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Genetic Diversity (genetic + diversity)
Kinds of Genetic Diversity Terms modified by Genetic Diversity Selected AbstractsA METAPOPULATION PERSPECTIVE ON GENETIC DIVERSITY AND DIFFERENTIATION IN PARTIALLY SELF-FERTILIZING PLANTSEVOLUTION, Issue 12 2002Pärk. Ingvarsson Abstract., Partial self-fertilization is common in higher plants. Mating system variation is known to have important consequences for how genetic variation is distributed within and among populations. Selfing is known to reduce effective population size, and inbreeding species are therefore expected to have lower levels of genetic variation than comparable out crossing taxa. However, several recent empirical studies have shown that reductions in genetic diversity within populations of inbreeding species are far greater than the expected reductions based on the reduced effective population size. Two different processes have been argued to cause these patterns, selective sweeps (or hitchhiking) and background selection. Both are expected to be most effective in reducing genetic variation in regions of low recombination rates. Selfing is known to reduce the effective recombination rate, and inbreeding taxa are thus thought to be particularly vulnerable to the effects of hitchhiking or background selection. Here I propose a third explanation for the lower-than-expected levels of genetic diversity within populations of selfing species; recurrent extinctions and recolonizations of local populations, also known as metapopulation dynamics. I show that selfing in a metapopulation setting can result in large reductions in genetic diversity within populations, far greater than expected based the lower effective population size inbreeding species is expected to have. The reason for this depends on an interaction between selfing and pollen migration. [source] GENETIC DIVERSITY AND INTROGRESSION IN TWO CULTIVATED SPECIES (PORPHYRA YEZOENSIS AND PORPHYRA TENERA) AND CLOSELY RELATED WILD SPECIES OF PORPHYRA (BANGIALES, RHODOPHYTA),JOURNAL OF PHYCOLOGY, Issue 2 2009Kyosuke Niwa We investigated the genetic variations of the samples that were tentatively identified as two cultivated Porphyra species (Porphyra yezoensis Ueda and Porphyra tenera Kjellm.) from various natural populations in Japan using molecular analyses of plastid and nuclear DNA. From PCR-RFLP analyses using nuclear internal transcribed spacer (ITS) rDNA and plastid RUBISCO spacer regions and phylogenetic analyses using plastid rbcL and nuclear ITS-1 rDNA sequences, our samples from natural populations of P. yezoensis and P. tenera showed remarkably higher genetic variations than found in strains that are currently used for cultivation. In addition, it is inferred that our samples contain four wild Porphyra species, and that three of the four species, containing Porphyra kinositae, are closely related to cultivated Porphyra species. Furthermore, our PCR-RFLP and molecular phylogenetic analyses using both the nuclear and plastid DNA demonstrated the occurrence of plastid introgression from P. yezoensis to P. tenera and suggested the possibility of plastid introgression from cultivated P. yezoensis to wild P. yezoensis. These results imply the importance of collecting and establishing more strains of cultivated Porphyra species and related wild species from natural populations as genetic resources for further improvement of cultivated Porphyra strains. [source] Phylogenetic Comparative Methods Strengthen Evidence for Reduced Genetic Diversity among Endangered TetrapodsCONSERVATION BIOLOGY, Issue 5 2010PATRICK A. FLIGHT evolución de la historia de vida; extinción; heterocigosidad de proteínas; regresión filogenética; tamaño poblacional efectivo Abstract:,The fitness of species with little genetic diversity is expected to be affected by inbreeding and an inability to respond to environmental change. Conservation theory suggests that endangered species will generally demonstrate lower genetic diversity than taxa that are not threatened. This hypothesis has been challenged because the time frame of anthropogenic extinction may be too fast to expect genetic factors to significantly contribute. I conducted a meta-analysis to examine how genetic diversity in 894 tetrapods correlates with extinction threat level. Because species are not evolutionarily independent, I used a phylogenetic regression framework to address this issue. Mean genetic diversity of tetrapods, as assessed by protein heterozygosity, was 29.7,31.5% lower on average in threatened species than in their nonthreatened relatives, a highly significant reduction. Within amphibians as diversity decreased extinction risk increased in phylogenetic models, but not in nonphylogenetic regressions. The effects of threatened status on diversity also remained significant after accounting for body size in mammals. These results support the hypothesis that genetic effects on population fitness are important in the extinction process. Resumen:,Se espera que la adaptabilidad de una especie con poca diversidad genética sea afectada por la endogamia y una incapacidad para responder a cambios ambientales. La teoría de la conservación sugiere que las especies en peligro generalmente muestran menor diversidad genética que taxa que no están amenazados. Esta hipótesis ha sido cuestionada porque el período de tiempo de la extinción antropogénica puede ser muy rápido para esperar que los factores genéticos contribuyan significativamente. Realice un meta-análisis para examinar cómo se correlaciona la diversidad genética de 894 tetrápodos con el nivel de amenaza de extinción. Debido a que las especies no son independientes evolutivamente, utilice un marco de regresión filogenética para abordar este tema. La media de la diversidad genética de tetrápodos, medida como la heterocigosidad de proteínas, fue 29.7,31.5% menor en las especies amenazadas que en sus parientes no amenazados, una reducción altamente significativa. En anfibios, a medida que disminuía la diversidad el riesgo de extinción incrementaba en los modelos filogenéticos, pero no en las regresiones no filogenéticas. El efecto del estatus de amenaza sobre la biodiversidad también permaneció significativo después de considerar el tamaño corporal de mamíferos. Estos resultados dan soporte a la hipótesis de que los efectos genéticos sobre la adaptabilidad de la población son importantes en el proceso de extinción. [source] Effectiveness of Conservation Targets in Capturing Genetic DiversityCONSERVATION BIOLOGY, Issue 1 2003Maile C. Neel We used empirical data from four rare plant taxa to assess these consequences in terms of how well allele numbers ( all alleles and alleles occurring at a frequency openface>0.05 in any population ) and expected heterozygosity are represented when different numbers of populations are conserved. We determined sampling distributions for these three measures of genetic diversity using Monte Carlo methods. We assessed the proportion of alleles included in the number of populations considered adequate for conservation, needed to capture all alleles, and needed to meet an accepted standard of genetic-diversity conservation of having a 90,95% probability of including all common alleles. We also assessed the number of populations necessary to obtain values of heterozygosity within ±10% of the value obtained from all populations. Numbers of alleles were strongly affected by the number of populations sampled. Heterozygosity was only slightly less sensitive to numbers of populations than were alleles. On average, currently advocated conservation intensities represented 67,83% of all alleles and 85,93% of common alleles. The smallest number of populations to include all alleles ranged from 6 to 17 ( 42,57% ), but <0.2% of 1000 samples of these numbers of populations included them all. It was necessary to conserve 16,29 ( 53,93% ) of the sampled populations to meet the standard for common alleles. Between 20% and 64% of populations were needed to reliably represent species-level heterozygosity. Thus, higher percentages of populations are needed than are currently considered adequate to conserve genetic diversity if populations are selected without genetic data. Resumen: Cualquier acción de conservación que preserve algunas poblaciones y no otras tendrá consecuencias genéticas. Utilizamos datos empíricos de cuatro taxones de plantas raras para evaluar estas consecuencias en términos de lo bien representados que están los números de alelos ( todos los alelos ocurriendo a una frecuencia>0.05 en cualquier población ) y la heterocigosidad esperada cuando se conservan diferentes números de poblaciones. Las distribuciones de muestreo de estas tres medidas de la diversidad genética fueron determinadas utilizando métodos Monte Carlo. Evaluamos la proporción de alelos incluida en números de poblaciones: consideradas adecuadas para la conservación; requeridas para capturar todos los alelos; y las requeridas para alcanzar un estándar de conservación de diversidad genética aceptable del 90,95% de probabilidad de incluir todos los alelos comunes. También evaluamos el número de poblaciones necesarias para obtener valores de heterocigosidad que caigan dentro de ±10% del valor obtenido de todas las poblaciones. Los números de alelos fueron afectados significativamente por el número de poblaciones muestreadas. La heterocigosidad solo fue ligeramente menos sensible a los números de poblaciones de lo que fueron los alelos. Las intensidades de conservación propugnadas actualmente representaron en promedio el 67,83% de todos los alelos y el 85,93% de los alelos comunes. El menor número de poblaciones para incluir a todos los alelos varió de 6 a 17 ( 42,57% ), pero <0.2% de 1000 muestras de esos números de poblaciones los incluyó a todos. Fue necesario conservar de 16 a 29 ( 53,93% ) de las poblaciones muestreadas para alcanzar el estándar para los alelos comunes. Se requirió entre 20% y 64% de las poblaciones para representar la heterocigosidad a nivel de especie confiablemente. Por lo tanto, se requieren mayores porcentajes de poblaciones que los actualmente considerados adecuados para conservar la diversidad genética si las poblaciones son seleccionadas sin datos genéticos. [source] The Speke's Gazelle Breeding Program as an Illustration of the Importance of Multilocus Genetic Diversity in Conservation Biology: Response to Kalinowski et al.CONSERVATION BIOLOGY, Issue 4 2002Alan R. Templeton First page of article [source] Genetic Diversity and Tests of the Hybrid Origin of the Endangered Yellow LarkspurCONSERVATION BIOLOGY, Issue 6 2001Jason A. Koontz The total number of individuals in these two populations is estimated to be <100. We used allozyme and random amplified polymorphic DNA ( RAPD) markers to (1) assess levels and patterns of genetic diversity in one wild population and two cultivated populations and (2) test the hypothesis that D. luteum is of hybrid origin between D. decorum and D. nudicaule. These data will be used to aid in developing a management plan to conserve the species. The wild population maintains high levels of genetic diversity. Genetic data indicate that both cultivated populations, especially the north Sonoma population, have several allozymes and RAPD markers not found in the wild population and could be used to establish new populations of D. luteum or to enhance the diversity and size of the wild population. The allozyme data did not reveal any fixed differences between D. decorum and D. nudicaule, although allele frequencies of the putative parental populations differed. At these loci, D. luteum resembled D. nudicaule more than D. decorum . Many unique RAPD markers distinguish each of the three species. The diagnostic markers from populations of D. nudicaule and D. decorum were not additive in the putative hybrid, and these data indicate that D. luteum is not of recent hybrid origin. Conservation of the yellow larkspur should include strategies that use the cultivated populations of D. luteum, but hybridizing D. decorum and D. nudicaule to "recreate"D. luteum is not recommended. Resumen:Delphidium luteum ( Ranunculaceae), un delfinio en peligro de extinción, está restringido a dos poblaciones silvestres cerca de Bodega Bay, California. Se estima que el total de individuos en estas dos poblaciones es de <100. Utilizamos marcadores de alozimas y RAPD para (1) evaluar los niveles y patrones de diversidad genética en una población silvestre y dos poblaciones cultivadas y (2) probar la hipótesis de que D. luteum es de origen híbrido entre D. decorum y D. nudicaule. Estos datos serán utilizados para ayudar a desarrollar un plan de manejo para conservar la especie. La población silvestre mantiene altos niveles de diversidad genética. Los datos genéticos indican que ambas poblaciones cultivadas, especialmente en la población de Sonoma norte, tienen varias alozimas y marcadores RAPD que no se encuentran en poblaciones silvestres y podrían utilizarse para establecer nuevas poblaciones de D. luteum o reforzar la diversidad y tamaño de la población silvestre. Los datos de alozimas no revelaron diferencias fijas entre D. decorum y D. nudicaule, aunque las frecuencias alélicas de las poblaciones parentales putativas fueron diferentes. En estos loci, D. luteum fue más semejante a D. nudicaule que a D. decorum. Muchos marcadores RADP únicos distinguen a cada una de las tres especies. Los marcadores diagnóstico de poblaciones de D. decorum y D. nudicaule no fueron aditivos en el híbrido putativo, y estos datos indican que D. luteum no es de origen híbrido reciente. La conservación del delfinio amarillo debería incluir estrategias que usen las poblaciones cultivadas de D. luteum; sin embargo, no se recomienda la hibridación de D. decorum y D. nudicaule para "recrear" a D. luteum. [source] Genetic Diversity and Association Analysis for Salinity Tolerance, Heading Date and Plant Height of Barley Germplasm Using Simple Sequence Repeat MarkersJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 8 2008Lilia Eleuch Abstract The objective of this study was to investigate the genetic diversity of barley accessions. Additionally, association trait analysis was conducted for grain yield under salinity, heading date and plant height. For this purpose, 48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat (SSR) markers. Four of the 22 markers (Bmac316, scssr03907, HVM67 and Bmag770) were able to differentiate all barley genotypes. Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region. The genotypes used in this study have been evaluated for agronomic performance in different environments. Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 (2H, bin 13) in two different environments with common significant alleles (175, 177), whereas the HVHOTR1 marker (2H, bin 3) was only significant in Sakhar_Egypt with alleles size being 158 and 161. Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmac0415 markers in three different agro climatic locations, whereas HVCMA, scssr00103 and HVM67 were linked to heading date in the Egyptian environment only. The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398. [source] Genetic Diversity: Geographical Distribution and Toxin Profiles of Microcystis Strains (Cyanobacteria) in ChinaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 3 2007Zhong-Xing Wu Abstract Twenty strains of Microcystis Kütz were isolated from different freshwater bodies in China to analyze the diversity, geographical distribution and toxin profiles. Based on whole-cell polymerase chain reaction of cpcBA-IGS nucleotide sequence, the derived neighbor-joining (NJ) and maximum parsimony (MP) trees indicate that these strains of Microcystis can be divided into four clusters. The strains from south, middle and north region of China formed distinct lineages, suggesting high diversity and a geographical distribution from south to north locations. Moreover, the results being indicating high variable genotypes of the strains of the Microcystis strains from the same lake show that there is high diversity of Microcystis within a water bloom population. Comparing the results of the present study with those reported for compared with 43 strains of Microcystis from other locations, also reveals Chinese strains have high similarity with those from regions in the North Hemispherical. This suggests that the Microcystis strains in the world might have a geographical distribution. Analysis of 30 strains using the primers MCF/TER and TOX2P/TOX2M showed that there was no correlation between the gene of cpcBA-IGS and the presence of mcy. Toxic strains were founded to be predominant in different water bodies throughout China. [source] ISSR Analysis of the Genetic Diversity of the Endangered Species Sinopodophyllum hexandrum (Royle) Ying from Western Sichuan Province, ChinaJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 10 2006Meng Xiao Abstract Sinopodophyllum hexandrum (Royle) Ying is an important medicinal and endangered species. Inter-simple sequence repeats (ISSR) analysis was conducted on seven natural populations from western Sichuan Province to investigate the genetic diversity of S. hexandrum. Leaf samples of 140 individuals were collected. Of the 139 discernible fragments generated by 12 selected primers (among 100 primers), 54 appeared to be polymorphic. The percentage of polymorphic bands (PPB) was 38.85% at the species level, and PPB within a population ranged from 7.91% to 23.74%. Low levels of genetic variation (He= 0.092, Ho= 0.142) and high levels of genetic differentiation among the populations (Gst= 62.25%) was detected on the basis of results from POPGENE and analysis of molecular variance (AMOVA), respectively. Furthermore, the limited gene flow (Nm= 0.361) may result from biological characteristics, such as self-pollination and short distance seed dispersal. Based on the genetic and ecological information available for S. hexandrum, we propose some appropriate strategies for the conservation of the endangered medicinal species in this region, namely rescuing and conserving the core populations for in situ conservation and sampling and preserving more populations with fewer individuals from each population for ex situ conservation. (Managing editor: Li-Hui Zhao) [source] Genetic Diversity of Landraces in Gossypium arboreum L. Race sinense Assessed with Simple Sequence Repeat MarkersJOURNAL OF INTEGRATIVE PLANT BIOLOGY, Issue 9 2006Wang-Zhen Guo Abstract Asiatic cotton (Gossypium arboreum L.) is an "Old World" cultivated cotton species, the sinense race of which is planted extensively in China. This species is still used in the current tetraploid cotton breeding program as an elite germplasm line, and is also used as a model for genomic research in Gossypium. In the present study, 60 cotton microsatellite markers, averaging 4.6 markers for each A-genome chromosome, were chosen to assess the genetic diversity of 109 accessions. These included 106 G. arboreum landraces, collected from 18 provinces throughout four Asiatic cotton-growing regions in China. A total of 128 alleles were detected, with an average of 2.13 alleles per locus. The largest number of alleles, as well as the maximum number of polymorphic loci, was detected in the A03 linkage group. No polymorphic alleles were detected on chromosome 10. The polymorphism information content for the 22 polymorphic microsatellite loci varied from 0.52 to 0.98, with an average of 0.89. Genetic diversity analysis revealed that the landraces in the Southern region had more genetic variability than those from the other two regions, and no significant difference was detected between landraces in the Yangtze and the Yellow River Valley regions. These findings are consistent with the history of sinense introduction, with the Southern region being the presumed center of origin for Chinese Asiatic cotton, and with subsequent northeastward extension to the Yangtze and Yellow River Valleys. Cluster analysis, based on simple sequence repeat data for 60 microsatellite loci, clearly differentiated Vietnamese and G. herbaceum landraces from the sinense landrace. No relationship between inter-variety similarity and geographical ecological region was observed. The present findings indicate that the Southern region landraces may have been directly introduced into the provinces in the middle and lower Yangtze River Valley, where Asiatic cotton was most extensively grown, and further race sinense crops were subsequently produced. (Managing editor: Ya-Qin Han) [source] Assessment of Genetic Diversity in Thai Isolates of Pyricularia grisea by Random Amplification of Polymorphic DNAJOURNAL OF PHYTOPATHOLOGY, Issue 4 2008P. Sirithunya Abstract One hundred and seventy-four isolates of Pyricularia grisea were collected from various hosts such as barley, rice, weed and wild rice in Thailand. Seven arbitrary decamer primers from the set of University of British Columbia were employed and nine lineages were classified. Lineages B, C and H were predominant, contributing up to 70% of total pathogens in this study. Analysis showed that the distribution of each lineage differs from the predominant lineages across Thailand in such that other lineages were restricted in particular area. For instance, lineage A was limited only in southern Thailand, whereas wide distribution of lineages B and C reflected an influence of both biological and physical effects on pathogen variation. Principal component analysis resulted in a total of four groups of blast pathogen with small distinctions between barley-, rice-, weed- and wild rice-infected blast. Bridging relationships occurred among border isolates of weed and rice blast suggesting a chance of migrations between hosts. Higher diversity was observed in northern, north-eastern and central Thailand while eastern and southern parts were rather low. Genetic diversity indices elucidated an abundance of pathogen lineages existing in northern Thailand suggesting that it should be the centre of diversity. [source] Genetic Diversity of Cryphonectria hypovirus 1 in China, Japan and ItalyJOURNAL OF PHYTOPATHOLOGY, Issue 11-12 2007F.-X. Liu Abstract The aim of this study was to examine the origin of Cryphonectria hypovirus 1 (CHV1) which infects chestnut blight fungus, Cryphonectria parasitica. The genetic diversity of 39 CHV1 isolates from China, Japan and Italy was assessed by combining sequencing and restriction fragment length polymorphic (RFLP) experiments. Based on their partial sequences, 26 CHV1 isolates within 26 haplotypes were grouped into three subtypes. The 17 viruses from China were distributed between subtypes I and III, while all four of the isolates from Japan were subtype II. Of the five isolates from Italy, four were subtype I, and one (IT 192) was subtype III. Our analysis of the geographic distribution of the isolates indicated that all but one of the Chinese subtype III CHV1s are present in northern China; meanwhile all but three of the Chinese subtype I CHV1s are present in South China. Unlike in Europe where there is one predominant CHV1 subtype, our distribution analysis indicates that there has been gene flow between the populations in Asia. Cluster analysis based on the RFLP banding patterns showed that the viral isolates could be separated into four clusters. Most of the viral isolates (29 of 39, 74.4%) were grouped into one large cluster. Greater genetic diversity was observed among the CHV1s from China than among those from Japan and Italy. The Italian isolates were genetically more similar to the Japanese and South Chinese isolates than to the North Chinese isolates, indicating that CHV1 in Italy may have originated from Japan and/or South China. [source] Estimating Genetic Diversity in Durum and Bread Wheat Cultivars from Turkey using AFLP and SAMPL MarkersPLANT BREEDING, Issue 1 2008S. Alt Abstract Since 1925, more than 100 wheat varieties were developed and released in Turkey, and many more were introduced from abroad, but no systematic analysis of their genetic diversity has been performed yet. In this research, a total of 34 domestic and foreign cultivars (12 durum and 22 bread wheats), released in Turkey between 1936 and 2000, were fingerprinted by means of five amplified fragment length polymorphism and three selective amplification of microsatellite polymorphic loci (SAMPL) primer combinations, to evaluate their genetic variation and to determine the existence of cultivar-specific bands. Among the 344 amplicons scored, 214 were polymorphic. The primer combination EACG/MAGG yielded the highest number and the primer combination SAMPL,6/M AGA produced the lowest number of polymorphic bands. Most cultivars were molecularly very similar, although a few distinct ones (the durum wheat ,Kunduru,1149' and the bread wheat ,,kizce,96') were also identified. Seven cultivar-specific markers for different bread wheat cultivars (,Golia', ,Seri,82', ,Adana,99', ,Pandas' and ,Sertak,52') and six cultivar-specific markers for durum wheat cv ,Kunduru' were observed. Our results show that genetic diversity among old and present,day wheat cultivar commonly grown in Turkey is limited. [source] Genetic Diversity in Restoration Materials and the Impacts of Seed Collection in Colorado's Restoration Plant Production IndustryRESTORATION ECOLOGY, Issue 3 2007Sierra L. Smith Abstract The ever increasing demand for native plants and seed for use in restoration and revegetation has created a sizable industry. The large-scale production and planting of native plants have given rise to a suite of ecological concerns including collection impacts, genetic diversity, and provenance. This study examines the practices and beliefs of 12 restoration plant production companies in Colorado with regard to arising ecological issues and identifies where further research is needed. We found that native seed collection in Colorado was largely unregulated and unmonitored and impacts were unknown. Maintaining genetic diversity in restoration materials is costly and does not have universal support. The use of provenance material (or local ecotypes) was hotly contested with strong and sound arguments on both sides of the issue. Procurement of pure ecotypes was difficult because of the variety of institutions involved in production and complications such as artificial selection and cross-pollination. [source] Limited Reintroduction Does Not Always Lead to Rapid Loss of Genetic Diversity: An Example from the American Chestnut (Castanea dentata; Fagaceae)RESTORATION ECOLOGY, Issue 3 2007Sarah A. M. Pierson Abstract In restoring species, reasons for introducing limited numbers of individuals at different locations include costs of introduction and maintenance, limited founder supply, and risk "bet hedging." However, populations initiated from few founders may experience increased genetic drift, inbreeding, and diversity loss. We examined the genetic diversity of an isolated stand of more than 5,000 American chestnut trees relative to that of the 9 surviving stand founders (out of 10 total) planted in the 1880s. We used minisatellite DNA probes to reveal 84 genetic markers (circa 24 loci) among the nine founders, and their genetic diversity was compared with three separate plots of descendant trees, as well as with two natural stands. The descendants were circa 7.3% more heterozygous than the founders (mean estimated H= 0.556 vs. 0.518, respectively; p < 0.0001). Genetic differentiation was not pronounced (FST < 0.031), and no markers, including those at low frequency among the founders, were lost in the descendants. The founders and natural transects were not significantly different in H or similarity (mean proportion of bands shared). Special planting or mating protocols for establishment of a vigorous American chestnut population from a low number of founders may not be required to avoid strong effects of genetic drift and inbreeding. These results demonstrate that loss of genetic diversity following reintroduction of a limited number of founders is not always inevitable, such as this case where the species is highly outcrossing, expression of heterozygous advantage may occur, the original founders remain as gene contributors over generations, and the establishing population expands constantly and rapidly. [source] Genetic Diversity of Populations of Monilinia fructicola (Fungi, Ascomycota, Helotiales) from ChinaTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 2 2010JIN-YAN FAN ABSTRACT. The genetic variation among 128 isolates of Monilinia fructicola (Fungi, Ascomycota, Helotiales) from China was analyzed using Inter-Simple Sequence Repeat (ISSR) markers and compared with those of samples from California, USA and New Zealand. A total of 72 reproducible DNA fragments were scored, of which 87.5% (63/72) were polymorphic. The Nei's gene diversity and Shannon's diversity indices of three Chinese regional populations were very similar to that from California. However, several differences were observed among geographic populations of M. fructicola from both within China and between China and California. The analysis of molecular variance (AMOVA) of isolates from different geographic locations suggested that most of the observed genetic variation was found within populations. Results of this study are inconsistent with the hypothesis that the Chinese populations of M. fructicola were derived from a single or few recent migrants from other countries. Instead, our results suggest that M. fructicola has been in China long before its first official recording in 2003. [source] Genetic Diversity of Parasitic Dinoflagellates in the Genus Amoebophrya and Its Relationship to Parasite Biology and BiogeographyTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 1 2008SUNJU KIM ABSTRACT. We determined 18S rRNA gene sequences of Amoebophrya strains infecting the thecate dinoflagellates Alexandrium affine and Gonyaulax polygramma from Korean coastal waters and compared those data with previously reported sequences of Amoebophrya from cultures, infected cells concentrated from field samples, and environmental 18S rRNA gene sequences obtained from a variety of marine environments. Further, we used these data to examine genetic diversity in Amoebophrya strains relative to geographic origin, host phylogeny, site of infection, and host specificity. In our analyses of known dinoflagellate taxa, the 13 available Amoebophrya sequences clustered together within the dinoflagellates as three groups forming a monophyletic group with high bootstrap support (maximum likelihood, ML: 100%) or a posterior probability (PP) of 1. When the Amoebophrya sequences were analyzed along with environmental sequences associated with Marine Alveolate Group II, nine subgroups formed a monophyletic group with high bootstrap support (ML: 100%) and PP of 1. Sequences known to be from Amoebophrya spp. infecting dinoflagellate hosts were distributed in seven of those subgroups. Despite differences in host species and geographic origin (Korea, United States, and Europe), Amoebophrya strains (Group II) from Gymnodinium instriatum, A. affine, Ceratium tripos (AY208892), Prorocentrum micans, and Ceratium lineatum grouped together by all of our tree construction methods, even after adding the environmental sequences. By contrast, strains within Groups I and III divided into several lineages following inclusion of environmental sequences. While Amoebophrya strains within Group II mostly developed within the host cytoplasm, strains in Groups I and III formed infections inside the host nucleus, a trait that appeared across several of the subgroups. Host specificity varied from moderately to extremely species-specific within groups, including Group II. Taken together, our results imply that genetic diversity in Amoebophrya strains does not always reflect parasite biology or biogeography. [source] There are High Levels of Functional and Genetic Diversity in Oxyrrhis marinaTHE JOURNAL OF EUKARYOTIC MICROBIOLOGY, Issue 3 2005CHRIS D. LOWE Abstract. Oxyrrhis marina, a widely distributed marine protist, is used to model heterotrophic flagellate responses in microbial food webs. Although clonal variability occurs in protists, assessments of intraspecific diversity are rare; such assessments are critical, particularly where species are used as models in ecological studies. To address the extent of intraspecific variation within O. marina, we assessed diversity among 11 strains using 5.8S rDNA and ITS sequences. The 5.8S rDNA and ITS regions revealed high divergence between strains: 63.1% between the most diverse. To compare O. marina diversity relative to other alveolates, 18S rDNA sequences for five strains were analysed with sequences from representatives of the major alveolate groups. 18S rDNA also revealed high divergence in O. marina. Additionally, consistent with phylogenies based on protein coding genes, maximum likelihood analysis indicated that O. marina was monophyletic and ancestral to the dinoflagellates. To assess ecophysiological differences, growth rates of seven O. marina strains were measured at 10 salinities (10,55,). Two salinity responses occurred: one group achieved highest growth rates at high salinities; the other grew best at low salinities. There was no clear correlation between molecular, ecophysiological, or geographical differences. However, salinity tolerance was associated with habitat type: intertidal strains grew best at high salinities; open-water strains grew best at low salinities. These data indicate the need to examine many strains of a species in both phylogenetic and ecological studies, especially where key-species are used to model ecological processes. [source] Genetic Diversity of the Fragile X Syndrome Gene (FMR1) in a Large Sub-Saharan West African PopulationANNALS OF HUMAN GENETICS, Issue 4 2010Emmanuel K. Peprah Summary Fragile X syndrome (OMIM #300624) is caused by the expansion of a CGG trinucleotide repeat found in the 5, untranslated region of the X-linked FMR1 gene. Although examinations of characteristics associated with repeat instability and expansion of the CGG repeat upon transmission from parent to offspring has occurred in various world populations, none has been conducted in large Sub-Saharan African populations. We have examined the FMR1 CGG repeat structure in a sample of 350 males drawn from the general population of Ghana. We found that Ghanaians and African Americans have similar allele frequency distributions of CGG repeat and its flanking STR markers, DXS548 and FRAXAC1. However, the distribution of the more complex marker, FRAXAC2, is significantly different. The haplotype structure of the FMR1 locus indicated that Ghanaians share several haplotypes with African Americans and Caucasians that are associated with the expanded full mutation. In Ghanaians, the majority of repeat structures contained two AGG interruptions, however, the majority of intermediate alleles (35,49) lacked AGG interruptions. Overall, we demonstrate that allelic diversity of the FMR1 locus among Ghanaians is comparable to African Americans, but includes a minority of CGG array structures not found in other populations. [source] Elucidation of CYP2D6 Genetic Diversity in a Unique African Population: Implications for the Future Application of Pharmacogenetics in the Xhosa PopulationANNALS OF HUMAN GENETICS, Issue 4 2010Galen E. B. Wright Summary Genetic variation of the CYP2D6 gene has been associated with altered drug metabolism; however, limited studies have investigated CYP2D6 sequence diversity in African populations. We devised a CYP2D6 genotyping strategy to analyse the South African Xhosa population and genotype a Xhosa schizophrenia cohort, as CYP2D6 metabolises many antipsychotics and antidepressants. The entire CYP2D6 gene locus was sequenced in 15 Xhosa control individuals and the data generated were used to design a comprehensive genotyping strategy. Over 25 CYP2D6 alleles were genotyped in Xhosa controls and Xhosa schizophrenia patients using long-range PCR, DNA sequencing and single nucleotide primer extension analysis. Bioinformatic algorithms were used to predict the functional consequences of relevant mutations and samples were assigned CYP2D6 activity scores. A unique allele distribution was revealed and two rare novel alleles, CYP2D6*73 and CYP2D6*74, were identified. No significant differences in allele frequencies were detected between Xhosa controls and schizophrenia patients. This study provides i) comprehensive data on a poorly characterised population, ii) a valuable CYP2D6 genotyping strategy and iii) due to their unique genetic profile, provides the basis for pharmacogenetic intervention for Xhosa individuals. [source] Inter- and Extra-Indian Admixture and Genetic Diversity in Reunion Island Revealed by Analysis of Mitochondrial DNAANNALS OF HUMAN GENETICS, Issue 3 2009Vincent Dubut Summary Reunion Island is a French territory located in the western Indian Ocean. The genetic pattern of the Reunionese population has been shaped by contributions from highly contrasting regions of the world. Over the last 350 years, several migration waves and cultural and socio-economic factors have led to the emergence of six main ethnic groups in Reunion. India is one of the principal regions that contributed to the setting up of the Reunionese population. Diversity, demographic and admixture analyses were performed on mtDNA variation of the Reunionese of Indian ancestry, including the Malbar and Zarab ethnic groups, in order to question their history. Using a phylogeographical approach, we generated and analysed quantitative data on the contribution of the Indian parental populations. Furthermore, we showed that the settlement of Reunion Island by Indians did not involve a founder effect, except in the very beginning of the Reunionese settlement (at the end of the 17th century). The accuracy of our results was optimised by a re-evaluation of the classification of the Southern Asian mtDNA haplogroups. Finally, by comparing our results to a previous study dealing with the Reunionese population, we highlighted how ethno-historical data are critical for reconstructing the complex history of multiethnic populations. [source] Susceptibility of Common and Rare Plant Species to the Genetic Consequences of Habitat FragmentationCONSERVATION BIOLOGY, Issue 3 2007OLIVIER HONNAY diversidad genética; endogamia; fragmentación de hábitat; sistema reproductivo; tamaño poblacional Abstract:,Small plant populations are more prone to extinction due to the loss of genetic variation through random genetic drift, increased selfing, and mating among related individuals. To date, most researchers dealing with genetic erosion in fragmented plant populations have focused on threatened or rare species. We raise the question whether common plant species are as susceptible to habitat fragmentation as rare species. We conducted a formal meta-analysis of habitat fragmentation studies that reported both population size and population genetic diversity. We estimated the overall weighted mean and variance of the correlation coefficients among four different measures of genetic diversity and plant population size. We then tested whether rarity, mating system, and plant longevity are potential moderators of the relationship between population size and genetic diversity. Mean gene diversity, percent polymorphic loci, and allelic richness across studies were positively and highly significantly correlated with population size, whereas no significant relationship was found between population size and the inbreeding coefficient. Genetic diversity of self-compatible species was less affected by decreasing population size than that of obligate outcrossing and self-compatible but mainly outcrossing species. Longevity did not affect the population genetic response to fragmentation. Our most important finding, however, was that common species were as, or more, susceptible to the population genetic consequences of habitat fragmentation than rare species, even when historically or naturally rare species were excluded from the analysis. These results are dramatic in that many more plant species than previously assumed may be vulnerable to genetic erosion and loss of genetic diversity as a result of ongoing fragmentation processes. This implies that many fragmented habitats have become unable to support plant populations that are large enough to maintain a mutation-drift balance and that occupied habitat fragments have become too isolated to allow sufficient gene flow to enable replenishment of lost alleles. Resumen:,Las poblaciones pequeñas de plantas son más propensas a la extinción debido a la pérdida de variación genética por medio de la deriva génica aleatoria, el incremento de autogamia y la reproducción entre individuos emparentados. A la fecha, la mayoría de los investigadores que trabajan con erosión genética en poblaciones fragmentadas de plantas se han enfocado en las especies amenazadas o raras. Cuestionamos si las especies de plantas comunes son tan susceptibles a la fragmentación del hábitat como las especies raras. Realizamos un meta análisis formal de estudios de fragmentación que reportaron tanto tamaño poblacional como diversidad genética. Estimamos la media general ponderada y la varianza de los coeficientes de correlación entre cuatro medidas de diversidad genética y de tamaño poblacional de las plantas. Posteriormente probamos si la rareza, el sistema reproductivo y la longevidad de la planta son moderadores potenciales de la relación entre el tamaño poblacional y la diversidad genética. La diversidad genética promedio, el porcentaje de loci polimórficos y la riqueza alélica en los estudios tuvieron una correlación positiva y altamente significativa con el tamaño poblacional, mientras que no encontramos relación significativa entre el tamaño poblacional y el coeficiente de endogamia. La diversidad genética de especies auto compatibles fue menos afectada por la reducción en el tamaño poblacional que la de especies exogámicas obligadas y especies auto compatibles, pero principalmente exogámicas. La longevidad no afectó la respuesta genética de la población a la fragmentación. Sin embargo, nuestro hallazgo más importante fue que las especies comunes fueron tan, o más, susceptibles a las consecuencias genéticas de la fragmentación del hábitat que las especies raras, aun cuando las especies histórica o naturalmente raras fueron excluidas del análisis. Estos resultados son dramáticos porque muchas especies más pueden ser vulnerables a la erosión genética y a la pérdida de diversidad genética como consecuencia de los procesos de fragmentación que lo se asumía previamente. Esto implica que muchos hábitats fragmentados han perdido la capacidad para soportar poblaciones de plantas lo suficientemente grandes para mantener un equilibrio mutación-deriva y que los fragmentos de hábitat ocupados están tan aislados que el flujo génico es insuficiente para permitir la reposición de alelos perdidos. [source] BIODIVERSITY RESEARCH: Genetic diversity in two introduced biofouling amphipods (Ampithoe valida & Jassa marmorata) along the Pacific North American coast: investigation into molecular identification and cryptic diversityDIVERSITY AND DISTRIBUTIONS, Issue 5 2010Erik M. Pilgrim Abstract Aim, We investigated patterns of genetic diversity among invasive populations of Ampithoe valida and Jassa marmorata from the Pacific North American coast to assess the accuracy of morphological identification and determine whether or not cryptic diversity and multiple introductions contribute to the contemporary distribution of these species in the region. Location, Native range: Atlantic North American coast; Invaded range: Pacific North American coast. Methods, We assessed indices of genetic diversity based on DNA sequence data from the mitochondrial cytochrome c oxidase subunit I (COI) gene, determined the distribution of COI haplotypes among populations in both the invasive and putative native ranges of A. valida and J. marmorata and reconstructed phylogenetic relationships among COI haplotypes using both maximum parsimony and Bayesian approaches. Results, Phylogenetic inference indicates that inaccurate species-level identifications by morphological criteria are common among Jassa specimens. In addition, our data reveal the presence of three well supported but previously unrecognized clades of A. valida among specimens in the north-eastern Pacific. Different species of Jassa and different genetic lineages of Ampithoe exhibit striking disparity in geographic distribution across the region as well as substantial differences in genetic diversity indices. Main conclusions, Molecular genetic methods greatly improve the accuracy and resolution of identifications for invasive benthic marine amphipods at the species level and below. Our data suggest that multiple cryptic introductions of Ampithoe have occurred in the north-eastern Pacific and highlight uncertainty regarding the origin and invasion histories of both Jassa and Ampithoe species. Additional morphological and genetic analyses are necessary to clarify the taxonomy and native biogeography of both amphipod genera. [source] Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and AfricaDIVERSITY AND DISTRIBUTIONS, Issue 5 2009Sébastien Calvignac Abstract Aim, Middle East brown bears (Ursus arctos syriacus Hemprich and Ehrenberg, 1828) are presently on the edge of extinction. However, little is known of their genetic diversity. This study investigates that question as well as that of Middle East brown bear relationships to surrounding populations of the species. Location, Middle East region of south-western Asia. Methods, We performed DNA analyses on 27 brown bear individuals. Twenty ancient bone samples (Late Pleistocene to 20th century) from natural populations and seven present-day samples obtained from captive individuals were analysed. Results, Phylogenetic analyses of the mitochondrial sequences obtained from seven ancient specimens identify three distinct maternal clades, all unrelated to one recently described from North Africa. Brown bears from Iran exhibit striking diversity (three individuals, three haplotypes) and form a unique clade that cannot be linked to any extant one. Individuals from Syria belong to the Holarctic clade now observed in Eastern Europe, Turkey, Japan and North America. Specimens from Lebanon surprisingly appear as tightly linked to the clade of brown bears now in Western Europe. Moreover, we show that U. a. syriacus in captivity still harbour haplotypes closely linked to those found in ancient individuals. Main conclusion, This study brings important new information on the genetic diversity of brown bear populations at the crossroads of Europe, Asia and Africa. It reveals a high level of diversity in Middle East brown bears and extends the historical distribution of the Western European clade to the East. Our analyses also suggest the value of a specific breeding programme for captive populations. [source] Genetic diversity of the toxic cyanobacterium Microcystis in Lake MikataENVIRONMENTAL TOXICOLOGY, Issue 3 2005Mitsuhiro Yoshida Abstract The aim of the present study was to clarify the bloom dynamics and community composition of hepatotoxin microcystin-producing and non-microcystin-producing Microcystis genotypes in the environment. In Lake Mikata (Fukui, Japan) from April 2003 to January 2004, seasonal variation in the number of cells with microcystin (mcy) genotypes and the genetic diversity of the total population were investigated using quantitative competitive PCR and a 16S rDNA clone library, respectively. Using competitive PCR, cells with mcyA genotypes were quantified in August and October, and the ratio of the number of these mcyA genotypes to colony-forming Microcystis cells was 0.37 and 2.37, respectively. The 16S rDNA clones obtained could be divided into 12 ribotypes: a,l. Sixty-one Microcystis strains isolated from Lake Mikata during the sampling period were subjected to toxicity tests using HPLC and ELISA, PCR-based detection of the mcyA gene, and sequence analysis of the 16S rDNA. All isolates could be differentiated into 11 ribotypes (a, b, d, f, h, i, and m,q). Ribotypes b, f, i, m, n, and p had at least one strain that was a microcystin producer. In natural communities ribotypes b and f accounted for 85% of the 16S rDNA clones in August, and ribotypes b and i accounted for 24% of the clones in October. Thus, in some bloom stages the presence of microcystin genotypes identified using the 16S rDNA clone library correlated with that of mcy genotypes determined using competitive PCR. © 2005 Wiley Periodicals, Inc. Environ Toxicol 20: 229,234, 2005. [source] Genetic diversity of Clethrionomys glareolus populations from highly contaminated sites in the Chornobyl region, UkraineENVIRONMENTAL TOXICOLOGY & CHEMISTRY, Issue 8 2000Cole W. Matson Abstract At radioactive sites, at least two mechanisms may affect the genetic diversity of populations of a given species. Increased mutation rates due to radiation exposure may increase the amount of genetic diversity in a population. Alternatively, population bottlenecks exacerbated by environmental degradation may lead to a reduction of