Journal articles: 'Clonal and genetic diversity'

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Rozenfeld, Alejandro F., Sophie Arnaud-Haond, Emilio Hernández-García, Víctor M. Eguíluz, Manuel A. Matías, Ester Serrão, and Carlos M. Duarte. "Spectrum of genetic diversity and networks of clonal organisms." Journal of The Royal Society Interface 4, no. 17 (May 2007): 1093–102. http://dx.doi.org/10.1098/rsif.2007.0230.

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Clonal reproduction characterizes a wide range of species including clonal plants in terrestrial and aquatic ecosystems, and clonal microbes such as bacteria and parasitic protozoa, with a key role in human health and ecosystem processes. Clonal organisms present a particular challenge in population genetics because, in addition to the possible existence of replicates of the same genotype in a given sample, some of the hypotheses and concepts underlying classical population genetics models are irreconcilable with clonality. The genetic structure and diversity of clonal populations were examined using a combination of new tools to analyse microsatellite data in the marine angiosperm Posidonia oceanica . These tools were based on examination of the frequency distribution of the genetic distance among ramets, termed the spectrum of genetic diversity (GDS), and of networks built on the basis of pairwise genetic distances among genets. Clonal growth and outcrossing are apparently dominant processes, whereas selfing and somatic mutations appear to be marginal, and the contribution of immigration seems to play a small role in adding genetic diversity to populations. The properties and topology of networks based on genetic distances showed a ‘small-world’ topology, characterized by a high degree of connectivity among nodes, and a substantial amount of substructure, revealing organization in subfamilies of closely related individuals. The combination of GDS and network tools proposed here helped in dissecting the influence of various evolutionary processes in shaping the intra-population genetic structure of the clonal organism investigated; these therefore represent promising analytical tools in population genetics.

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Black, James R. M., and Nicholas McGranahan. "Genetic and non-genetic clonal diversity in cancer evolution." Nature Reviews Cancer 21, no. 6 (March 16, 2021): 379–92. http://dx.doi.org/10.1038/s41568-021-00336-2.

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Stelzer, H. E. "Evaluating genetic diversity concerns in clonal deployments." Canadian Journal of Forest Research 27, no. 3 (March 1, 1997): 438–41. http://dx.doi.org/10.1139/x96-201.

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Reisch, Christoph, Stefanie Meier, Christoph Schmid, and Maik Bartelheimer. "Clonal diversity and genetic variation of the sedge Carex nigra in an alpine fen depend on soil nutrients." PeerJ 8 (June 3, 2020): e8887. http://dx.doi.org/10.7717/peerj.8887.

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In this study we analysed the impact of water regime and soil nutrients on the clonal diversity and genetic variation of the sedge Carex nigra in a central alpine fen. For our analysis, we established 16 study plots randomly distributed over the fen. We determined the exact elevation of each plot as an indicator for the water regime and measured the content of phosphorous and potassium in the soil of each plot. Clonal diversity and genetic variation of C. nigra were assessed with nuclear microsatellites using leaf material collected in 20 subplots along a diagonal cross within each study plot. The influence of water regime and soil mineral nutrients on clonal diversity and genetic variation was estimated by Bayesian multiple regression. Our study revealed a clear impact of soil nutrient conditions on clonal diversity and genetic variation of C. nigra, which increased with the concentration of phosphorous and decreased with the concentration of potassium. Key background to these findings seems to be the relative offspring success from generative as compared to clonal propagation. Phosphorous acquisition is essential during seedling establishment. Clonal diversity and genetic variation increase, therefore, at sites with higher phosphorous contents due to more successful recruitment. High levels of clonal diversity and genetic variation at sites of low potassium availability may in contrast be mainly caused by increased plant susceptibility to abiotic stress under conditions of potassium deficiency, which brings about more gaps in C. nigra stands and favors the ingrowth from other clones or recruitment from seeds.

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Balloux, François, Laurent Lehmann, and Thierry de Meeûs. "The Population Genetics of Clonal and Partially Clonal Diploids." Genetics 164, no. 4 (August 1, 2003): 1635–44. http://dx.doi.org/10.1093/genetics/164.4.1635.

