premutation alleles has no effect on illness severity.

  8. Carriage of One or Two FMR1 Premutation Alleles Seems to Have No Effect on Illness Severity in a FXTAS Female with an Autozygous FMR1 Premutation Allele.

    PubMed

    Rodriguez-Revenga, Laia; Pagonabarraga, Javier; Gómez-Anson, Beatriz; López-Mourelo, Olga; Izquierdo, Silvia; Alvarez-Mora, Maria Isabel; Granell, Esther; Madrigal, Irene; Milà, Montserrat

    2016-10-01

    Fragile X-associated tremor/ataxia syndrome (FXTAS) is a late-onset neurodegenerative disorder that occurs in FMR1 premutation carriers. The prevalence of FMR1 premutation carriers in the general population is relatively high, and although rare, a premutation in both X chromosomes may occur in females inheriting a premutation allele from each of both parent carriers. Here, we report the first female with an autozygous (homozygous by descendent) FMR1 premutation allele, who fulfills neurological and radiological FXTAS findings/criteria. Molecular characterization included CGG repeat length, AGG interruption pattern, FMR1 messenger RNA (mRNA), fragile X mental retardation protein (FMRP) level quantification, and single-nucleotide polymorphism (SNP) microarray. Neuroradiological assessment of 3-T magnetic resonance imaging and neurological and cognitive/neuropsychological evaluations were performed. Neurological and neuroradiological examination of the female with the same FMR1 allele in the premutation range (77 CGGs) demonstrated FXTAS features. Further familial evaluation showed a similar neuropsychiatric profile, with impairments in cognitive flexibility and visuospatial function, mainly. A unique family with an autozygous FMR1 premutation female is presented. Neurological/cognitive and neuroradiological examinations revealed FXTAS-specific findings in the female with the autozygous FMR1 premutation allele. The consistent molecular and cognitive/psychiatric phenotype in family members suggests that carrying one or two FMR1 premutation alleles has no effect on illness severity. PMID:27315125

  9. Allele frequency data of 15 autosomal STR loci in four major population groups of South Africa.

    PubMed

    Lucassen, Anton; Ehlers, Karen; Grobler, Paul J; Shezi, Adeline L

    2014-03-01

    Allele frequency distributions for 15 tetrameric short tandem repeat (STR) loci were determined using the AmpFlSTR® Identifiler Plus™ PCR amplification kit. There was little evidence of departures from Hardy-Weinberg equilibrium or association of alleles of different loci in the population samples. The probability of identity values for the different populations range from 1/3.3 × 10(17) (White) to 1/1.88 × 10(18) (Coloured). The combined probability of paternal exclusion for the different population groups ranges from 0.9995858 (Coloured) to 0.9997874 (Indian).

  10. Functional isogenic modeling of BRCA1 alleles reveals distinct carrier phenotypes.

    PubMed

    Cochran, Rory L; Cidado, Justin; Kim, Minsoo; Zabransky, Daniel J; Croessmann, Sarah; Chu, David; Wong, Hong Yuen; Beaver, Julia A; Cravero, Karen; Erlanger, Bracha; Parsons, Heather; Heaphy, Christopher M; Meeker, Alan K; Lauring, Josh; Park, Ben Ho

    2015-09-22

    Clinical genetic testing of BRCA1 and BRCA2 is commonly performed to identify specific individuals at risk for breast and ovarian cancers who may benefit from prophylactic therapeutic interventions. Unfortunately, it is evident that deleterious BRCA1 alleles demonstrate variable penetrance and that many BRCA1 variants of unknown significance (VUS) exist. In order to further refine hereditary risks that may be associated with specific BRCA1 alleles, we performed gene targeting to establish an isogenic panel of immortalized human breast epithelial cells harboring eight clinically relevant BRCA1 alleles. Interestingly, BRCA1 mutations and VUS had distinct, quantifiable phenotypes relative to isogenic parental BRCA1 wild type cells and controls. Heterozygous cells with known deleterious BRCA1 mutations (185delAG, C61G and R71G) demonstrated consistent phenotypes in radiation sensitivity and genomic instability assays, but showed variability in other assays. Heterozygous BRCA1 VUS cells also demonstrated assay variability, with some VUS demonstrating phenotypes more consistent with deleterious alleles. Taken together, our data suggest that BRCA1 deleterious mutations and VUS can differ in their range of tested phenotypes, suggesting they might impart varying degrees of risk. These results demonstrate that functional isogenic modeling of BRCA1 alleles could aid in classifying BRCA1 mutations and VUS, and determining BRCA allele cancer risk. PMID:26246475

  11. Functional isogenic modeling of BRCA1 alleles reveals distinct carrier phenotypes

    PubMed Central

    Cochran, Rory L.; Cidado, Justin; Kim, Minsoo; Zabransky, Daniel J.; Croessmann, Sarah; Chu, David; Wong, Hong Yuen; Beaver, Julia A.; Cravero, Karen; Erlanger, Bracha; Parsons, Heather; Heaphy, Christopher M.; Meeker, Alan K.; Lauring, Josh; Park, Ben Ho

    2015-01-01

    Clinical genetic testing of BRCA1 and BRCA2 is commonly performed to identify specific individuals at risk for breast and ovarian cancers who may benefit from prophylactic therapeutic interventions. Unfortunately, it is evident that deleterious BRCA1 alleles demonstrate variable penetrance and that many BRCA1 variants of unknown significance (VUS) exist. In order to further refine hereditary risks that may be associated with specific BRCA1 alleles, we performed gene targeting to establish an isogenic panel of immortalized human breast epithelial cells harboring eight clinically relevant BRCA1 alleles. Interestingly, BRCA1 mutations and VUS had distinct, quantifiable phenotypes relative to isogenic parental BRCA1 wild type cells and controls. Heterozygous cells with known deleterious BRCA1 mutations (185delAG, C61G and R71G) demonstrated consistent phenotypes in radiation sensitivity and genomic instability assays, but showed variability in other assays. Heterozygous BRCA1 VUS cells also demonstrated assay variability, with some VUS demonstrating phenotypes more consistent with deleterious alleles. Taken together, our data suggest that BRCA1 deleterious mutations and VUS can differ in their range of tested phenotypes, suggesting they might impart varying degrees of risk. These results demonstrate that functional isogenic modeling of BRCA1 alleles could aid in classifying BRCA1 mutations and VUS, and determining BRCA allele cancer risk. PMID:26246475

  12. Functional isogenic modeling of BRCA1 alleles reveals distinct carrier phenotypes.

    PubMed

    Cochran, Rory L; Cidado, Justin; Kim, Minsoo; Zabransky, Daniel J; Croessmann, Sarah; Chu, David; Wong, Hong Yuen; Beaver, Julia A; Cravero, Karen; Erlanger, Bracha; Parsons, Heather; Heaphy, Christopher M; Meeker, Alan K; Lauring, Josh; Park, Ben Ho

    2015-09-22

    Clinical genetic testing of BRCA1 and BRCA2 is commonly performed to identify specific individuals at risk for breast and ovarian cancers who may benefit from prophylactic therapeutic interventions. Unfortunately, it is evident that deleterious BRCA1 alleles demonstrate variable penetrance and that many BRCA1 variants of unknown significance (VUS) exist. In order to further refine hereditary risks that may be associated with specific BRCA1 alleles, we performed gene targeting to establish an isogenic panel of immortalized human breast epithelial cells harboring eight clinically relevant BRCA1 alleles. Interestingly, BRCA1 mutations and VUS had distinct, quantifiable phenotypes relative to isogenic parental BRCA1 wild type cells and controls. Heterozygous cells with known deleterious BRCA1 mutations (185delAG, C61G and R71G) demonstrated consistent phenotypes in radiation sensitivity and genomic instability assays, but showed variability in other assays. Heterozygous BRCA1 VUS cells also demonstrated assay variability, with some VUS demonstrating phenotypes more consistent with deleterious alleles. Taken together, our data suggest that BRCA1 deleterious mutations and VUS can differ in their range of tested phenotypes, suggesting they might impart varying degrees of risk. These results demonstrate that functional isogenic modeling of BRCA1 alleles could aid in classifying BRCA1 mutations and VUS, and determining BRCA allele cancer risk.

  13. Initial invasion of gametophytic self-incompatibility alleles in the absence of tight linkage between pollen and pistil S alleles.

    PubMed

    Sakai, Satoki; Wakoh, Haluka

    2014-08-01

    In homomorphic self-incompatibility (SI) systems of plants, the loci controlling the pollen and pistil types are tightly linked, and this prevents the generation of compatible combinations of alleles expressing pollen and pistil types, which would result in self-fertilization. We modeled the initial invasion of the first pollen and pistil alleles in gametophytic SI to determine whether these alleles can stably coexist in a population without tight linkage. We assume pollen and pistil loci each carry an incompatibility allele S and an allele without an incompatibility function N. We assume that pollen with an S allele are incompatible with pistils carrying S alleles, whereas other crosses are compatible. Ovules in pistils carrying an S allele suffer viability costs because recognition consumes resources. We found that the cost of carrying a pistil S allele allows pollen and pistil S alleles to coexist in a stable equilibrium if linkage is partial. This occurs because parents that carry pistil S alleles but are homozygous for pollen N alleles cannot avoid self-fertilization; however, they suffer viability costs. Hence, pollen N alleles are selected again. When pollen and pistil S alleles can coexist in a polymorphic equilibrium, selection will favor tighter linkage.

  14. Microsatellite-based genetic diversity patterns in disjunct populations of a rare orchid.

    PubMed

    Pandey, Madhav; Richards, Matt; Sharma, Jyotsna

    2015-12-01

    We investigated the patterns of genetic diversity and structure in seven disjunct populations of a rare North American orchid, Cypripedium kentuckiense by including populations that represented the periphery and the center of the its range. Eight nuclear and two chloroplast microsatellites were used. Genetic diversity was low across the sampled populations of C. kentuckiense based on both nuclear (average An = 4.0, Ho = 0.436, He = 0.448) and cpDNA microsatellites (average An = 1.57, Nh = 1.57 and H = 0.133). The number of private alleles ranged from one to four per population with a total of 17 private alleles detected at five nuclear microsatellites. One private allele at one cpDNA microsatellite was also observed. Although the absolute values for nuclear microsatellite based population differentiation were low (Fst = 0.075; ϕPT = 0.24), they were statistically significant. Pairwise Fst values ranged from 0.038 to 0.123 and each comparison was significant. We also detected isolation by distance with nDNA microsatellites based on the Mantel test (r(2) = 0.209, P = 0.05). STRUCTURE analysis and the neighbor joining trees grouped the populations similarly whereby the geographically proximal populations were genetically similar. Our data indicate that the species is genetically depauperate but the diversity is distributed more or less equally across its range. Population differentiation and isolation by distance were detectable, which indicates that genetic isolation is beginning to manifest itself across the range in this rare species.

  15. Analysis and frequency of bovine lymphocyte antigen DRB3.2 alleles in Jersey cows.

    PubMed

    Gilliespie, B E; Jayarao, B M; Dowlen, H H; Oliver, S P

    1999-09-01

    Jersey cows (n = 172) were genotyped for the bovine lymphocyte antigen (BoLA)-DRB3.2 allele by polymerase chain reaction and restriction fragment length polymorphism analysis. Bovine DNA was isolated from aliquots of whole blood. A two-step polymerase chain reaction followed by digestion with restriction endonucleases RsaI, BstyI, and HaeIII was conducted on the DNA from Jersey cattle. Twenty-four BoLA-DRB3.2 alleles were identified with frequencies ranging from 0.3 to 22.9%. Thirteen allele types were similar to those reported previously; and 11 were new allele types that have not been reported previously. Allele types reported previously include: BoLA-DRB3.2*2, *8, *10, *15, *17, *20, *21, *22, *23, *25, *28, *36, and *37. Their frequencies were 0.3, 11.3, 22.9, 13.6, 5.5, 3.7, 10.7, 3.5, 0.9, 0.3, 4.7, 9.3, and 0.9%, respectively. Of the new allele types detected, *ibe occurred at the highest frequency (6.1%) in Jersey cows from this herd. The six most frequently isolated alleles (BoLA-DRB3.2*8, *10, *15, *21, *36, and *ibe) accounted for 73.9% of the alleles in the population of this herd. Results of this study demonstrate that the BoLA-DRB3.2 locus is highly polymorphic in Jersey cattle.

  16. Patterns of microsatellite polymorphism in the range-restricted bonobo (Pan paniscus): considerations for interspecific comparison with chimpanzees (P. troglodytes).

    PubMed

    Reinartz, G E; Karron, J D; Phillips, R B; Weber, J L

    2000-03-01

    The endangered great ape, Pan paniscus (bonobo) has the smallest range of the African apes. Virtually nothing is known about the genetic diversity or genetic structure of this species, while substantial amounts of polymorphism have been reported for the bonobo's widespread congener, the chimpanzee (P. troglodytes). Given its restricted range, what is the extent of genetic variation in the bonobo relative to the chimpanzee, and is the bonobo genetically depauperate? To investigate patterns of genetic polymorphism, bonobos of wild origin were genotyped for 28 microsatellite loci. The mean number of alleles per locus (5.2) and the mean observed heterozygosity (0.52) in bonobos were similar to variation observed in a wild chimpanzee community (P. t. schweinfurthii). The rarer bonobo is not genetically depauperate and may have genetic diversity comparable to the eastern chimpanzee subspecies. Bonobos have approximately 55% of the allelic diversity and 66% of the observed heterozygosity exhibited by all three chimpanzee subspecies sampled across equatorial Africa. Resampling techniques were used to quantify the effects of sample size differences and number and choice of loci between bonobos and chimpanzees. The examination of these variables underscores their importance in accurately interpreting interspecific comparisons of diversity estimates.

  17. Do Heliconius butterfly species exchange mimicry alleles?

    PubMed

    Smith, Joel; Kronforst, Marcus R

    2013-08-23

    Hybridization has the potential to transfer beneficial alleles across species boundaries, and there are a growing number of examples in which this has apparently occurred. Recent studies suggest that Heliconius butterflies have transferred wing pattern mimicry alleles between species via hybridization, but ancestral polymorphism could also produce a signature of shared ancestry around mimicry genes. To distinguish between these alternative hypotheses, we measured DNA sequence divergence around putatively introgressed mimicry loci and compared this with the rest of the genome. Our results reveal that putatively introgressed regions show strongly reduced sequence divergence between co-mimetic species, suggesting that their divergence times are younger than the rest of the genome. This is consistent with introgression and not ancestral variation. We further show that this signature of introgression occurs at sites throughout the genome, not just around mimicry genes.

  18. Genetic diversity and differentiation of sea trout (Salmo trutta) populations in Lithuanian rivers assessed by microsatellite DNA variation.

    PubMed

    Samuiloviene, Aurelija; Kontautas, Antanas; Gross, Riho

    2009-11-01

    The genetic diversity and differentiation of sea trout were studied in three river basins in Lithuania: Akmena-Dane, Bartuva, and Nemunas. A total of 282 individuals were genotyped at eight microsatellite loci. A similar level of genetic diversity was found in all of the populations studied: mean allelic richness ranged from 3.64 to 5.03, and average expected heterozygosity ranged from 0.588 to 0.721. Significant genetic divergence was observed among the different river basins as well as between populations within the drainages. All pairwise F (ST) values were highly significant, ranging from 0.027 to 0.197. The analysis of molecular variance showed rather weak hierarchical population structuring within the Nemunas basin, which may be explained by extensive gene flow among different river basins or, alternatively, reflect the influence of artificial breeding. Information on genetic diversity and differentiation of the Lithuanian sea trout populations will be useful for future management decisions.

  19. Genetic Diversity in Nothofagus alessandrii (Fagaceae), an Endangered Endemic Tree Species of the Coastal Maulino Forest of Central Chile

    PubMed Central

    Torres-Díaz, Cristian; Ruiz, Eduardo; González, Fidelina; Fuentes, Glenda; Cavieres, Lohengrin A.

    2007-01-01

    Background and Aims The endemic tree Nothofagus alessandrii (Fagaceae) has been historically restricted to the coastal range of Region VII of central Chile, and its forests have been increasingly destroyed and fragmented since the end of the 19th century. In this study, the patterns of within- and among-population genetic diversity in seven fragments of this endangered narrowly endemic tree were examined. Methods Allozyme electrophoresis of seven loci of N. alessandrii was used to estimate genetic diversity, genetic structure and gene flow. Key Results High levels of genetic diversity were found as shown by mean expected heterozygosity (He = 0·182 ± 0·034), percentage of polymorphic loci (Pp = 61·2 %), mean number of alleles per locus (A = 1·8) and mean number of alleles per polymorphic locus (Ap = 2·3). Genetic differentiation was also high (GST = 0·257 and Nm = 0·7). These values are high compared with more widespread congeneric species. Conclusions Despite its endemic status and restricted geographical range N. alessandrii showed high levels of genetic diversity. The observed patterns of diversity are explained in part by historical processes and more recent human fragmentation. PMID:17513870

  20. Microsatellite DNA marker analysis of genetic diversity in wild common carp (Cyprinus carpio L.) populations.

    PubMed

    Li, Dayu; Kang, Dahai; Yin, Qianqian; Sun, Xiaowen; Liang, Liqun

    2007-11-01

    Thirty microsatellite loci were used for analyzing six wild populations of common carp (Cyprinus carpio L.). Observed (H(o)) and expected (H(e)) heterozygosity values, polymorphic information content (PIC), and number of effective alleles (A(e)) were all detected. Genetic similarity index and genetic distance were computed based on the allele frequency. The Hardy-Weinberg Equilibrium was checked according to the test of chi2. Genetic differentiation and hierarchical partition of genetic diversity were evaluated by F(ST) and N(m). A clustering dendrogram was made based on the results of UPGMA methods using the PHYLIP software package (version 3.63). There were totally 8,136 fragments ranging from 125 bp to 414 bp in length. Three to thirteen alleles were amplified in 30 loci and 210 alleles in all six populations. The average number of alleles in each locus was seven. The result showed that 1) the level of genetic variability was moderate in the six populations. Polymorphic information contents of the six wild common carp populations were 0.44, 0.52, 0.53, 0.57, 0.63, and 0.64 respectively. Effective alleles were from 1.04 to 4.72, the average numbers in each population were 2.19, 2.60, 2.42, 2.43, 2.45, and 2.33. The average expected heterozygosity values were 0.50, 0.59, 0.56, 0.56, 0.57, and 0.54 respectively; 2) the highest genetic similarity index that came from the populations of BR and ZL was 0.8511 and the lowest index was 0.6688, and it came from the populations of BR and HN. There was a correlation between the clustering result and the geographical distribution. PMID:18037135

  1. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth. PMID:21684917

  2. Genetic diversity and population structure of Yucca filamentosa (Agavaceae).

    PubMed

    Massey, L; Hamrick, J

    1998-03-01

    Using 19 allozyme loci we studied genetic diversity in 18 populations of Yucca filamentosa (Agavaceae) from the southeastern United States. Of the 19 loci surveyed, 17 (89.5%) were polymorphic in at least one of the populations sampled. There was considerable variation among populations in the percentage of polymorphic loci (range = 31.6-84.2%, mean = 67.6%). Similar heterogeneity among populations was observed for mean number of alleles per polymorphic locus (range = 2.0-3.0; mean = 2.48) and mean expected heterozygosity (range = 0.113-0.288; mean = 0.213). On average, 83% of the total genetic diversity was found within populations. Duplications of three allozyme loci were detected in several populations. The life-history characteristics of Y. filamentosa (a long-lived, semiwoody, predominantly outcrossing monocot with a large geographical range) may contribute to the maintenance of such high levels of genetic diversity. These results contradict expectations of the genetic structure of Y. filamentosa based on observations of the dispersal and pollination behavior of its sole pollinator, Tegeticula yuccasella, the yucca moth.

  3. Assessment of genetic diversity in broomcorn millet (Panicum miliaceum L.) using SSR markers.

    PubMed

    Hu, Xingyu; Wang, Jianfei; Lu, Ping; Zhang, Hongsheng

    2009-08-01

    The genetic diversity of 118 accessions of broomcorn millet (Panicum miliaceum L.), collected from various ecological areas, was analyzed. Using 46 SSR (Simple Sequence Repeat) polymorphic markers from rice, wheat, oat and barley, a total of 226 alleles were found, which exhibited moderate level of diversity. The number of alleles per primer ranged from two to nine, with an average of 4.91. The range of polymorphism information content (PIC) was 0.284-0.980 (average, 0.793). The expected heterozygosity (He) varied from 0.346 to 0.989, with an average of 0.834. The average coefficient of the genetic similarity of SSR markers among the 118 accessions was 0.609, and it ranged from 0.461 to 0.851. The UPGMA (Unweight Pair Group Method with Arithmetic Mean) clustering analysis at the genetic similarity value of 0.609 grouped the 118 accessions into five groups. Mantel test meant that geographical origin and genetic distance presented positive correlation. The clustering results were consistent with known information on ecological growing areas. The genetic similarity coefficient of the accessions in the Loess Plateau ecotype was significantly lower than those in the other ecotypes. It indicates that the highest level of genetic diversity occurred in the Loess Plateau, which is probably the original site of Panicum miliaceum. PMID:19683672

  4. Genetic diversity and species diversity of stream fishes covary across a land-use gradient

    USGS Publications Warehouse

    Blum, M.J.; Bagley, M.J.; Walters, D.M.; Jackson, S.A.; Daniel, F.B.; Chaloud, D.J.; Cade, B.S.