diversity. The relationship between these two contradictory forces is complex. To explore this relationship, long-term monitoring of a genetic marker within a population is needed. To provide baseline data on the population genetics of the bank vole (Clethrionomys glareolus) living in the most contaminated regions at Chornobyl, Ukraine, we have sequenced 291 base pairs of the mitochondrial DNA control region. Bank voles were chosen as a model system because they have the highest levels of internal dose of cesium-134, cesium-137, and strontium-90 within the Chornobyl exclusion zone. We sampled three geographic sites, which were Oranoe, a reference site with virtually no radioactive contamination (<2 Ci/km2), and two highly contaminated sites, Glyboke Lake and the Red Forest (both 1,000 Ci/km2). Genetic diversity in the population from Red Forest (0.722 ± 0.024) was significantly greater than at the Oranoe reference site (0.615 ± 0.039), while genetic diversity at Glyboke Lake (0.677 ± 0.068) was intermediate. It is concluded that long-term studies of historical and demographic characteristics for experimental and reference populations are required in order to employ population genetics to understand the biological impact of environmental contaminants on the genetics of natural populations. [source] DOES MATE LIMITATION IN SELF-INCOMPATIBLE SPECIES PROMOTE THE EVOLUTION OF SELFING?EVOLUTION, Issue 6 2010THE CASE OF LEAVENWORTHIA ALABAMICA Genetic diversity at the S-locus controlling self-incompatibility (SI) is often high because of negative frequency-dependent selection. In species with highly patchy spatial distributions, genetic drift can overwhelm balancing selection and cause stochastic loss of S-alleles. Natural selection may favor the breakdown of SI in populations with few S-alleles because low S-allele diversity constrains the seed production of self-incompatible plants. We estimated S-allele diversity, effective population sizes, and migration rates in Leavenworthia alabamica, a self-incompatible mustard species restricted to discrete habitat patches in rocky glades. Patterns of polymorphism were investigated at the S-locus and 15 neutral microsatellites in three large and three small populations with 100-fold variation in glade size. Populations on larger glades maintained more S-alleles, but all populations were estimated to harbor at least 20 S-alleles, and mate availabilities typically exceeded 0.80, which is consistent with little mate limitation in nature. Estimates of the effective size (Ne) in each population ranged from 600 to 1600, and estimated rates of migration (m) ranged from 3 × 10,4 to nearly 1 × 10,3. According to theoretical models, there is limited opportunity for genetic drift to reduce S-allele diversity in populations with these attributes. Although pollinators or resources limit seed production in small glades, limited S-allele diversity does not appear to be a factor promoting the incipient breakdown of SI in populations of this species that were studied. [source] Genetic diversity and biogeography of haloalkaliphilic sulphur-oxidizing bacteria belonging to the genus ThioalkalivibrioFEMS MICROBIOLOGY ECOLOGY, Issue 1 2006Mirjam Foti Abstract A group of 85 isolates of haloalkaliphilic obligately chemolithoautotrophic sulphur-oxidizing bacteria belonging to the genus Thioalkalivibrio were recently obtained from soda lakes in Mongolia, Kenya, California, Egypt and Siberia. They have been analyzed by repetitive extragenic palindromic (rep)-PCR genomic fingerprinting technique with BOX- and (GTG)5-primer set. Cluster analysis was performed using combined fingerprint profiles and a dendrogram similarity value (r) of 0.8 was used to define the same genotype. Fifty-six genotypes were found among the isolates, revealing a high genetic diversity. The strains can be divided into two major clusters, including isolates from the Asiatic (Siberia and Mongolia) and the African (Kenya and Egypt) continents, respectively. The majority (85.9%) of the genotypes were found in only one area, suggesting an endemic character of the Thioalkalivibrio strains. Furthermore, a correlation between fingerprint clustering, geographic origin and the characteristics of the lake of origin was found. [source] Genetic diversity and distribution of periphytic Synechococcus spp. in biofilms and picoplankton of Lake ConstanceFEMS MICROBIOLOGY ECOLOGY, Issue 2 2004Sven Becker Abstract In various water depths of the littoral zone of Lake Constance (Bodensee) cyanobacteria of the Synechococcus -type were isolated from biofilms (periphyton) on three natural substrates and an artificial one (unglazed tiles). From one tile three strains of phycoerythrin (PE)-rich Synechococcus spp. were isolated, the first examples of these organisms in the epibenthos. Phylogenetic inference based on the 16S,23S rRNA intergenic spacer (ITS-1) assigned all periphytic isolates to two clusters of the picophytoplankton clade (evolutionary lineage VI of cyanobacteria). The sequence divergence in the ITS-1 was used to design specific PCR primers to allow direct, culture-independent detection and quantification of isolated Synechococcus strains in natural periphytic and pelagic samples. Denaturing gradient gel electrophoresis (DGGE) analysis revealed depth-related differences of Synechococcus spp. distribution on tiles placed in the littoral zone. Synechococcus genotypes were observed which occurred in both the periphyton (on tiles) and in the pelagic picoplankton. A strain with one of these genotypes, Synechococcus sp. BO 8805, was isolated from the pelagic zone in 1988. Its genotype was found on tiles that had been exposed at different water depths in the littoral zone in spring and autumn of the year 2000. Quantitative analysis with a genotype-specific TaqMan probe and real-time Taq nuclease assays (TNA) confirmed its presence in the pelagic zone, although appearance of this and related genotypes was highly irregular and exhibited strong differences between consecutive years. Our results show that the ability to form significant subpopulations in pelagic and periphytic communities exists in three out of four phylogenetic clusters of Synechococcus spp. in Lake Constance. This versatility may be a key feature in the ubiquity of the evolutionary lineage VI of cyanobacteria. [source] Genetic diversity in Nordic and Baltic populations of Chondrostereum purpureum: a potential herbicide biocontrol agentFOREST PATHOLOGY, Issue 6 2008H. Vartiamäki Summary We analysed genetic variation in the natural populations of a potential herbicide biocontrol agent, Chondrostereum purpureum, in Nordic and Baltic countries using random amplified microsatellite markers. The results showed high genetic diversity among the populations of this fungus, but almost a complete lack of local differentiation. The results implicate that any local strain from the area can be used as a biocontrol agent without a fear of introducing new genotypes to treatment areas. 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