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Abstract The consequences of variable rates of clonal reproduction on the population genetics of neutral markers are explored in diploid organisms within a subdivided population (island model). We use both analytical and stochastic simulation approaches. High rates of clonal reproduction will positively affect heterozygosity. As a consequence, nearly twice as many alleles per locus can be maintained and population differentiation estimated as FST value is strongly decreased in purely clonal populations as compared to purely sexual ones. With increasing clonal reproduction, effective population size first slowly increases and then points toward extreme values when the reproductive system tends toward strict clonality. This reflects the fact that polymorphism is protected within individuals due to fixed heterozygosity. Contrarily, genotypic diversity smoothly decreases with increasing rates of clonal reproduction. Asexual populations thus maintain higher genetic diversity at each single locus but a lower number of different genotypes. Mixed clonal/sexual reproduction is nearly indistinguishable from strict sexual reproduction as long as the proportion of clonal reproduction is not strongly predominant for all quantities investigated, except for genotypic diversities (both at individual loci and over multiple loci).

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Duchmann, Matthieu, Lucie Laplane, and Raphael Itzykson. "Clonal Architecture and Evolutionary Dynamics in Acute Myeloid Leukemias." Cancers 13, no. 19 (September 29, 2021): 4887. http://dx.doi.org/10.3390/cancers13194887.

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Acute myeloid leukemias (AML) results from the accumulation of genetic and epigenetic alterations, often in the context of an aging hematopoietic environment. The development of high-throughput sequencing—and more recently, of single-cell technologies—has shed light on the intratumoral diversity of leukemic cells. Taking AML as a model disease, we review the multiple sources of genetic, epigenetic, and functional heterogeneity of leukemic cells and discuss the definition of a leukemic clone extending its definition beyond genetics. After introducing the two dimensions contributing to clonal diversity, namely, richness (number of leukemic clones) and evenness (distribution of clone sizes), we discuss the mechanisms at the origin of clonal emergence (mutation rate, number of generations, and effective size of the leukemic population) and the causes of clonal dynamics. We discuss the possible role of neutral drift, but also of cell-intrinsic and -extrinsic influences on clonal fitness. After reviewing available data on the prognostic role of genetic and epigenetic diversity of leukemic cells on patients’ outcome, we discuss how a better understanding of AML as an evolutionary process could lead to the design of novel therapeutic strategies in this disease.

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Maley, Carlo C., Patricia C. Galipeau, Jennifer C. Finley, V. Jon Wongsurawat, Xiaohong Li, Carissa A. Sanchez, Thomas G. Paulson, et al. "Genetic clonal diversity predicts progression to esophageal adenocarcinoma." Nature Genetics 38, no. 4 (March 26, 2006): 468–73. http://dx.doi.org/10.1038/ng1768.

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Nakajima, Yuichi, Yu Matsuki, Miguel D. Fortes, Wilfredo H. Uy, Wilfredo L. Campos, Kazuo Nadaoka, and Chunlan Lian. "Strong Genetic Structure and Limited Gene Flow among Populations of the Tropical Seagrass Thalassia hemprichii in the Philippines." Journal of Marine Science and Engineering 11, no. 2 (February 5, 2023): 356. http://dx.doi.org/10.3390/jmse11020356.

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Seagrasses are marine angiosperms, and seagrass beds maintain the species diversity of tropical and subtropical coastal ecosystems. For proper understanding, management and conservation of coastal ecosystems, it is essential to understand seagrass population dynamics. Population genetic studies can cover large geographic scales and contribute to a comprehensive understanding of reproductive dynamics and potential dispersal among locations. The clonal and genetic diversity and genetic connectivity of Thalassia hemprichii in the Philippines were estimated by a population genetics approach. The geographic scale of this study has a direct distance of approximately 1600 km. Although high clonal diversity was found in some sites (R = 0.07–1.00), both sexual and asexual reproduction generally maintains separate populations. Genetic diversity is not definitely correlated with latitude, and genetic differentiation is significant in all pairs of sites (FST = 0.026–0.744). Complex genetic structure was found in some regions, even at a fine geographic scale. The migration of fruits and seedlings was elucidated as an infrequent and stochastic event. These results suggest the necessity for the conservation of this species due to a deficiency in migrants from external regions.

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Ebert, Benjamin L. "Clonal Diversity and Mutated Genes in Myelodysplastic Syndromes." Blood 126, no. 23 (December 3, 2015): SCI—3—SCI—3. http://dx.doi.org/10.1182/blood.v126.23.sci-3.sci-3.

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Myelodysplastic syndromes (MDS) are driven by somatic genetic mutations that drive clonal explansion of neoplastic cells. The identification of these lesions has enabled large-scale studies to assess the association of genetic lesions with clinical and biological phenotype. Single mutations in driver genes in isolation, without concurrent mutations in additional driver genes, commonly do not cause overt disease, but rather cause an expanded population of blood cells without cytopenias, a condition that we have termed clonal hematopoiesis of indeterminate potential (CHIP). CHIP is common in the general population and is associated with age, risk of hematologic malignancy, and overall mortality. In contrast, patients with MDS generally have mutations in multiple genes as well as the disease-defining morphologic dysplastia and peripheral blood cytopenias. The particular mutations that drive MDS in an individual patient are powerfully associated with clinical phenotype, including cytopenias, specific morphologic abnormalities, blast percentage, overall survival, and response to therapy. Clonal architecture adds an additional layer of complexity as disease progression or response to therapy may be associated with shifts in the dominant genetic clone in the bone marrow. As the availability of genetic testing for panels of genes becomes widespread as a clinical assay, current endeavors are to move validated research findings into routine clinical use and to employ deep genetic analyses to evaluate response to investigational therapies in clinical trials. Disclosures Ebert: Genoptix: Consultancy, Patents & Royalties; H3 Biomedicine: Consultancy; Celgene: Consultancy.

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Lusasi, Justin. "Cyperus papyrus in Lake Victoria: Genetic Information, Utilisation and Resource Sustainability." JOURNAL OF THE GEOGRAPHICAL ASSOCIATION OF TANZANIA 36, no. 2 (July 10, 2021): 73–118. http://dx.doi.org/10.56279/jgat.v36i2.152.

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Many wetlands in the Lake Victoria basin are dominated by Cyperus papyrus, which are very productive and, therefore, have an important role both ecologically and socially. The increasing harvesting pressure of papyrus threatens its future. Thus, a conservation approach was employed to determine the intensity of the pressure and threat to the papyrus diversity at clonal level. Eight microsatellite loci were used for analysing the clonal diversity and genetic diversity of Cyperus papyrus in 6 swamps of Mwanza bay (Tanzania) and 5 swamps of Nyanza bay (Kenya). From 304 individuals, we observed a total of 49 alleles in Mwanza bay and 44 alleles in Nyanza bay, a high clonal diversity (R = 0.64 to 1 Mwanza bay and R=0.70 to 1 in Nyanza bay), and a high genetic diversity (HE) with an average of 0.558 and 0.493 for Mwanza and Nyanza bay, respectively. The analysis of molecular variance showed that most of the allelic variances were within individuals. This resulted in a moderate differentiation (FST, 0.126 and Nm, 1.7) from all studied population in Lake Victoria. Gene flow was high between populations within each bay of the Lake (Nm > 4). The observed disturbance in the swamps showed no effects on any of the papyrus diversity variables. The clonal diversity (R) was even higher in the disturbed swamps than in pristine ones, with values ranging from 0.78 to 1 for disturbed, and 0.64 to 1 for pristine swamps. This explains that, although it is a clonal plant, papyrus maintains sexual reproduction and successful seed dispersal, making them resilient to even strong environmental and anthropogenic disturbance.

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Stein, Katharina, Christoph Rosche, Heidi Hirsch, Anke Kindermann, Julia Köhler, and Isabell Hensen. "The influence of forest fragmentation on clonal diversity and genetic structure in Heliconia angusta, an endemic understorey herb of the Brazilian Atlantic rain forest." Journal of Tropical Ecology 30, no. 3 (February 24, 2014): 199–208. http://dx.doi.org/10.1017/s0266467414000030.

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Abstract:Fragmented populations are usually exposed to the negative effects of reduced gene flow, genetic drift and population differentiation. These effects result in the collective loss of genetic variation, thereby reducing the probability of population adaptation to new environmental conditions and increasing the risk of extinction. Forest fragments commonly exhibit suboptimal site conditions, which can result in enhanced clonal reproduction, and a potential reduction in clonal diversity due to increased selfing and inbreeding depression. The clonal diversity, genetic diversity and structure of Heliconia angusta (Heliconiaceae) were assessed using AFLP-markers. We analysed six patches in the continuous forest (Atlantic rain forest, State of Rio de Janeiro) and eight patches (155 leaf samples in total) in five nearby forest fragments (age of oldest fragment: c. 50 y; size range: < 5–100 ha). Clonal diversity (Pd) of patches was slightly, yet significantly, lower in forest fragments compared with continuous forest. Measures of genetic diversity of patches in forest fragments did not differ from those in the continuous forest. A STRUCTURE analysis did not show any clear clustering of patches in the continuous forest and forest fragments. Our results suggest that H. angusta has not yet suffered from the anticipated negative effects of fragmentation.

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Timmer, Margriet R., Chiu T. Lau, Sybren L. Meijer, Paul Fockens, Erik A. J. Rauws, Cyriel Y. Ponsioen, Silvia Calpe, and Kausilia K. Krishnadath. "Genetic Abnormalities in Biliary Brush Samples for Distinguishing Cholangiocarcinoma from Benign Strictures in Primary Sclerosing Cholangitis." Gastroenterology Research and Practice 2016 (2016): 1–9. http://dx.doi.org/10.1155/2016/4381513.

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Background. Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease and is strongly associated with cholangiocarcinoma (CCA). The lack of efficient diagnostic methods for CCA is a major problem. Testing for genetic abnormalities may increase the diagnostic value of cytology.Methods.We assessed genetic abnormalities forCDKN2A,TP53,ERBB2,20q,MYC, and chromosomes 7 and 17 and measures of genetic clonal diversity in brush samples from 29 PSC patients with benign biliary strictures and 12 patients with sporadic CCA or PSC-associated CCA. Diagnostic performance of cytology alone and in combination with genetic markers was evaluated by sensitivity, specificity, and area under the curve analysis.Results. The presence ofMYCgain andCDKN2Aloss as well as a higher clonal diversity was significantly associated with malignancy.MYCgain increased the sensitivity of cytology from 50% to 83%. However, the specificity decreased from 97% to 76%. The diagnostic accuracy of the best performing measures of clonal diversity was similar to the combination of cytology andMYC. AddingCDKN2Aloss to the panel had no additional benefit.Conclusion. Evaluation ofMYCabnormalities and measures of clonal diversity in brush cytology specimens may be of clinical value in distinguishing CCA from benign biliary strictures in PSC.

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Park, Ji-Min, Soon-Ho Kwon, He-Jin Lee, Sung-Joon Na, Yousry A. El-Kassaby, and Kyu-Suk Kang. "Integrating fecundity variation and genetic relatedness in estimating the gene diversity of seed crops: Pinus koraiensis seed orchard as an example." Canadian Journal of Forest Research 47, no. 3 (March 2017): 366–70. http://dx.doi.org/10.1139/cjfr-2016-0223.

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The genetic gain and gene diversity of seed crops from a 1.5-generation clonal seed orchard of Pinus koraiensis Siebold & Zucc. were estimated under consideration of parental genetic values and fecundity variation. Fecundity variation among clones was estimated for 5 consecutive years (2010–2014) as the sibling coefficient, which was drawn from clonal contribution to the total production of seed conelet. To monitor gene diversity, status number was estimated by the integration of fecundity variation and group coancestry. Group coancestry was calculated as the average of genetic relatedness (coancestry) among orchard clones. The averages of conelet production were high in 2010 and 2011, moderate in 2013 and 2014, and poor in 2012 with a grand mean of 13.7. Correlation analysis showed that good conelet producers consistently gave good production. Cumulative distribution of clonal conelet production was presented as a function of the total conelet yield, and this distribution indicated deviation from the expected clonal equal production. