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DNA Variation (dna + variation)
Kinds of DNA Variation Selected AbstractsChloroplast DNA Variation and Biogeography in the Genus Rorippa Scop. (Brassicaceae)PLANT BIOLOGY, Issue 1 2002W. Bleeker Abstract: Phylogenetic relationships and biogeography of 25 Rorippa species were studied using sequences of two non-coding regions of chloroplast DNA (trnL intron, trnL/F spacer). Our results indicate a close relationship between European (R. islandica ssp. islandica, R. pyrenaica) and North American (R. curvipes, R. sinuata) mountain species. The polyploid European lowland species R. amphibia, R. palustris and R. sylvestris are much younger than the mountain species and have their closest relatives in western Asia and Siberia. Different colonization routes of the southern hemisphere are discussed for Rorippa. Australasia was colonized at least twice, most likely via the Malayan route. A molecular clock approach dates the first colonization to the end of Pliocene or early Pleistocene. R. gigantea reached Australia later in the Pleistocene. Our data provide evidence for an amphitropical disjunction between the South American (R. philippiana) and North American (R. curvisiliqua) species. Long-distance dispersal via migrating birds is the most likely explanation for this intercontinental disjunction. Two of the analysed African species (R. nudiuscula, R. madagascariensis) have their closest relative (R. austriaca) in eastern Europe and western Asia. The lack of sequence divergence among these species indicates a colonization event probably not earlier than 100 000 years ago. [source] SNPlexing the human Y-chromosome: A single-assay system for major haplogroup screeningELECTROPHORESIS, Issue 18 2007Gemma Berniell-Lee Abstract SNPs are one of the main sources of DNA variation among humans. Their unique properties make them useful polymorphic markers for a wide range of fields, such as medicine, forensics, and population genetics. Although several high-throughput techniques have been (and are being) developed for the vast typing of SNPs in the medical context, population genetic studies involve the typing of few and select SNPs for targeted research. This results in SNPs having to be typed in multiple reactions, consuming large amounts of time and of DNA. In order to improve the current situation in the area of human Y-chromosome diversity studies, we decided to employ a system based on a multiplex oligo ligation assay/PCR (OLA/PCR) followed by CE to create a Y multiplex capable of distinguishing, in a single reaction, all the major haplogroups and as many subhaplogroups on the Y-chromosome phylogeny as possible. Our efforts resulted in the creation of a robust and accurate 35plex (35 SNPs in a single reaction) that when tested on 165 human DNA samples from different geographic areas, proved capable of assigning samples to their corresponding haplogroup. [source] INTEGRATING EVOLUTIONARY AND FUNCTIONAL APPROACHES TO INFER ADAPTATION AT SPECIFIC LOCIEVOLUTION, Issue 9 2010Jay F. Storz Inferences about adaptation at specific loci are often exclusively based on the static analysis of DNA sequence variation. Ideally, population-genetic evidence for positive selection serves as a stepping-off point for experimental studies to elucidate the functional significance of the putatively adaptive variation. We argue that inferences about adaptation at specific loci are best achieved by integrating the indirect, retrospective insights provided by population-genetic analyses with the more direct, mechanistic insights provided by functional experiments. Integrative studies of adaptive genetic variation may sometimes be motivated by experimental insights into molecular function, which then provide the impetus to perform population genetic tests to evaluate whether the functional variation is of adaptive significance. In other cases, studies may be initiated by genome scans of DNA variation to identify candidate loci for recent adaptation. Results of such analyses can then motivate experimental efforts to test whether the identified candidate loci do in fact contribute to functional variation in some fitness-related phenotype. Functional studies can provide corroborative evidence for positive selection at particular loci, and can potentially reveal specific molecular mechanisms of adaptation. [source] Phylogeographical structure in the coastal species Senecio rodriguezii (Asteraceae), a narrowly distributed endemic Mediterranean plantJOURNAL OF BIOGEOGRAPHY, Issue 7 2009Arántzazu Molins Abstract Aim, Our goals were (1) to assess the levels of chloroplast DNA variation in a narrowly distributed plant restricted to continental islands, (2) to ascertain whether a phylogeographical structure is present in plants restricted to coastal linear systems, and (3) to interpret the results in the light of the known palaeogeography of these islands. Location, The Eastern Balearic Islands (Majorca and Minorca) in the Western Mediterranean Basin. Methods, Sampling included 134 individuals from 28 populations of Senecio rodriguezii covering the entire range of the species. Sequences of the chloroplast genome (trnT,trnL spacer) were obtained and parameters of population genetic diversity and substructure were determined (hsht, Gst). The geographical structure of genetic variation was assessed by an analysis of molecular variance (AMOVA). Additionally, a spatial AMOVA (SAMOVA) was used to identify groups of populations that were geographically homogeneous and maximally differentiated from each other. Finally, a pattern of isolation by distance was assessed by testing the correlation between the matrix of pairwise ,ST values and the matrix of geographical distances between pairs of populations using a Mantel test. Results, Seven haplotypes were detected in S. rodriguezii. Only two of them were shared between islands; all of the others were restricted to Majorca (two) or Minorca (three). Overall, we found high levels of genetic diversity and significant geographical structuring of cpDNA markers. Most of the variation detected can be attributed to differences among populations (84.6%), but there was also a significant differentiation between the islands. Main conclusions, Our results support the view that the Balearic Islands constitute a reservoir of genetic diversity, not only for widespread Mediterranean taxa, but also for endemic ones. The intraspecific genetic structure found in S. rodriguezii suggests that its population history was dominated by both expansion and contraction events. This has resulted in a species that is highly structured genetically, showing very few shared haplotypes between islands, and a high number of haplotypes restricted to small geographical areas within the islands. Changes in habitat availability and dynamic processes of population fragmentation and connectivity due to repeated cycles of sea-level changes during the Quaternary are the possible underlying factors that have shaped the cpDNA pool of this endemic species on a regional scale. [source] Fitness differences associated with Pgi SNP genotypes in the Glanville fritillary butterfly (Melitaea cinxia)JOURNAL OF EVOLUTIONARY BIOLOGY, Issue 2 2009L. ORSINI Abstract Allozyme variation at the phosphoglucose isomerase (PGI) locus in the Glanville fritillary butterfly (Melitaea cinxia) is associated with variation in flight metabolic rate, dispersal rate, fecundity and local population growth rate. To map allozyme to DNA variation and to survey putative functional variation in genomic DNA, we cloned the coding sequence of Pgi and identified nonsynonymous variable sites that determine the most common allozyme alleles. We show that these single-nucleotide polymorphisms (SNPs) exhibit significant excess of heterozygotes in field-collected population samples as well as in laboratory crosses. This is in contrast to previous results for the same species in which other allozymes and SNPs were in Hardy,Weinberg equilibrium or exhibited an excess of homozygotes. Our results suggest that viability selection favours Pgi heterozygotes. Although this is consistent with direct overdominance at Pgi, we cannot exclude the possibility that heterozygote advantage is caused by the presence of one or more deleterious alleles at linked loci. [source] Mitochondrial DNA variation of an isolated population of the Adriatic brook lamprey Lampetra zanandreai (Agnatha: Petromyzontidae): phylogeographic and phylogenetic inferencesJOURNAL OF FISH BIOLOGY, Issue 9 2009V. Caputo Two mitochondrial genes were examined to compare an isolated population of the Adriatic brook lamprey Lampetra zanandreai in central Italy with other populations in the species range (Po plain) and with parasitic and freshwater lampreys. A single haplotype, identical to one in a Venetian sample, was found in 10 individuals from the isolated population. The reduced variability is consistent with a history of dispersal after the Pleistocene expansion of the Po basin. The results support the hypothesis of an origin of L. zanandreai and L. fluviatilis,L. planeri from a common anadromous ancestor. [source] Stepping stone gene flow in an estuarine-dwelling sparid from south-east AustraliaJOURNAL OF FISH BIOLOGY, Issue 4 2004C. P. Burridge Allozyme and mitochondrial DNA variation was surveyed in Acanthopagrus butcheri to examine the pattern of gene flow among estuaries in south-east Australia. Allozymes distinguished two peripheral estuaries from the remaining six, although the pattern of genetic variation could owe more to selection than reproductive isolation, and overall structure was small (, = 0·012). In contrast, mitochondrial DNA revealed a high degree of genetic structure (, = 0·263), and a significant relationship with geographic isolation. Consequently, contemporary gene flow mostly between adjacent estuaries, consistent with a one-dimensional stepping stone model, is evident in south-east Australia. The data indicate that management of A. butcheri within the study range should be conducted at the scale of individual or geographically proximate estuaries. [source] Microsatellite DNA variation in Bornean orangutans (Pongo pygmaeus)JOURNAL OF MEDICAL PRIMATOLOGY, Issue 2 2000K.S. Warren Orangutans (Pongo pygmaeus) on the islands of Borneo and Sumatra are considered two separate subspecies. However, the genetic relationships between isolated populations on Borneo are not clear. This study determined the extent of variation within the Bornean subspecies of orangutan, using microsatellite DNA analysis. Blood samples were collected from 96 individuals of known origin from East, West and Central Kalimantan. Human microsatellite primer pairs located at human map position D2S141, D4S431, D11S925, D16S420 and D17S791 were suitable for use in primates. D4S431 appeared monomorphic for all orangutans. In three cases (D2S141 East and West and D16S420 West), a highly significant excess of homozygous allele frequencies was detected, but with other primer pairs no significant difference in allele frequencies occurred. We conclude that the divergence between the different populations on Borneo is less than the variation within the populations. There was also evidence that inbreeding occurred within the populations. [source] Geographical patterns of mitochondrial DNA variation in Apis mellifera iberiensis (Hymenoptera: Apidae)JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH, Issue 1 2008F. Cánovas Abstract An extensive survey of mitochondrial haplotypes in honeybee colonies from the Iberian Peninsula has corroborated previous hypotheses about the existence of a joint clinal variation of African (A) and west European (M) evolutionary lineages. It has been found that the Iberian Peninsula is the European region with the highest haplotype diversity (12 haplotypes detected of the M lineage and 10 of the A lineage). The frequency of A haplotypes decreases in a SW-NE trend, while that of M haplotypes increases. These results are discussed in relation to hypotheses about the African origin of Apis mellifera and an early colonization of west Europe during intermediate Pleistocene glaciation events, followed by a regional differentiation. The extant pattern of haplotype frequency and distribution seems to be influenced at a regional scale by adaptation to local climatic conditions and the mobile beekeeping that has become a large-scale practice during the last decades. Other previous anthropogenic influences (Greek, Roman and Arab colonizations) are thought to be of minor importance in present day populations. Resumen Un extenso estudio de los haplotipos mitocondriales en colonias de la abeja doméstica de la Péninsula Ibérica ha corroborado las hipótesis previas acerca de la existencia de una variación clinal conjunta de los linajes evolutivos africano (A) y europeo occidental (M). Se ha encontrado que la Peninsula Ibérica es la región europea con la mayor diversidad (12 haplotipos detectados pertenecientes al linaje M y 10 al linaje A). La frecuencia de los haplotipos africanos disminuye en la orientación SW-NE, al tiempo que aumenta proporcionalmente la de los M. Estos resultados se analizan en relación a las hipótesis recientes que ubican el origen de Apis mellifera en África, junto con otras que postulan una colonización temprana de esta especie en Europa occidental, seguida de una diferenciación durante el Pleistoceno. El patrón geográfico actual de haplotipos y frecuencias a escala regional, parece estar influido por la adaptación a las condiciones climáticas locales y la trashumancia, práctica que ha adquirido grandes proporciones en las últimas décadas. Otras influencias antrópicas acontecidas como las colonizaciones de griegos, romanos y árabes han tenido posiblemente poca influencia sobre las poblaciones ibéricas actuales. [source] Phylogeography of Douglas-fir based on mitochondrial and chloroplast DNA sequences: testing hypotheses from the fossil recordMOLECULAR ECOLOGY, Issue 9 2010PAUL F. GUGGER Abstract The integration of fossil and molecular data can provide a synthetic understanding of the ecological and evolutionary history of an organism. We analysed range-wide maternally inherited mitochondrial DNA and paternally inherited chloroplast DNA sequence data with coalescent simulations and traditional population genetic methods to test hypotheses of population divergence generated from the fossil record of Douglas-fir (Pseudotsuga menziesii), an ecologically and economically important western North American conifer. Specifically, we tested (i) the hypothesis that the Pliocene orogeny of the Cascades and Sierra Nevada caused the divergence of coastal and Rocky Mountain Douglas-fir varieties; and (ii) the hypothesis that multiple glacial refugia existed on the coast and in the Rocky Mountains. We found that Douglas-fir varieties diverged about 2.11 Ma (4.37 Ma,755 ka), which could be consistent with a Pliocene divergence. Rocky Mountain Douglas-fir probably resided in three or more glacial refugia. More variable molecular markers would be required to detect the two coastal refugia suggested in the fossil record. Comparison of mitochondrial DNA and chloroplast DNA variation revealed that gene flow via pollen linked populations isolated from seed exchange. Postglacial colonization of Canada from coastal and Rocky Mountain refugia near the ice margin at the Last Glacial Maximum produced a wide hybrid zone among varieties that formed almost exclusively by pollen exchange and chloroplast DNA introgression, not seed exchange. Postglacial migration rates were 50,165 m/year, insufficient to track projected 21st century warming in some regions. Although fossil and genetic data largely agree, each provides unique insights. [source] Population genetics of a marine bivalve, Pinctada maxima, throughout the Indo-Australian Archipelago shows differentiation and decreased diversity at range limitsMOLECULAR ECOLOGY, Issue 24 2007CURTIS E. LIND Abstract 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 (FST = 0.027; RST = 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. [source] Evolutionary history of lamprey paired species Lampetra fluviatilis (L.) and Lampetra planeri (Bloch) as inferred from mitochondrial DNA variationMOLECULAR ECOLOGY, Issue 9 2007RUTE ESPANHOL Abstract A remarkable trend in the evolution of lampreys is the occurrence in most genera of ,paired species', in which the parasitic anadromous lampreys are believed to have given rise to nonparasitic freshwater resident populations. The present work examines the phylogeography of the European paired species Lampetra fluviatilis and Lampetra planeri, in an attempt to elucidate species pair evolutionary history. We studied sequence variation in cytochrome b and ATPase 6, 8 mitochondrial genes in 63 individuals from 21 localities of the paired species throughout their distribution range. Results from the phylogenetic and nested clade analyses were largely consistent, suggesting the existence of three major evolutionary lineages: lineage I and possibly lineage II are widespread throughout Europe, while the most ancestral lineage III is apparently restricted to the Iberian Peninsula. The high genetic diversity observed in the Iberian Peninsula is probably the result of refugial persistence and subsequent accumulation of variation over several ice ages, whereas the low levels of genetic diversity observed in central and northern Europe should reflect a rapid postglacial colonization. Results suggest that L. planeri originated within at least two distinct evolutionary lineages, rejecting the single origin hypothesis. The observed lack of taxa monophyly within lineage I may be the result of ongoing gene flow if the two taxa are alternate life-history forms of a single species. However, structure within lineage I is also consistent with the hypothesis of divergence of taxa after postglacial dispersion (around 2000 generations ago) with incomplete lineage sorting. Further testing of the alternative hypotheses is warranted. [source] Comparative phylogeography of eastern chipmunks and white-footed mice in relation to the individualistic nature of speciesMOLECULAR ECOLOGY, Issue 13 2006KEVIN C. ROWE Abstract Palaeoecological studies have demonstrated that ecological communities as a whole did not remain stable throughout the climatic fluctuations of the Quaternary. The result is that long-term associations of species cannot be inferred by contemporary associations in ecological communities. Therefore, the evolutionary significance of any contemporary ecological interactions among species and of the biotic community within which species have evolved also cannot be assumed from contemporary conditions. Comparative phylogeographic data provide a method to identify species within ecological communities that have shared biogeographic histories. We present an example of a long-term association between populations of two mammalian species, eastern chipmunks (Tamias striatus) and white-footed mice (Peromyscus leucopus), which are commonly associated with deciduous forest habitats. The distribution of mitochondrial DNA variation in T. striatus and P. leucopus from previously glaciated regions of the eastern United States support the hypothesis that, in at least part of their range, genetic lineages of the two species have expanded from similar population sources since the Last Glacial Maximum. In addition, the spatial concordance of genetic lineages of T. striatus and P. leucopus with the oak-savannah forest formations of Wisconsin and Illinois, suggest that populations associated with this community colonized the area in association with a set of arboreal species that comprise their deciduous forest habitat. [source] Genetic drift outweighs balancing selection in shaping post-bottleneck major histocompatibility complex variation in New Zealand robins (Petroicidae)MOLECULAR ECOLOGY, Issue 12 2004HILARY C. MILLER Abstract The Chatham Island black robin, Petroica traversi, is a highly inbred, endangered passerine with extremely low levels of variation at hypervariable neutral DNA markers. In this study we investigated variation in major histocompatibility complex (MHC) class II genes in both the black robin and its nonendangered relative, the South Island robin Petroica australis australis. Previous studies have shown that Petroica have at least four expressed class II B MHC genes. In this study, the sequences of introns flanking exon 2 of these loci were characterized to design primers for peptide-binding region (PBR) sequence analysis. Intron sequences were comprised of varying numbers of repeated units, with highly conserved regions immediately flanking exon 2. Polymerase chain reaction primers designed to this region amplified three or four sequences per black robin individual, and eight to 14 sequences per South Island robin individual. MHC genes are fitness-related genes thought to be under balancing selection, so they may be more likely to retain variation in bottlenecked populations. To test this, we compared MHC variation in the black robin with artificially bottlenecked populations of South Island robin, and with their respective source populations, using restriction fragment length polymorphism analyses and DNA sequencing of the PBR. Our results indicate that the black robin is monomorphic at class II B MHC loci, while both source and bottlenecked populations of South Island robin have retained moderate levels of variation. Comparison of MHC variation with minisatellite DNA variation indicates that genetic drift outweighs balancing selection in determining MHC diversity in the bottlenecked populations. However, balancing selection appears to influence MHC diversity over evolutionary timescales, and the effects of gene conversion are evident. [source] Plastid DNA variation in the Dactylorhiza incarnata/maculata polyploid complex and the origin of allotetraploid D. sphagnicola (Orchidaceae)MOLECULAR ECOLOGY, Issue 10 2003M. Hedrén Abstract To obtain further information on the polyploid dynamics of the the Dactylorhiza incarnata/maculata polyploid complex and the origin of the allotetraploid D. sphagnicola (Orchidaceae), plastid DNA variation was studied in 400 plants from from Sweden and elsewhere in Europe and Asia Minor by means of polymerase chain reaction,restriction fragment length polymorphisms (PCR-RFLPs) and sequencing. Allotetraploid taxa in Europe are known have evolved by multiple independent polyploidization events following hybridization between the same set of two distinct ancestral lineages. Most allotetraploids have inherited the plastid genome from parents similar to D. maculata sensu lato, which includes, e.g. the diploid D. fuchsii and the autotetraploid D. maculata sensu stricto. D. sphagnicola carries a separate plastid haplotype different from the one found in other allotetraploid taxa, which is in agreement with an independent origin from the parental lineages. Some of the remaining allotetraploids have local distributions and appear to be of postglacial origin, whereas still other allotetraploids may be of higher age, carrying plastid haplotypes that have not been encountered in present day representatives of the parental lineages. Introgression and hybridization between diploids and allotetraploids, and between different independently derived allotetraploids may further have contributed to genetic diversity at the tetraploid level. Overall, the Dactylorhiza polyploid complex illustrates how taxon diversity and genetic diversity may be replenished rapidly in a recently glaciated area. [source] How mitochondrial DNA diversity can help to understand the dynamics of wild-cultivated complexes.MOLECULAR ECOLOGY, Issue 12 2001The case of Medicago sativa in Spain Abstract In order to clarify the relationships (genetic exchange and shared ancestry) between natural and cultivated populations of alfalfa (Medicago sativa L.) in Spain, we investigated the patterns of mitochondrial DNA variation (characterized through restriction fragment length polymorphism) for 248 individuals in seven natural and six cultivated populations of this species. Mitochondrial variation was evidenced in both natural and cultivated populations of M. sativa. Among the seven mitotypes idengified in the species, two were specific of the natural populations, a result attesting the fact that the Spanish wild form of M. sativa is an original genetic pool compared to the cultivated one. Other mitotypes were observed in both natural and cultivated populations, suggesting the occurrence of gene flow through seeds from cultivated towards natural populations. Comparisons with previously gathered nuclear and phenotypic data give insights into the different evolutionary forces acting on the different kinds of Spanish natural populations examined so far. [source] Mitochondrial DNA variation and biogeography of eastern gorillasMOLECULAR ECOLOGY, Issue 9 2001M. I. Jensen-Seaman Abstract Mitochondrial DNA variation in 109 individuals from four populations of wild living gorillas in East Africa was ascertained by sequencing the first hypervariable segment of the control region, or ,d-loop', amplified from noninvasively collected hair and faeces. d- loop haplotypes from eastern gorillas fell into two distinct clades, each with low levels of genetic diversity; most observed haplotypes within each clade differing by only one or two mutations. Both clades show evidence of population bottlenecks in the recent past, perhaps concomitant with the tropical forest reduction and fragmentation brought on by global cooling and drying associated with the last glacial maximum. [source] Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variationMOLECULAR ECOLOGY, Issue 4 2001T. L. King Abstract Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5,37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available. [source] The comparative phylogeography of Neotropical mammals: patterns of intraspecific mitochondrial DNA variation among bats contrasted to nonvolant small mammalsMOLECULAR ECOLOGY, Issue 9 2000A. D. Ditchfield Abstract The major aim of this study was to compare the phylogeographic patterns of codistributed bats and small nonvolant Neotropical mammals. Cytochrome b sequences (mitochondrial DNA) were obtained for a total of 275 bats representing 17 species. The tissue samples were collected in coastal Brazil, and were available from Mexico and the Guyana. The study concentrates on four species (Artibeus lituratus, Carollia perspicillata, Sturnira lilium and Glossophaga soricina) which were well represented. The other 13 species were sequenced to test the generality of the patterns observed. In general, sequence divergence values within species were low, with most bat species presenting less than 4% average sequence divergence, and usually between 1 and 2.5%. Clades of highly similar haplotypes enjoyed broad distribution on a continental scale. These clades were not usually geographically structured, and at a given locality the number of haplotypes was high (8,10). As distance increased, some moderately divergent clades were found, although the levels of divergence were low. This suggests a geographical effect that varied depending on species and scale. Small nonvolant mammals almost invariably have high levels of sequence divergence (> 10%) for cytochrome b over much shorter distances (< 1000 km). The grain of intraspecific variation found in small nonvolant mammals is much finer than in bats. Low levels of geographical structuring cannot be attributed to a slower evolutionary rate of bat DNA in relation to other mammalian taxa. The phylogeographic pattern of bats contrasts sharply with the pattern found for Neotropical rodents and marsupials. [source] Chloroplast diversity in Vouacapoua americana (Caesalpiniaceae), a neotropical forest treeMOLECULAR ECOLOGY, Issue 9 2000C. Dutech Abstract The chloroplast genome has been widely used to describe genetic diversity in plant species. Its maternal inheritance in numerous angiosperm species and low mutation rate are suitable characters when inferring historical events such as possible recolonization routes. Here we have studied chloroplast DNA variation using PCR,RFLP (polymerase chain reaction,restriction fragment length polymorphism) with seven pairs of primers and four restriction enzymes in 14 populations of Vouacapoua americana (Caesalpiniaceae) a neotropical tree sampled throughout French Guiana. Population diversity (Hs), total gene diversity (Ht) and differentiation among populations (GST) were estimated using Nei's method as 0.09, 0.87 and 0.89, respectively. This is consistent with the limited gene flow associated with synzoochory in this species. The genetic structure observed in the north of French Guiana suggests that historical events such as contractions and recent recolonizations have had a large impact on the distribution of genetic diversity in this species. [source] Climate and Growth Form: The Consequences for Genome Size in PlantsPLANT BIOLOGY, Issue 5 2005D. Ohri Abstract: The adaptive significance of nuclear DNA variation in angiosperms is still widely debated. The discussion mainly revolves round the causative factors influencing genome size and the adaptive consequences to an organism according to its growth form and environmental conditions. Nuclear DNA values are now known for 3874 angiosperm species (including 773 woody species) from over 219 families (out of a total of 500) and 181 species of woody gymnosperms, representing all the families. Therefore, comparisons have been made on not only angiosperms, taken as a whole, but also on the subsets of data based on taxonomic groups, growth forms, and environment. Nuclear DNA amounts in woody angiosperms are restricted to less than 23.54 % of the total range of herbaceous angiosperms; this range is further reduced to 6.8 % when woody and herbaceous species of temperate angiosperms are compared. Similarly, the tropical woody dicots are restricted to less than 50.5 % of the total range of tropical herbaceous dicots, while temperate woody dicots are restricted to less than 10.96 % of the total range of temperate herbaceous dicots. In the family Fabaceae woody species account for less than 14.1 % of herbaceous species. Therefore, in the total angiosperm sample and in subsets of data, woody growth form is characterized by a smaller genome size compared with the herbaceous growth form. Comparisons between angiosperm species growing in tropical and temperate regions show highly significant differences in DNA amount and genome size in the total angiosperm sample. However, when only herbaceous angiosperms were considered, significant differences were obtained in DNA amount, while genome size showed a non-significant difference. An atypical result was obtained in the case of woody angiosperms where mean DNA amount of tropical species was almost 25.04 % higher than that of temperate species, which is because of the inclusion of 85 species of woody monocots in the tropical sample. The difference becomes insignificant when genome size is compared. Comparison of tropical and temperate species among dicots and monocots and herbaceous monocots taken separately showed significant differences both in DNA amount and genome size. In herbaceous dicots, while DNA amount showed significant differences the genome size varies insignificantly. There was a non-significant difference among tropical and temperate woody dicots. In three families, i.e., Poaceae, Asteraceae, and Fabaceae the temperate species have significantly higher DNA amount and genome size than the tropical ones. Woody gymnosperms had significantly more DNA amount and genome size than woody angiosperms, woody eudicots, and woody monocots. Woody monocots also had significantly more DNA amount and genome size than woody eudicots. Lastly, there was no significant difference between deciduous and evergreen hardwoods. The significance of these results in relation to present knowledge on the evolution of genome size is discussed. [source] Expression of the porcine adrenergic receptor beta 2 gene in longissimus dorsi muscle is affected by cis -regulatory DNA variationANIMAL GENETICS, Issue 1 2009E. Muráni Summary The beta-2 adrenergic receptor (AR) mediates metabolic actions of catecholamines, including glycogenolysis, lipolysis and proteolysis, in muscle and adipose tissue. Factors influencing the density of beta-2 ARs thus might affect carcass composition and meat quality. One such factor might represent cis -regulatory DNA variation affecting mRNA expression of the adrenergic receptor beta 2 (ADRB2) gene in relevant tissues. To identify potential cis -regulatory DNA variation of porcine ADRB2, we comparatively sequenced part of the 5, flanking region and identified 10 single nucleotide polymorphisms (SNPs). The SNP at position g.673C>T (AF000134) resides in an evolutionarily conserved region (ECR) in an in silico predicted androgen response element. Quantification of total transcript levels and allelic expression imbalance (AEI) revealed significant variability in mRNA expression of ADRB2 in longissimus dorsi muscle of slaughter pigs, partly attributable to cis -regulatory DNA variation. However, the g.673C>T SNP has, in the given temporo-spatial context, no significant effect but is apparently in linkage disequilibrium with the causal cis -regulatory DNA variant. We used the g.673C>T SNP as a marker to study the association of ADRB2 variation with carcass and meat quality in four commercial lines. We found association with the pH of loin at 45 min and 24 h postmortem (p.m.) and with the pH of ham at 24 h p.m. Supporting evidence for ADRB2 as a candidate gene for pork quality is provided by our assignment of the gene to the telomeric end of the q arm of porcine chromosome 2, where several quantitative trait loci for meat quality were reported. [source] Phylogenetic relationships within Plantago (Plantaginaceae): evidence from nuclear ribosomal ITS and plastid trnL-F sequence dataBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2002NINA RØNSTED A molecular phylogenetic study of Plantago L. (Plantaginaceae) analysed nucleotide variation in the internal transcribed spacers (ITS) of nuclear ribosomal and plastid trnL-F regions. Included are 57 Plantago species, with two Aragoa species as the ingroup and three Veronica species as the outgroup. Phylogenetic analysis using maximum parsimony identified five major clades, corresponding to the taxonomic groups Plantago subgenera Plantago, Coronopus, Psyllium, Littorella and Bougueria. Aragoa is sister to genus Plantago. Plantago subgenus Littorella is sister to the other subgenera of Plantago. The results are in general correlated with a morphological phylogenetic study and iridoid glucoside patterns, but Plantago subgenus Albicans is paraphyletic and should be included in Plantago subgenus Psyllium sensu lato to obtain a monophyletic clade with six sections. Plantago section Hymenopsyllium is more closely related to section Gnaphaloides than to section Albicans. Plantago subgenus Bougueria is sister to subgenus Psyllium s.l. section Coronopus in Plantago subgenus Coronopus is subdivided in two series. Only some of the sections can be resolved into series. DNA variation within genus Plantago is high, a result that would not have been predicted on the basis of morphology, which is relatively stereotyped. If we calibrate a molecular clock based on the divergence of P. stauntoni, endemic to New Amsterdam in the southern Indian Ocean, we calculate the time of the split between Plantago and Aragoa to be 7.1 million years ago, which is congruent with the fossil record. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 2002, 139, 323,338. [source] Functional analysis helps to clarify the clinical importance of unclassified variants in DNA mismatch repair genes,HUMAN MUTATION, Issue 11 2007Jianghua Ou Abstract Hereditary nonpolyposis colorectal cancer (HNPCC) or Lynch syndrome is caused by DNA variations in the DNA mismatch repair (MMR) genes MSH2, MLH1, MSH6, and PMS2. Many of the mutations identified result in premature termination of translation and thus in loss-of-function of the encoded mutated protein. These DNA variations are thought to be pathogenic mutations. However, some patients carry other DNA mutations, referred to as unclassified variants (UVs), which do not lead to such a premature termination of translation; it is not known whether these contribute to the disease phenotype or merely represent rare polymorphisms. This is a major problem which has direct clinical consequences. Several criteria can be used to classify these UVs, such as: whether they segregate with the disease within pedigrees, are absent in control individuals, show a change of amino acid polarity or size, provoke an amino acid change in a domain that is evolutionary conserved and/or shared between proteins belonging to the same protein family, or show altered function in an in vitro assay. In this review we discuss the various functional assays reported for the HNPCC-associated MMR proteins and the outcomes of these tests on UVs identified in patients diagnosed with or suspected of having HNPCC. We conclude that a large proportion of MMR UVs are likely to be pathogenic, suggesting that missense variants of MMR proteins do indeed play a role in HNPCC. Hum Mutat 28(11), 1047,1054, 2007. © 2007 Wiley-Liss, Inc. [source] Inherited defects of coagulation Factor V: the thrombotic sideJOURNAL OF THROMBOSIS AND HAEMOSTASIS, Issue 1 2006H. L. VOS Summary., DNA variations in the Factor V gene have played a major role in thrombosis research ever since the discovery of Factor V Leiden. Here, all relatively common DNA variations in the coding regions of the Factor V gene are discussed. Many of them have been associated with venous thrombosis or related diseases. However, most variations have been studied separately, without taking the presence of other variations in the same gene into account. This means that their association with disease should be interpreted with caution, as it may reflect linkage with another variation. An approach in which a haplotype-based analysis of the Factor V gene is combined with in vitro assays of recombinant proteins is advocated. Finally, a possible reason for the relatively polymorphic nature of the Factor V protein is discussed. [source] Mitochondrial DNA patterns in the Iberian Northern plateau: Population dynamics and substructure of the Zamora provinceAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 4 2010Luis Alvarez Abstract Several studies have shown the importance of recent events in the configuration of the genetic landscape of a specific territory. In this context, due to the phenomena of repopulation and demographic fluctuations that took place in recent centuries, the Iberian Northern plateau is a very interesting case study. The main aim of this work is to check if recent population movements together with existing boundaries (geographical and administrative) have influenced the current genetic composition of the area. To accomplish this general purpose, mitochondrial DNA variations of 214 individuals from a population located in the Western region of the Iberian Northern plateau (the province of Zamora) were analyzed. Results showed a typical Western European mitochondrial DNA haplogroup composition. However, unexpected high frequencies of U5, HV0, and L haplogroups were found in some regions. The analyses of microdifferentiation showed that there are differences between regions, but no geographic substructure organization can be noticed. It can be stated that the differences observed in the genetic pool of the sampled area at regional level results from the mixture of different populations carrying new lineages into this area at different points in history. Am J Phys Anthropol 142:531,539, 2010. © 2010 Wiley-Liss, Inc. [source] Prehistorical East,West admixture of maternal lineages in a 2,500-year-old population in XinjiangAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 2 2010Fan Zhang Abstract As an area of contact between Asia and Europe, Central Asia witnessed a scenario of complex cultural developments, extensive migratory movements, and biological admixture between West and East Eurasians. However, the detanglement of this complexity of diversity requires an understanding of prehistoric contacts of the people from the West and the East on the Eurasia continent. We demonstrated the presence of genetic admixture of West and East in a population of 35 inhabitants excavated in Gavaerk in southern Xinjiang and dated 2,800,2,100 years before present by analyzing their mitochondrial DNA variations. This result indicates that the initial contact of the East and the West Eurasians occurred further east than Central Asia as early as 2,500 years ago. Am J Phys Anthropol, 2010. © 2009 Wiley-Liss, Inc. [source] Integration of Ranked Lists via Cross Entropy Monte Carlo with Applications to mRNA and microRNA StudiesBIOMETRICS, Issue 1 2009Shili Lin Summary One of the major challenges facing researchers studying complex biological systems is integration of data from -omics platforms. Omic-scale data include DNA variations, transcriptom profiles, and RAomics. Selection of an appropriate approach for a data-integration task is problem dependent, primarily dictated by the information contained in the data. In situations where modeling of multiple raw datasets jointly might be extremely challenging due to their vast differences, rankings from each dataset would provide a commonality based on which results could be integrated. Aggregation of microRNA targets predicted from different computational algorithms is such a problem. Integration of results from multiple mRNA studies based on different platforms is another example that will be discussed. Formulating the problem of integrating ranked lists as minimizing an objective criterion, we explore the usage of a cross entropy Monte Carlo method for solving such a combinatorial problem. Instead of placing a discrete uniform distribution on all the potential solutions, an iterative importance sampling technique is utilized "to slowly tighten the net" to place most distributional mass on the optimal solution and its neighbors. Extensive simulation studies were performed to assess the performance of the method. With satisfactory simulation results, the method was applied to the microRNA and mRNA problems to illustrate its utility. [source] | |||||||||||||||||||||||||||||||