    2012-01-01

    Genetic diversity and species diversity are expected to covary according to area and isolation, but may not always covary with environmental heterogeneity. In this study, we examined how patterns of genetic and species diversity in stream fishes correspond to local and regional environmental conditions. To do so, we compared population size, genetic diversity and divergence in central stonerollers (Campostoma anomalum) to measures of species diversity and turnover in stream fish assemblages among similarly sized watersheds across an agriculture-forest land-use gradient in the Little Miami River basin (Ohio, USA). Significant correlations were found in many, but not all, pair-wise comparisons. Allelic richness and species richness were strongly correlated, for example, but diversity measures based on allele frequencies and assemblage structure were not. In-stream conditions related to agricultural land use were identified as significant predictors of genetic diversity and species diversity. Comparisons to population size indicate, however, that genetic diversity and species diversity are not necessarily independent and that variation also corresponds to watershed location and glaciation history in the drainage basin. Our findings demonstrate that genetic diversity and species diversity can covary in stream fish assemblages, and illustrate the potential importance of scaling observations to capture responses to hierarchical environmental variation. More comparisons according to life history variation could further improve understanding of conditions that give rise to parallel variation in genetic diversity and species diversity, which in turn could improve diagnosis of anthropogenic influences on aquatic ecosystems. ?? 2011 Springer-Verlag.

  5. Mutant maize variety containing the glt1-1 allele

    DOEpatents

    Nelson, Oliver E.; Pan, David

    1994-01-01

    A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating.

  6. Mutant maize variety containing the glt1-1 allele

    DOEpatents

    Nelson, O.E.; Pan, D.

    1994-07-19

    A maize plant has in its genome a non-mutable form of a mutant allele designated vitX-8132. The allele is located at a locus designated as glt which conditions kernels having an altered starch characteristic. Maize plants including such a mutant allele produce a starch that does not increase in viscosity on cooling, after heating. 2 figs.

  7. Increasing long term response by selecting for favorable minor alleles

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Long-term response of genomic selection can be improved by considering allele frequencies of selected markers or quantitative trait loci (QTLs). A previous formula to weight allele frequency of favorable minor alleles was tested, and 2 new formulas were developed. The previous formula used nonlinear...

  8. D9S1120, a simple STR with a common Native American-specific allele: forensic optimization, locus characterization and allele frequency studies.

    PubMed

    Phillips, C; Rodriguez, A; Mosquera-Miguel, A; Fondevila, M; Porras-Hurtado, L; Rondon, F; Salas, A; Carracedo, A; Lareu, M V

    2008-12-01

    The simple tetrameric STR D9S1120 exhibits a common population-specific allele of 9 repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent. Apart from the presence of 9RA in two northeast Siberian populations, D9S1120 shows variability exclusive to, and universal in all American populations studied to date. This STR therefore provides an informative forensic marker applicable in countries with significant proportions of Native American populations or ancestry. We have re-designed PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120. The 9RA allele shares the same repeat structure as the majority of other D9S1120 alleles and so originates from a slippage-diminution mutation rather than an independent deletion. We confirm the previously reported allele frequencies from a range of populations indicating a global heterozygosity range for D9S1120 of 66-75% and estimate the proportion of Native American-diagnostic genotypes to average 53%, underlining the potential usefulness of this STR in both forensic identification and in population genetics studies of the Americas.

  9. Natural variation in maize architecture is mediated by allelic differences at the PINOID co-ortholog barren inflorescence2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We characterized allelic variation at barren inflorescence2 (bif2), a maize co-ortholog of the Arabidopsis PINOID protein kinase (PID), and tested for trait associations with bif2 in both an association mapping population of 277 diverse maize inbreds and in the inter-mated B73-Mo17 (IBM) linkage pop...

  10. Allelic Expression Imbalance of JAK2 V617F Mutation in BCR-ABL Negative Myeloproliferative Neoplasms

    PubMed Central

    Kim, Yeo-Kyeoung; Kim, Hyeoung-Joon; Shin, Jong-Hee; Suh, Soon-Pal; Ryang, Dong-Wook; Shin, Myung-Geun

    2013-01-01

    The discovery of a single point mutation in the JAK2 gene in patients with BCR/ABL-negative myeloproliferative neoplasms (MPNs) has not only brought new insights and pathogenesis, but also has made the diagnosis of MPNs much easier. Although, to date, several mechanisms for the contribution of single JAK2V617F point mutation to phenotypic diversity of MPNs have been suggested in multiple studies, but it is not clear how a unique mutation can cause the phenotypic diversity of MPNs. In this study, our results show that allelic expression imbalance of JAK2 V617F mutant frequently occurs and contributes to phenotypic diversity of BCR-ABL-negative MPNs. The proportion of JAK2 V617F mutant allele was significantly augmented in RNA levels as compared with genomic DNA differently by distinct MPNs subtypes. In detail, preferential expression of JAK2 mutant allele showed threefold increase from the cDNA compared with the genomic DNA from patients with essential thrombocythemia and twofold increase in polycythemia vera. In conclusion, allelic expression imbalance of JAK2 V617F mutant proposes another plausible mechanism for the contribution of single JAK2 point mutation to phenotypic diversity of MPNs. PMID:23349688

  11. Always Look on Both Sides: Phylogenetic Information Conveyed by Simple Sequence Repeat Allele Sequences

    PubMed Central

    Barthe, Stéphanie; Gugerli, Felix; Barkley, Noelle A.; Maggia, Laurent; Cardi, Céline; Scotti, Ivan

    2012-01-01

    Simple sequence repeat (SSR) markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM). Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR) sequences), it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker’s sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

  12. Identification of the third/extra allele for forensic application in cases with TPOX tri-allelic pattern.

    PubMed

    Picanço, Juliane Bentes; Raimann, Paulo Eduardo; da Motta, Carlos Henrique Ares Silveira; Rodenbusch, Rodrigo; Gusmão, Leonor; Alho, Clarice Sampaio

    2015-05-01

    Genotyping of polymorphic short tandem repeats (STRs) loci is widely used in forensic DNA analysis. STR loci eventually present tri-allelic pattern as a genotyping irregularity and, in that situation, the doubt about the tri-allele locus frequency calculation can reduce the analysis strength. In the TPOX human STR locus, tri-allelic genotypes have been reported with a widely varied frequency among human populations. We investigate whether there is a single extra allele (the third allele) in the TPOX tri-allelic pattern, what it is, and where it is, aiming to understand its genomic anatomy and to propose the knowledge of this TPOX extra allele from genetic profile, thus preserving the two standard TPOX alleles in forensic analyses. We looked for TPOX tri-allelic subjects in 75,113 Brazilian families. Considering only the parental generation (mother+father) we had 150,226 unrelated subjects evaluated. From this total, we found 88 unrelated subjects with tri-allelic pattern in the TPOX locus (0.06%; 88/150,226). Seventy three of these 88 subjects (73/88; 83%) had the Clayton's original Type 2 tri-allelic pattern (three peaks of even intensity). The remaining 17% (15/88) show a new Type 2 derived category with heterozygote peak imbalance (one double dose peak plus one regular sized peak). In this paper we present detailed data from 66 trios (mother+father+child) with true biological relationships. In 39 of these families (39/66; 59%) the extra TPOX allele was transmitted either from the mother or from the father to the child. Evidences indicated the allele 10 as the extra TPOX allele, and it is on the X chromosome. The present data, which support the previous Lane hypothesis, improve the knowledge about tri-allelic pattern of TPOX CODIS' locus allowing the use of TPOX profile in forensic analyses even when with tri-allelic pattern. This evaluation is now available for different forensic applications.

  13. Empirical evaluations of analytical issues arising from predicting HLA alleles using multiple SNPs

    PubMed Central

    2011-01-01

    Background Numerous immune-mediated diseases have been associated with the class I and II HLA genes located within the major histocompatibility complex (MHC) consisting of highly polymorphic alleles encoded by the HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1 loci. Genotyping for HLA alleles is complex and relatively expensive. Recent studies have demonstrated the feasibility of predicting HLA alleles, using MHC SNPs inside and outside of HLA that are typically included in SNP arrays and are commonly available in genome-wide association studies (GWAS). We have recently described a novel method that is complementary to the previous methods, for accurately predicting HLA alleles using unphased flanking SNPs genotypes. In this manuscript, we address several practical issues relevant to the application of this methodology. Results Applying this new methodology to three large independent study cohorts, we have evaluated the performance of the predictive models in ethnically diverse populations. Specifically, we have found that utilizing imputed in addition to genotyped SNPs generally yields comparable if not better performance in prediction accuracies. Our evaluation also supports the idea that predictive models trained on one population are transferable to other populations of the same ethnicity. Further, when the training set includes multi-ethnic populations, the resulting models are reliable and perform well for the same subpopulations across all HLA genes. In contrast, the predictive models built from single ethnic populations have superior performance within the same ethnic population, but are not likely to perform well in other ethnic populations. Conclusions The empirical explorations reported here provide further evidence in support of the application of this approach for predicting HLA alleles with GWAS-derived SNP data. Utilizing all available samples, we have built "state of the art" predictive models for HLA-A, -B, -C, -DRB1, -DQB1 and -DPB1. The HLA allele

  14. Catalogue of alleles of gliadin-coding loci in durum wheat (Triticum durum Desf.).

    PubMed

    Melnikova, N V; Kudryavtseva, A V; Kudryavtsev, A M

    2012-02-01

    Gliadins are seed storage proteins which are characterized by high intervarietal polymorphism and can be used as genetic markers. As a result of our work, a considerably extended catalogue of allelic variants of gliadin component blocks was compiled for durum wheat; 74 allelic variants for four gliadin-coding loci were identified for the first time. The extended catalogue includes a total of 131 allelic variants: 16 for locus Gli-A1(d), 19 for locus Gli-B1(d), 41 for locus Gli-A2(d), and 55 for locus Gli-B2(d). The electrophoretic pattern of the standard cultivar and a diagram are provided for every block identified. The number of alleles per family is quite small for loci Gli-A1(d) and Gli-B1(d) of durum wheat, as contrasted to loci Gli-A2(d) and Gli-B2(d) that are characterized by large families including many alleles. The presence of large block families determines a higher diversity of durum wheat for loci Gli-A2(d) and Gli-B2(d) as compared to Gli-A1(d) and Gli-B1(d). The catalogue of allelic variants of gliadin component blocks can be used by seed farmers to identify durum wheat cultivars and evaluate their purity; by breeders, to obtain homogenous cultivars and control the initial stages of selection; by gene bank experts, to preserve native varieties and the original biotypic composition of cultivars. PMID:21946233

  15. Genetic Exchange of Fimbrial Alleles Exemplifies the Adaptive Virulence Strategy of Porphyromonas gingivalis

    PubMed Central

    Kerr, Jennifer E.; Abramian, Jared R.; Dao, Doan-Hieu V.; Rigney, Todd W.; Fritz, Jamie; Pham, Tan; Gay, Isabel; Parthasarathy, Kavitha; Wang, Bing-yan; Zhang, Wenjian; Tribble, Gena D.

    2014-01-01

    Porphyromonas gingivalis is a gram–negative anaerobic bacterium, a member of the human oral microbiome, and a proposed “keystone” pathogen in the development of chronic periodontitis, an inflammatory disease of the gingiva. P. gingivalis is a genetically diverse species, and is able to exchange chromosomal DNA between strains by natural competence and conjugation. In this study, we investigate the role of horizontal DNA transfer as an adaptive process to modify behavior, using the major fimbriae as our model system, due to their critical role in mediating interactions with the host environment. We show that P. gingivalis is able to exchange fimbrial allele types I and IV into four distinct strain backgrounds via natural competence. In all recombinants, we detected a complete exchange of the entire fimA allele, and the rate of exchange varies between the different strain backgrounds. In addition, gene exchange within other regions of the fimbrial genetic locus was identified. To measure the biological implications of these allele swaps we compared three genotypes of fimA in an isogenic background, strain ATCC 33277. We demonstrate that exchange of fimbrial allele type results in profound phenotypic changes, including the quantity of fimbriae elaborated, membrane blebbing, auto-aggregation and other virulence-associated phenotypes. Replacement of the type I allele with either the type III or IV allele resulted in increased invasion of gingival fibroblast cells relative to the isogenic parent strain. While genetic variability is known to impact host-microbiome interactions, this is the first study to quantitatively assess the adaptive effect of exchanging genes within the pan genome cloud. This is significant as it presents a potential mechanism by which opportunistic pathogens may acquire the traits necessary to modify host-microbial interactions. PMID:24626479

  16. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast.

    PubMed

    Salinas, Francisco; de Boer, Carl G; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F; Martínez, Claudio; Cubillos, Francisco A

    2016-01-01

    Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

  17. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast

    PubMed Central

    Salinas, Francisco; de Boer, Carl G.; Abarca, Valentina; García, Verónica; Cuevas, Mara; Araos, Sebastian; Larrondo, Luis F.; Martínez, Claudio; Cubillos, Francisco A.

    2016-01-01

    Linkage mapping studies in model organisms have typically focused their efforts in polymorphisms within coding regions, ignoring those within regulatory regions that may contribute to gene expression variation. In this context, differences in transcript abundance are frequently proposed as a source of phenotypic diversity between individuals, however, until now, little molecular evidence has been provided. Here, we examined Allele Specific Expression (ASE) in six F1 hybrids from Saccharomyces cerevisiae derived from crosses between representative strains of the four main lineages described in yeast. ASE varied between crosses with levels ranging between 28% and 60%. Part of the variation in expression levels could be explained by differences in transcription factors binding to polymorphic cis-regulations and to differences in trans-activation depending on the allelic form of the TF. Analysis on highly expressed alleles on each background suggested ASN1 as a candidate transcript underlying nitrogen consumption differences between two strains. Further promoter allele swap analysis under fermentation conditions confirmed that coding and non-coding regions explained aspartic and glutamic acid consumption differences, likely due to a polymorphism affecting Uga3 binding. Together, we provide a new catalogue of variants to bridge the gap between genotype and phenotype. PMID:26898953

  18. Update on allele nomenclature for human cytochromes P450 and the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Database.

    PubMed

    Sim, Sarah C; Ingelman-Sundberg, Magnus

    2013-01-01

    Interindividual variability in xenobiotic metabolism and drug response is extensive and genetic factors play an important role in this variation. A majority of clinically used drugs are substrates for the cytochrome P450 (CYP) enzyme system and interindividual variability in expression and function of these enzymes is a major factor for explaining individual susceptibility for adverse drug reactions and drug response. Because of the existence of many polymorphic CYP genes, for many of which the number of allelic variants is continually increasing, a universal and official nomenclature system is important. Since 1999, all functionally relevant polymorphic CYP alleles are named and published on the Human Cytochrome P450 Allele (CYP-allele) Nomenclature Web site (http://www.cypalleles.ki.se). Currently, the database covers nomenclature of more than 660 alleles in a total of 30 genes that includes 29 CYPs as well as the cytochrome P450 oxidoreductase (POR) gene. On the CYP-allele Web site, each gene has its own Webpage, which lists the alleles with their nucleotide changes, their functional consequences, and links to publications identifying or characterizing the alleles. CYP2D6, CYP2C9, CYP2C19, and CYP3A4 are the most important CYPs in terms of drug metabolism, which is also reflected in their corresponding highest number of Webpage hits at the CYP-allele Web site.The main advantage of the CYP-allele database is that it offers a rapid online publication of CYP-alleles and their effects and provides an overview of peer-reviewed data to the scientific community. Here, we provide an update of the CYP-allele database and the associated nomenclature.

  19. Genetic diversity of Ovis aries populations near domestication centers and in the New World.

    PubMed

    Blackburn, H D; Toishibekov, Y; Toishibekov, M; Welsh, C S; Spiller, S F; Brown, M; Paiva, S R

    2011-09-01

    Domestic sheep in Kazakhstan may provide an interesting source of genetic variability due to their proximity to the center of domestication and the Silk Route. Additionally, those breeds have never been compared to New World sheep populations. This report compares genetic diversity among five Kazakhstan (KZ) and 13 United States (US) sheep breeds (N = 442) using 25 microsatellite markers from the FAO panel. The KZ breeds had observed and expected measures of heterozygosity greater than 0.60 and an average number of alleles per locus of 7.8. In contrast, US sheep breeds had observed heterozygosity ranged from 0.37 to 0.62 and had an average number of alleles of 5.7. A Bayesian analysis indicated there were two primary populations (K = 2). Surprisingly, the US breeds were near evenly split between the two clusters, while all of the KZ breeds were placed in one of the two clusters. Pooling breeds within country of sample origin showed KZ and US populations to have similar levels of expected heterozygosity and the average number of alleles per locus. The results of breeds pooled within country suggest that there was no difference between countries for these diversity measures using this set of neutral markers. This finding suggests that populations' geographically isolated from centers of domestication can be more diverse than previously thought, and as a result, conservation strategies can be adjusted accordingly. Furthermore, these results suggest there may be limited need for countries to alter the protocols for trade and exchange of animal genetic resources that are in place today, since no one population has a unique set of private alleles.

  20. Composition and functional analysis of low-molecular-weight glutenin alleles with Aroona near-isogenic lines of bread wheat

    PubMed Central

    2012-01-01

    composition and function of 18 LMW-GS alleles in bread wheat. The variation of i-type genes mainly contributed to the high diversity of Glu-A3 alleles, and the differences among Glu-B3 alleles were mainly derived from the high polymorphism of s-type genes. Among LMW-GS alleles, Glu-A3e and Glu-B3c represented inferior alleles for bread-making quality, whereas Glu-A3d, Glu-B3b, Glu-B3g and Glu-B3i were correlated with superior bread-making quality. Glu-D3 alleles played minor roles in determining quality variation in bread wheat. Thus, LMW-GS alleles not only affect dough extensibility but greatly contribute to the dough resistance, glutenin macro-polymers and bread quality. PMID:23259617

  1. Determination of DQB1 alleles using PCR amplification and allele-specific primers.

    PubMed

    Lepage, V; Ivanova, R; Loste, M N; Mallet, C; Douay, C; Naoumova, E; Charron, D

    1995-10-01

    Molecular genotyping of HLA class II genes is commonly carried out using polymerase chain reaction (PCR) in combination with sequence-specific oligotyping (PCR-SSO) or a combination of the PCR and restriction fragment length polymorphism methods (PCR-RFLP). However, the identification of the DQB1 type by PCR-SSO and PCR-RFLP is very time-consuming which is disadvantageous for the typing of cadaveric organ donors. We have developed a DQB1 typing method using PCR in combination with allele-specific amplification (PCR-ASA), which allows the identification of the 17 most frequent alleles in one step using seven amplification mixtures. PCR allele-specific amplification HLA-DQB1 typing is easy to perform, and the results are easy to interpret in routine clinical practice. The PCR-ASA method is therefore better suited to DQB1 typing for organ transplantation than other methods.

  2. Borrowed alleles and convergence in serpentine adaptation.

    PubMed

    Arnold, Brian J; Lahner, Brett; DaCosta, Jeffrey M; Weisman, Caroline M; Hollister, Jesse D; Salt, David E; Bomblies, Kirsten; Yant, Levi

    2016-07-19

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  3. Borrowed alleles and convergence in serpentine adaptation

    PubMed Central

    Arnold, Brian J.; Lahner, Brett; DaCosta, Jeffrey M.; Weisman, Caroline M.; Hollister, Jesse D.; Salt, David E.; Bomblies, Kirsten; Yant, Levi

    2016-01-01

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata. In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata. This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment. PMID:27357660

  4. Borrowed alleles and convergence in serpentine adaptation.

    PubMed

    Arnold, Brian J; Lahner, Brett; DaCosta, Jeffrey M; Weisman, Caroline M; Hollister, Jesse D; Salt, David E; Bomblies, Kirsten; Yant, Levi

    2016-07-19

    Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary genomic approach coupled with elemental profiling to assess how autotetraploid Arabidopsis arenosa adapted to a multichallenge serpentine habitat in the Austrian Alps. We first demonstrate that serpentine-adapted plants exhibit dramatically altered elemental accumulation levels in common conditions, and then resequence 24 autotetraploid individuals from three populations to perform a genome scan. We find evidence for highly localized selective sweeps that point to a polygenic, multitrait basis for serpentine adaptation. Comparing our results to a previous study of independent serpentine colonizations in the closely related diploid Arabidopsis lyrata in the United Kingdom and United States, we find the highest levels of differentiation in 11 of the same loci, providing candidate alleles for mediating convergent evolution. This overlap between independent colonizations in different species suggests that a limited number of evolutionary strategies are suited to overcome the multiple challenges of serpentine adaptation. Interestingly, we detect footprints of selection in A. arenosa in the context of substantial gene flow from nearby off-serpentine populations of A. arenosa, as well as from A. lyrata In several cases, quantitative tests of introgression indicate that some alleles exhibiting strong selective sweep signatures appear to have been introgressed from A. lyrata This finding suggests that migrant alleles may have facilitated adaptation of A. arenosa to this multihazard environment.

  5. Biased gene conversion skews allele frequencies in human populations, increasing the disease burden of recessive alleles.

    PubMed

    Lachance, Joseph; Tishkoff, Sarah A

    2014-10-01

    Gene conversion results in the nonreciprocal transfer of genetic information between two recombining sequences, and there is evidence that this process is biased toward G and C alleles. However, the strength of GC-biased gene conversion (gBGC) in human populations and its effects on hereditary disease have yet to be assessed on a genomic scale. Using high-coverage whole-genome sequences of African hunter-gatherers, agricultural populations, and primate outgroups, we quantified the effects of GC-biased gene conversion on population genomic data sets. We find that genetic distances (FST and population branch statistics) are modified by gBGC. In addition, the site frequency spectrum is left-shifted when ancestral alleles are favored by gBGC and right-shifted when derived alleles are favored by gBGC. Allele frequency shifts due to gBGC mimic the effects of natural selection. As expected, these effects are strongest in high-recombination regions of the human genome. By comparing the relative rates of fixation of unbiased and biased sites, the strength of gene conversion was estimated to be on the order of Nb ≈ 0.05 to 0.09. We also find that derived alleles favored by gBGC are much more likely to be homozygous than derived alleles at unbiased SNPs (+42.2% to 62.8%). This results in a curse of the converted, whereby gBGC causes substantial increases in hereditary disease risks. Taken together, our findings reveal that GC-biased gene conversion has important population genetic and public health implications.

  6. Patterns of neutral diversity under general models of selective sweeps.

    PubMed

    Coop, Graham; Ralph, Peter

    2012-09-01

    Two major sources of stochasticity in the dynamics of neutral alleles result from resampling of finite populations (genetic drift) and the random genetic background of nearby selected alleles on which the neutral alleles are found (linked selection). There is now good evidence that linked selection plays an important role in shaping polymorphism levels in a number of species. One of the best-investigated models of linked selection is the recurrent full-sweep model, in which newly arisen selected alleles fix rapidly. However, the bulk of selected alleles that sweep into the population may not be destined for rapid fixation. Here we develop a general model of recurrent selective sweeps in a coalescent framework, one that generalizes the recurrent full-sweep model to the case where selected alleles do not sweep to fixation. We show that in a large population, only the initial rapid increase of a selected allele affects the genealogy at partially linked sites, which under fairly general assumptions are unaffected by the subsequent fate of the selected allele. We also apply the theory to a simple model to investigate the impact of recurrent partial sweeps on levels of neutral diversity and find that for a given reduction in diversity, the impact of recurrent partial sweeps on the frequency spectrum at neutral sites is determined primarily by the frequencies rapidly achieved by the selected alleles. Consequently, recurrent sweeps of selected alleles to low frequencies can have a profound effect on levels of diversity but can leave the frequency spectrum relatively unperturbed. In fact, the limiting coalescent model under a high rate of sweeps to low frequency is identical to the standard neutral model. The general model of selective sweeps we describe goes some way toward providing a more flexible framework to describe genomic patterns of diversity than is currently available. PMID:22714413

  7. Characterizing allelic association in the genome era

    PubMed Central

    WEIR, B. S.; LAURIE, C. C.

    2015-01-01

    Summary Whole genome data are allowing the estimation of population genetic parameters with an accuracy not imagined 50 years ago. Variation in these parameters along the genome is being found empirically where once only approximate theoretical values were available. Along with increased information, however, has come the issue of multiple testing and the realization that high values of the coefficients of variation of quantities such as relatedness measures may make it difficult to draw inferences. This review concentrates on measures of allelic association within and between individuals and within and between populations. PMID:21429275

  8. Chromosome inversions, adaptive cassettes and the evolution of species' ranges.

    PubMed

    Kirkpatrick, Mark; Barrett, Brian

    2015-05-01

    A chromosome inversion can spread when it captures locally adapted alleles or when it is introduced into a species by hybridization with adapted alleles that were previously absent. We present a model that shows how both processes can cause a species range to expand. Introgression of an inversion that carries novel, locally adapted alleles is a particularly powerful mechanism for range expansion. The model supports the earlier proposal that introgression of an inversion triggered a large range expansion of a malaria mosquito. These results suggest a role for inversions as cassettes of genes that can accelerate adaptation by crossing species boundaries, rather than protecting genomes from introgression.

  9. Chromosome inversions, adaptive cassettes and the evolution of species' ranges.

    PubMed

    Kirkpatrick, Mark; Barrett, Brian

    2015-05-01

    A chromosome inversion can spread when it captures locally adapted alleles or when it is introduced into a species by hybridization with adapted alleles that were previously absent. We present a model that shows how both processes can cause a species range to expand. Introgression of an inversion that carries novel, locally adapted alleles is a particularly powerful mechanism for range expansion. The model supports the earlier proposal that introgression of an inversion triggered a large range expansion of a malaria mosquito. These results suggest a role for inversions as cassettes of genes that can accelerate adaptation by crossing species boundaries, rather than protecting genomes from introgression. PMID:25583098

  10. HLA-DR2 haplotypic diversity in populations of South-East Asia, northern China, Melanesia and Australian aborigines using PCR-RFLP for DRB1, DRB5, DQA1 and DQB1. A novel DRB1 allele: DRB1*16022.

    PubMed

    Trejaut, J; Bhatia, K; Greville, W D; Hu, K R; Duraisamy, G; Nuchprayoon, C; Donald, J; Aziz, A; Dunckley, H

    1996-12-01

    The polymorphism of the human leucocyte antigen HLA-DR2 and the heterogeneity of HLA-DR2 class II-related haplotypes (HLA-DRB1-DRB5-DQA1-DQB1) were investigated in four populations of east and south-east Asia (SEA) and five Melanesian populations using TaqI restriction fragment length polymorphism (RFLP) analysis, and the polymerase chain reaction (PCR) amplification-based techniques PCR-RFLP and sequence-specific oligonucleotide (SSO) typing. The haplotype DRB1*1502-DRB5*0101-DQA1*0102-DQB1*0601 was common in Malaysians, Javanese, Thursday Islanders, Madang, Goroka and the Australian Aborigines, while DRB1*16021-DRB5*0101-DQA1*0102-DQB1*0502 was common in the Thai and Thursday Islanders. DRB1*1501-DRB5*0101-DQA1*0102-DQB1*0602 was present at a high frequency in Northern Chinese, Goroka, Watut and Australian Aborigines. The study describes four rare or unusual haplotypes: HLA-DRB1*1501-DRB5*0101-DQA1*0101-DQB1*0601, DRB1*1502-DRB5*0101-DQA1*0101-DQB1*0502, DRB1*1502-DRB5*0102-DQA1* 0102-DQB1*0502 and DRB1*1501-DRB5*0101-DQA1*0101/2-DQB1*0503; the latter two were confirmed by segregation in two Javanese families. A new DR2 allele, initially detected by PCR-RFLP and confirmed by DNA sequencing as DRB1*16022 (previously designated DRB1*16Madang), was seen in a Madang individual. A new HLA-DR2 TaqI RFLP subtype, locally designated as DR15U, is also described. This RFLP subtype segregated in a Javanese family and correlated with a typically SEA haplotype, DRB1*1502-DRB5*0102-DQA1*0101-DQB1*0501. The allele HLA-DR16Thai, determined by TaqI DRB RFLP, was found by PCR-RFLP and SSO typing to correlate with a unique SEA haplotype, HLA-DRB1*16021-DRB5*0101-DQA1*0102-DQB1*0502, and was observed in the Thai, Malaysian, Thursday Islander, Javanese and Northern Chinese populations.

  11. Microsatellite Analysis of the Genetic Diversity and Population Structure in Dairy Goats in Thailand

    PubMed Central

    Seilsuth, Somkiat; Seo, Joo Hee; Kong, Hong Sik; Jeon, Gwang Joo

    2016-01-01

    The genetic relationships between different populations and breeds of exotic dairy goats in Thailand were studied using 12 microsatellite markers. Blood samples were obtained from 211 goats from Department of Livestock Development breeding and research farms: 29 Anglonubian (AN), 21 Alpine (AP), 23 Jamunapari (JAM), 50 Saanen (SN), and 88 Toggenburg (TG). Five of the 12 microsatellite markers were found to be polymorphic. A mean of 7.40 alleles per locus was found, with a range from 5 (SPS115 and ETH225) to 11 (TGLA122). We found 24, 27, 19, 32, and 24 alleles in the AN, AP, JAM, SN, and TG breeds, respectively; 37 alleles were present in all breeds. The mean number of alleles in each population ranged from 3.2 (ETH225 locus) to 7.6 (TGLA122 locus). Genetic variability within the breeds was moderate as evidenced by the mean expected heterozygosity of 0.539. The average observed heterozygosity across the 5 markers in all breeds was 0.529 with the maximum observed at the BM1818 locus (0.772) and the minimum at the ETH225 locus (0.248). The observed and expected heterozygosity for all breeds for the 5 microsatellite markers ranged from 0.419 to 0.772 and 0.227 to 0.792, respectively. On the basis of their means, the TGLA122 and BM1818 loci were the most suitable markers for distinguishing genetic diversity among the goats. The estimated average Fis value for the breeds ranged from −0.044 (ETH225) to 0.180 (SPS115), while the estimated average Fst value ranged from 0.021 (SPS115) to 0.104 (ETH10). These results indicated that TGLA122 and BM1818 markers are suitable to be used for aiding conservation and breeding improvement strategies of dairy. PMID:26950862

  12. Microsatellite Analysis of the Genetic Diversity and Population Structure in Dairy Goats in Thailand.

    PubMed

    Seilsuth, Somkiat; Seo, Joo Hee; Kong, Hong Sik; Jeon, Gwang Joo

    2016-03-01

    The genetic relationships between different populations and breeds of exotic dairy goats in Thailand were studied using 12 microsatellite markers. Blood samples were obtained from 211 goats from Department of Livestock Development breeding and research farms: 29 Anglonubian (AN), 21 Alpine (AP), 23 Jamunapari (JAM), 50 Saanen (SN), and 88 Toggenburg (TG). Five of the 12 microsatellite markers were found to be polymorphic. A mean of 7.40 alleles per locus was found, with a range from 5 (SPS115 and ETH225) to 11 (TGLA122). We found 24, 27, 19, 32, and 24 alleles in the AN, AP, JAM, SN, and TG breeds, respectively; 37 alleles were present in all breeds. The mean number of alleles in each population ranged from 3.2 (ETH225 locus) to 7.6 (TGLA122 locus). Genetic variability within the breeds was moderate as evidenced by the mean expected heterozygosity of 0.539. The average observed heterozygosity across the 5 markers in all breeds was 0.529 with the maximum observed at the BM1818 locus (0.772) and the minimum at the ETH225 locus (0.248). The observed and expected heterozygosity for all breeds for the 5 microsatellite markers ranged from 0.419 to 0.772 and 0.227 to 0.792, respectively. On the basis of their means, the TGLA122 and BM1818 loci were the most suitable markers for distinguishing genetic diversity among the goats. The estimated average F is value for the breeds ranged from -0.044 (ETH225) to 0.180 (SPS115), while the estimated average F st value ranged from 0.021 (SPS115) to 0.104 (ETH10). These results indicated that TGLA122 and BM1818 markers are suitable to be used for aiding conservation and breeding improvement strategies of dairy. PMID:26950862

  13. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction.

    PubMed

    Nayak, Spurthi N; Song, Jian; Villa, Andrea; Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C; Kuhn, David N; Glaz, Barry; Gilbert, Robert A; Comstock, Jack C; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.

  14. Promoting Utilization of Saccharum spp. Genetic Resources through Genetic Diversity Analysis and Core Collection Construction

    PubMed Central

    Pathak, Bhuvan; Ayala-Silva, Tomas; Yang, Xiping; Todd, James; Glynn, Neil C.; Kuhn, David N.; Glaz, Barry; Gilbert, Robert A.; Comstock, Jack C.; Wang, Jianping

    2014-01-01

    Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance. PMID:25333358

  15. Evaluation of genetic diversity in fig accessions by using microsatellite markers.

    PubMed

    do Val, A D B; Souza, C S; Ferreira, E A; Salgado, S M L; Pasqual, M; Cançado, G M A

    2013-04-25

    Fig (Ficus carica L.) is a fruit of great importance worldwide. Its propagation is carried out with stem cuttings, a procedure that favors the occurrence of synonymy among specimens. Thus, molecular markers have become an important tool for studies of DNA fingerprinting, germplasm characterization, and genetic diversity evaluation in this plant species. The aim of this study was the analysis of genetic diversity among accessions of fig and the detection of synonyms among samples using molecular markers. Five microsatellite markers previously reported as polymorphic to fig were used to characterize 11 fig cultivars maintained in the germplasm bank located in Lavras, Minas Gerais. A total of 21 polymorphic DNA fragments were amplified, with an average of 4.2 alleles per locus. The average allelic diversity and polymorphic information content were 0.6300 and 0.5644, respectively, whereas the total value for the probability of identity was 1.45 x 10(-4). The study allowed the identification of 10 genotypes and 2 synonymous individuals. The principal coordinate analysis showed no defined clusters despite the formation of groups according to geographical origin. However, neighbor-joining analysis identified the same case of synonymy detected using principal coordinate analysis. The data also indicated that the fig cultivars analyzed constitute a population of individuals with high genetic diversity and a broad range of genetic variation.

  16. Demographic history and the low genetic diversity in Dipteryx alata (Fabaceae) from Brazilian Neotropical savannas

    PubMed Central

    Collevatti, R G; Telles, M P C; Nabout, J C; Chaves, L J; Soares, T N

    2013-01-01

    Genetic effects of habitat fragmentation may be undetectable because they are generally a recent event in evolutionary time or because of confounding effects such as historical bottlenecks and historical changes in species' distribution. To assess the effects of demographic history on the genetic diversity and population structure in the Neotropical tree Dipteryx alata (Fabaceae), we used coalescence analyses coupled with ecological niche modeling to hindcast its distribution over the last 21 000 years. Twenty-five populations (644 individuals) were sampled and all individuals were genotyped using eight microsatellite loci. All populations presented low allelic richness and genetic diversity. The estimated effective population size was small in all populations and gene flow was negligible among most. We also found a significant signal of demographic reduction in most cases. Genetic differentiation among populations was significantly correlated with geographical distance. Allelic richness showed a spatial cline pattern in relation to the species' paleodistribution 21 kyr BP (thousand years before present), as expected under a range expansion model. Our results show strong evidences that genetic diversity in D. alata is the outcome of the historical changes in species distribution during the late Pleistocene. Because of this historically low effective population size and the low genetic diversity, recent fragmentation of the Cerrado biome may increase population differentiation, causing population decline and compromising long-term persistence. PMID:23591520

  17. Genetic diversity of functional food species Spinacia oleracea L. by protein markers.

    PubMed

    Rashid, M; Yousaf, Z; Haider, M S; Khalid, S; Rehman, H A; Younas, A; Arif, A

    2014-01-01

    Exploration of genetic diversity contributes primarily towards crop improvement. Spinaciaoleracea L. is a functional food species but unfortunately the genetic diversity of this vegetable is still unexplored. Therefore, this research was planned to explore the genetic diversity of S. oleracea by using morphological and protein markers. Protein profile of 25 accessions was generated on sodium dodecyl sulphate polyacrylamide gel. Total allelic variation of 27 bands was found. Out of these, 20 were polymorphic and the rest of the bands were monomorphic. Molecular weights of the bands ranged from 12.6 to 91.2 kDa. Major genetic differences were observed in accession 20541 (Peshawar) followed by 20180 (Lahore) and 19902 (AVRDC). Significant differences exist in the protein banding pattern. This variation can further be studied by advanced molecular techniques, including two-dimensional electrophoresis and DNA markers.

  18. Genetics of unstable alleles of the X chromosome genes isolated from natural populations of Drosophila melanogaster during the outburst of mutation yellow in 1982 to 1991 in Uman`

    SciTech Connect

    Zakharov, I.K.; Skibitskii, E.E.

    1995-08-01

    In 1982, a local increase of frequency of mutation yellow-2, which lasted for a decade, occurred in a population of Drosophila melanogaster from Uman` (Ukraine). Genetic properties (phenotypic difference, mutability, and pecularities of complementation) of alleles yellow-2, isolated from the population during the mutation outburst, and of their revertants, were studied. Allelic diversity, which reflected molecular differences in allele structure, was shown to appear. In addition to mutation yellow, isolated in 1990 from the Uman` population, mutational properties of other sex-linked genes (dusky, miniature, rudimentary, singed, and vermilion) isolated from natural populations in 1986 to 1990, were analyzed. Based on these data, the conclusion was drawn that the presence of unstable alleles in populations is not a sufficient condition for mutation outbursts. Comparative analysis of properties of yellow alleles obtained in different periods of the outburst continues. 17 refs., 4 tabs.

  19. Utility of nuclear allele networks for the analysis of closely related species in the genus Carabus, subgenus Ohomopterus.

    PubMed

    Sota, Teiji; Sasabe, Masataka

    2006-04-01

    Nuclear DNA sequence data for diploid organisms are potentially a rich source of phylogenetic information for disentangling the evolutionary relationships of closely related organisms, but present special phylogenetic problems owing to difficulties arising from heterozygosity and recombination. We analyzed allelic relationships for two nuclear gene regions (phosphoenolpyruvate carboxykinase and elongation factor-1a), along with a mitochondrial gene region (NADH dehydrogenase subunit 5), for an assemblage of closely related species of carabid beetles (Carabus subgenus Ohomopterus). We used a network approach to examine whether the nuclear gene sequences provide substantial phylogenetic information on species relationships and evolutionary history. The mitochondrial gene genealogy strongly contradicted the morphological species boundary as a result of introgression of heterospecific mitochondria. Two nuclear gene regions showed high allelic diversity within species, and this diversity was partially attributable to recombination between various alleles and high variability in the intron region. Shared nuclear alleles among species were rare and were considered to represent shared ancestral polymorphism. Despite the presence of recombination, nuclear allelic networks recovered species monophyly more often and presented genetic differentiation patterns (low to high) among species more clearly. Overall, nuclear gene networks provide clear evidence for separate biological species and information on the phylogenetic relationships among closely related carabid beetles.

  20. Predictable allele frequency changes due to habitat fragmentation in the Glanville fritillary butterfly.

    PubMed

    Fountain, Toby; Nieminen, Marko; Sirén, Jukka; Wong, Swee Chong; Hanski, Ilkka

    2016-03-01

    Describing the evolutionary dynamics of now extinct populations is challenging, as their genetic composition before extinction is generally unknown. The Glanville fritillary butterfly has a large extant metapopulation in the Åland Islands in Finland, but declined to extinction in the nearby fragmented southwestern (SW) Finnish archipelago in the 20th century. We genotyped museum samples for 222 SNPs across the genome, including SNPs from candidate genes and neutral regions. SW Finnish populations had significantly reduced genetic diversity before extinction, and their allele frequencies gradually diverged from those in contemporary Åland populations over 80 y. We identified 15 outlier loci among candidate SNPs, mostly related to flight, in which allele frequencies have changed more than the neutral expectation. At outlier loci, allele frequencies in SW Finland shifted in the same direction as newly established populations deviated from old local populations in contemporary Åland. Moreover, outlier allele frequencies in SW Finland resemble those in fragmented landscapes as opposed to continuous landscapes in the Baltic region. These results indicate selection for genotypes associated with good colonization capacity in the highly fragmented landscape before the extinction of the populations. Evolutionary response to habitat fragmentation may have enhanced the viability of the populations, but it did not save the species from regional extinction in the face of severe habitat loss and fragmentation. These results highlight a potentially common situation in changing environments: evolutionary changes are not strong enough to fully compensate for the direct adverse effects of environmental change and thereby rescue populations from extinction.

  1. Asymmetric dispersal allows an upstream region to control population structure throughout a species' range.

    PubMed

    Pringle, James M; Blakeslee, April M H; Byers, James E; Roman, Joe

    2011-09-13

    In a single well-mixed population, equally abundant neutral alleles are equally likely to persist. However, in spatially complex populations structured by an asymmetric dispersal mechanism, such as a coastal population where larvae are predominantly moved downstream by currents, the eventual frequency of neutral haplotypes will depend on their initial spatial location. In our study of the progression of two spatially separate, genetically distinct introductions of the European green crab (Carcinus maenas) along the coast of eastern North America, we captured this process in action. We documented the shift of the genetic cline in this species over 8 y, and here we detail how the upstream haplotypes are beginning to dominate the system. This quantification of an evolving genetic boundary in a coastal system demonstrates that novel genetic alleles or haplotypes that arise or are introduced into upstream retention zones (regions whose export of larvae is not balanced by import from elsewhere) will increase in frequency in the entire system. This phenomenon should be widespread when there is asymmetrical dispersal, in the oceans or on land, suggesting that the upstream edge of a species' range can influence genetic diversity throughout its distribution. Efforts to protect the upstream edge of an asymmetrically dispersing species' range are vital to conserving genetic diversity in the species. PMID:21876126

  2. Comparison of Campylobacter populations isolated from a free-range broiler flock before and after slaughter

    PubMed Central

    Colles, Frances M.; McCarthy, Noel D.; Sheppard, Samuel K.; Layton, Ruth; Maiden, Martin C.J.

    2014-01-01

    Relatively little is known about the Campylobacter genotypes colonizing extensively reared broiler flocks and their survival through the slaughter process, despite the increasing demand for free-range and organic products by the consumer. Campylobacter isolates from a free-range boiler flock, sampled before and after slaughter, were genotyped by MLST (multilocus sequence typing) and sequence analysis of the flaA short variable region (SVR). The Campylobacter genotypes isolated before and after slaughter were diverse, with up to five sequence types (STs) (seven-locus allelic profiles resulting from MLST) identified per live bird, up to eight STs identified per carcass and 31 STs identified in all. The majority (72.0%) of isolates sampled from carcasses post-slaughter were indistinguishable from those isolated from the live flock before slaughter by ST and flaA SVR type, however, sampling ‘on-farm’ failed to capture all of the diversity seen post-slaughter. There were statistically significant increases in the genetic diversity of Campylobacter (p=0.005) and the proportion of C. coli (p=0.002), with some evidence for differential survival of genotypes contaminating the end product. C. coli genotypes isolated after slaughter were more similar to those from free-range and organic meat products sampled nationally, than from the live flock sampled previously. This study demonstrated the utility of MLST in detecting genetic diversity before and after the slaughter process. PMID:20071049

  3. Assessment of allele-specific gene silencing by RNA interference with mutant and wild-type reporter alleles.

    PubMed

    Ohnishi, Yusuke; Tokunaga, Katsushi; Kaneko, Kiyotoshi; Hohjoh, Hirohiko

    2006-02-28

    Allele-specific gene silencing by RNA interference (RNAi) is therapeutically useful for specifically suppressing the expression of alleles associated with disease. To realize such allele-specific RNAi (ASPRNAi), the design and assessment of small interfering RNA (siRNA) duplexes conferring ASP-RNAi is vital, but is also difficult. Here, we show ASP-RNAi against the Swedish- and London-type amyloid precursor protein (APP) variants related to familial Alzheimer's disease using two reporter alleles encoding the Photinus and Renilla luciferase genes and carrying mutant and wild-type allelic sequences in their 3'-untranslated regions. We examined the effects of siRNA duplexes against the mutant alleles in allele-specific gene silencing and off-target silencing against the wild-type allele under heterozygous conditions, which were generated by cotransfecting the reporter alleles and siRNA duplexes into cultured human cells. Consistently, the siRNA duplexes determined to confer ASP-RNAi also inhibited the expression of the bona fide mutant APP and the production of either amyloid beta 40- or 42-peptide in Cos-7 cells expressing both the full-length Swedish- and wild-type APP alleles. The present data suggest that the system with reporter alleles may permit the preclinical assessment of siRNA duplexes conferring ASP-RNAi, and thus contribute to the design and selection of the most suitable of such siRNA duplexes.

  4. Deleterious alleles in the human genome are on average younger than neutral alleles of the same frequency.

    PubMed

    Kiezun, Adam; Pulit, Sara L; Francioli, Laurent C; van Dijk, Freerk; Swertz, Morris; Boomsma, Dorret I; van Duijn, Cornelia M; Slagboom, P Eline; van Ommen, G J B; Wijmenga, Cisca; de Bakker, Paul I W; Sunyaev, Shamil R

    2013-01-01

    Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations. A key challenge is to identify, among the myriad alleles, those variants that have an effect on molecular function, phenotypes, and reproductive fitness. Most non-neutral variation consists of deleterious alleles segregating at low population frequency due to incessant mutation. To date, studies characterizing selection against deleterious alleles have been based on allele frequency (testing for a relative excess of rare alleles) or ratio of polymorphism to divergence (testing for a relative increase in the number of polymorphic alleles). Here, starting from Maruyama's theoretical prediction (Maruyama T (1974), Am J Hum Genet USA 6:669-673) that a (slightly) deleterious allele is, on average, younger than a neutral allele segregating at the same frequency, we devised an approach to characterize selection based on allelic age. Unlike existing methods, it compares sets of neutral and deleterious sequence variants at the same allele frequency. When applied to human sequence data from the Genome of the Netherlands Project, our approach distinguishes low-frequency coding non-synonymous variants from synonymous and non-coding variants at the same allele frequency and discriminates between sets of variants independently predicted to be benign or damaging for protein structure and function. The results confirm the abundance of slightly deleterious coding variation in humans.

  5. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    PubMed

    Kasthurinaidu, Senthilkumar Pitchalu; Ramasamy, Thirumurugan; Ayyavoo, Jayachitra; Dave, Dhvani Kirtikumar; Adroja, Divya Anantray

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs.

  6. GST M1-T1 null Allele Frequency Patterns in Geographically Assorted Human Populations: A Phylogenetic Approach

    PubMed Central

    Ramasamy, Thirumurugan; Ayyavoo, Jayachitra

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs. PMID:25867025

  7. GST M1-T1 null allele frequency patterns in geographically assorted human populations: a phylogenetic approach.

    PubMed

    Kasthurinaidu, Senthilkumar Pitchalu; Ramasamy, Thirumurugan; Ayyavoo, Jayachitra; Dave, Dhvani Kirtikumar; Adroja, Divya Anantray

    2015-01-01

    Genetic diversity in drug metabolism and disposition is mainly considered as the outcome of the inter-individual genetic variation in polymorphism of drug-xenobiotic metabolizing enzyme (XME). Among the XMEs, glutathione-S-transferases (GST) gene loci are an important candidate for the investigation of diversity in allele frequency, as the deletion mutations in GST M1 and T1 genotypes are associated with various cancers and genetic disorders of all major Population Affiliations (PAs). Therefore, the present population based phylogenetic study was focused to uncover the frequency distribution pattern in GST M1 and T1 null genotypes among 45 Geographically Assorted Human Populations (GAHPs). The frequency distribution pattern for GST M1 and T1 null alleles have been detected in this study using the data derived from literatures representing 44 populations affiliated to Africa, Asia, Europe, South America and the genome of PA from Gujarat, a region in western India. Allele frequency counting for Gujarat PA and scattered plot analysis for geographical distribution among the PAs were performed in SPSS-21. The GST M1 and GST T1 null allele frequencies patterns of the PAs were computed in Seqboot, Gendist program of Phylip software package (3.69 versions) and Unweighted Pair Group method with Arithmetic Mean in Mega-6 software. Allele frequencies from South African Xhosa tribe, East African Zimbabwe, East African Ethiopia, North African Egypt, Caucasian, South Asian Afghanistan and South Indian Andhra Pradesh have been identified as the probable seven patterns among the 45 GAHPs investigated in this study for GST M1-T1 null genotypes. The patternized null allele frequencies demonstrated in this study for the first time addresses the missing link in GST M1-T1 null allele frequencies among GAHPs. PMID:25867025

  8. Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules

    PubMed Central

    Prevosto, Claudia; Usmani, M. Farooq; McDonald, Sarah; Gumienny, Aleksandra M.; Key, Tim; Goodman, Reyna S.; Gaston, J. S. Hill; Deery, Michael J.; Busch, Robert

    2016-01-01

    Major histocompatibility complex class I (MHCI) glycoproteins present cytosolic peptides to CD8+ T cells and regulate NK cell activity. Their heavy chains (HC) are expressed from up to three MHC gene loci (human leukocyte antigen [HLA]-A, -B, and -C in humans), whose extensive polymorphism maps predominantly to the antigen-binding groove, diversifying the bound peptide repertoire. Codominant expression of MHCI alleles is thus functionally critical, but how it is regulated is not fully understood. Here, we have examined the effect of polymorphism on the turnover rates of MHCI molecules in cell lines with functional MHCI peptide loading pathways and in monocyte-derived dendritic cells (MoDCs). Proteins were labeled biosynthetically with heavy water (2H2O), folded MHCI molecules immunoprecipitated, and tryptic digests analysed by mass spectrometry. MHCI-derived peptides were assigned to specific alleles and isotypes, and turnover rates quantified by 2H incorporation, after correcting for cell growth. MHCI turnover half-lives ranged from undetectable to a few hours, depending on cell type, activation state, donor, and MHCI isotype. However, in all settings, the turnover half-lives of alleles of the same isotype were similar. Thus, MHCI protein turnover rates appear to be allele-independent in normal human cells. We propose that this is an important feature enabling the normal function and codominant expression of MHCI alleles. PMID:27529174

  9. Allele-Independent Turnover of Human Leukocyte Antigen (HLA) Class Ia Molecules.

    PubMed

    Prevosto, Claudia; Usmani, M Farooq; McDonald, Sarah; Gumienny, Aleksandra M; Key, Tim; Goodman, Reyna S; Gaston, J S Hill; Deery, Michael J; Busch, Robert

    2016-01-01

    Major histocompatibility complex class I (MHCI) glycoproteins present cytosolic peptides to CD8+ T cells and regulate NK cell activity. Their heavy chains (HC) are expressed from up to three MHC gene loci (human leukocyte antigen [HLA]-A, -B, and -C in humans), whose extensive polymorphism maps predominantly to the antigen-binding groove, diversifying the bound peptide repertoire. Codominant expression of MHCI alleles is thus functionally critical, but how it is regulated is not fully understood. Here, we have examined the effect of polymorphism on the turnover rates of MHCI molecules in cell lines with functional MHCI peptide loading pathways and in monocyte-derived dendritic cells (MoDCs). Proteins were labeled biosynthetically with heavy water (2H2O), folded MHCI molecules immunoprecipitated, and tryptic digests analysed by mass spectrometry. MHCI-derived peptides were assigned to specific alleles and isotypes, and turnover rates quantified by 2H incorporation, after correcting for cell growth. MHCI turnover half-lives ranged from undetectable to a few hours, depending on cell type, activation state, donor, and MHCI isotype. However, in all settings, the turnover half-lives of alleles of the same isotype were similar. Thus, MHCI protein turnover rates appear to be allele-independent in normal human cells. We propose that this is an important feature enabling the normal function and codominant expression of MHCI alleles. PMID:27529174

  10. CYP2D6 allele distribution in Macedonians, Albanians and Romanies in the Republic of Macedonia

    PubMed Central

    Kuzmanovska, M; Dimishkovska, M; Maleva Kostovska, I; Noveski, P; Sukarova Stefanovska, E

    2015-01-01

    Abstract Cytochrome P450 2D6 (CYP2D6) is an enzyme of great importance for the metabolism of clinically used drugs. More than 100 variants of the CYP2D6 gene have been identified so far. The aim of this study was to investigate the allele distribution of CYP2D6 gene variants in 100 individuals of each of the Macedonian, Albanian and Romany population, by genotyping using long range polymerase chain reaction (PCR) and a multiplex single base extension method. The most frequent variants and almost equally distributed in the three groups were the fully functional alleles *1 and *2. The most common non functional allele in all groups was *4 that was found in 22.5% of the Albanians. The most common allele with decreased activity was *41 which was found in 23.0% of the Romany ethnic group, in 11.0% of the Macedonians and in 10.5% of the Albanians. Seven percent of the Albanians, 6.0% of the Romani and 4.0% of the Macedonians were poor metabolizers, while 5.0% of the Macedonians, 1.0% of Albanians and 1.0% of the Romanies were ultrarapid metabolizers. We concluded that the CYP2D6 gene locus is highly heterogeneous in these groups and that the prevalence of the CYP2D6 allele variants and genotypes in the Republic of Macedonia is in accordance with that of other European populations.

  11. Differential effects of the APOE e4 allele on different domains of cognitive ability across the life-course.

    PubMed

    Marioni, Riccardo E; Campbell, Archie; Scotland, Generation; Hayward, Caroline; Porteous, David J; Deary, Ian J

    2016-06-01

    The association between APOE genotype and cognitive function suggests a positive role for the e2 allele and a negative role for the e4 allele. Both alleles have relatively low frequencies in the general population; hence, meta-analyses have been based on many small, heterogeneous studies. Here, we report the APOE-cognition associations in the largest single analysis to date. APOE status and cognitive ability were measured in 18 337 participants from the Generation Scotland study between 2006 and 2011. The age range was 18-94 years with a mean of 47 (SD 15). Four cognitive domains were assessed: verbal declarative memory (paragraph recall), processing speed (digit symbol substitution), verbal fluency (phonemic verbal fluency), and vocabulary (Mill Hill synonyms). Linear regression was used to assess the associations between APOE genetic status and cognition. Possession of the e4 allele was associated with lower scores on the measures of memory and processing speed in subjects aged >60. Across all age ranges, the e4 allele was linked to better verbal fluency scores. In younger subjects (≤60 years) the e4 allele was linked to higher vocabulary scores. There were no associations between the e2 allele and cognitive ability. As seen in previous meta-analyses, the APOE e4 allele is linked to poorer cognitive performance in the domains of memory and processing speed. By contrast, positive associations were seen between the e4 allele and measures of verbal fluency and vocabulary. All associations were relatively small and, in many cases, nominally significant despite the very large sample size. PMID:26395552

  12. Dissecting Diversity Part II

    ERIC Educational Resources Information Center

    Matthews, Frank

    2005-01-01

    This article presents "Dissecting Diversity, Part II," the conclusion of a wide-ranging two-part roundtable discussion on diversity in higher education. The participants were as follows: Lezli Baskerville, J.D., President and CEO of the National Association for Equal Opportunity (NAFEO); Dr. Gerald E. Gipp, Executive Director of the American…

  13. Microarrays for high-throughput genotyping of MICA alleles using allele-specific primer extension.

    PubMed

    Baek, I C; Jang, J-P; Choi, H-B; Choi, E-J; Ko, W-Y; Kim, T-G

    2013-10-01

    The role of major histocompatibility complex (MHC) class I chain-related gene A (MICA), a ligand of NKG2D, has been defined in human diseases by its allele associations with various autoimmune diseases, hematopoietic stem cell transplantation (HSCT) and cancer. This study describes a practical system to develop MICA genotyping by allele-specific primer extension (ASPE) on microarrays. From the results of 20 control primers, strict and reliable cut-off values of more than 30,000 mean fluorescence intensity (MFI) as positive and less than 3000 MFI as negative, were applied to select high-quality specific extension primers. Among 55 allele-specific primers, 44 primers could be initially selected as optimal primer. Through adjusting the length, six primers were improved. The other failed five primers were corrected by refractory modification. MICA genotypes by ASPE on microarrays showed the same results as those by nucleotide sequencing. On the basis of these results, ASPE on microarrays may provide high-throughput genotyping for MICA alleles for population studies, disease-gene associations and HSCT.

  14. Allelic disequilibrium and allele frequency distribution as a function of social and demographic history.

    PubMed Central

    Thompson, E A; Neel, J V

    1997-01-01

    Allelic disequilibrium between closely linked genes is a common observation in human populations and often gives rise to speculation concerning the role of selective forces. In a previous treatment, we have developed a population model of the expected distribution of rare variants (including private polymorphisms) in Amerindians and have argued that, because of the great expansion of Amerindian numbers with the advent of agriculture, most of these rare variants are of relatively recent origin. Many other populations have similar histories of striking recent expansions. In this treatment, we demonstrate that, in consequence of this fact, a high degree of linkage disequilibrium between two nonhomologous alleles <0.5 cM apart is the "normal" expectation, even in the absence of selection. This expectation is enhanced by the previous subdivision of human populations into relatively isolated tribes characterized by a high level of endogamy and inbreeding. We also demonstrate that the alleles associated with a recessive disease phenotype are expected to exist in a population in very variable frequencies: there is no need to postulate positive selection with respect to the more common disease-associated alleles for such entities as phenylketonuria or cystic fibrosis. PMID:8981963

  15. [Screening and genetic diversity analysis of microsatellite markers in Chinese lobster (Panulirus stimpsoni)].

    PubMed

    Liu, Chu-Wu; Li, Jin-Ming; Liu, Li; Guo, Yu-Song

    2010-07-01

    With the construction of a library of partial fractionated genomic DNA of Panulirus stimpsoni Hoehuis, the microsatellite sequences of P. stimpsoni were screened by PCR technique. Then, the genetic diversity was analyzed with the microsatellite markers. Seventy-eight microsatellite sequences in 55 positive recombinant clones were obtained by PCR technique with primers of M13+/- and (CT)15, and (AT)15. Among these microsatellite sequences, the numbers of perfect, imperfect, compound perfect, and compound imperfect sequences were 50 (64%), 3 (3.8%), 5 (7.7%), and 19 (24.5%), respectively. To analyze genomic DNA diversity of P. stimpsoni, 15 pairs of primers were designed from the microsatellite flanking sequences. In these microsatellite loci, the alleles numbers ranged from 3 to 12; and the sizes of these alleles ranged from 78 to 425 bp, which are in accordance with their predicted size range. The expected heterozygosity (He) and the polymorphism information content (PIC) ranged from 0.48 to 0.87 and 0.44 to 0.84 with the average values of 0.71 and 0.60, respectively. These results showed that these microsatellite loci were suitable for P. stimpsoni molecule markers and genetic analysis because of their richness in genetic information.

  16. Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China.

    PubMed

    Liu, Wen; Shahid, Muhammad Qasim; Bai, Lin; Lu, Zhenzhen; Chen, Yuhong; Jiang, Lan; Diao, Mengyang; Liu, Xiangdong; Lu, Yonggen

    2015-01-01

    Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a period of almost two decades. We evaluated these accessions for 13 morphological or phenological traits and genotyped them for 36 DNA markers evenly distributed on the 12 chromosomes. The coefficient of variation of quantitative traits was 0.56 and ranged from 0.37 to 1.06. SSR markers detected 206 different alleles with an average of 6 alleles per locus. The mean polymorphism information content (PIC) was 0.64 in all populations, indicating that the marker loci have a high level of polymorphism and genetic diversity in all populations. Phylogenetic analyses based on morphological and molecular data revealed remarkable differences in the genetic diversity of common wild rice populations. The results showed that the Zengcheng, Gaozhou, and Suixi populations possess higher levels of genetic diversity, whereas the Huilai and Boluo populations have lower levels of genetic diversity than do the other populations. Based on their genetic distance, 130 accessions were selected as a core collection that retained over 90% of the alleles at the 36 marker loci. This genetically diverse core collection will be a useful resource for genomic studies of rice and for initiatives aimed at developing rice with improved agronomic traits.

  17. Evaluation of Genetic Diversity and Development of a Core Collection of Wild Rice (Oryza rufipogon Griff.) Populations in China

    PubMed Central

    Bai, Lin; Lu, Zhenzhen; Chen, Yuhong; Jiang, Lan; Diao, Mengyang; Liu, Xiangdong; Lu, Yonggen

    2015-01-01

    Common wild rice (Oryza rufipogon Griff.), the progenitor of Asian cultivated rice (O. sativa L.), is endangered due to habitat loss. The objectives of this research were to evaluate the genetic diversity of wild rice species in isolated populations and to develop a core collection of representative genotypes for ex situ conservation. We collected 885 wild rice accessions from eight geographically distinct regions and transplanted these accessions in a protected conservation garden over a perio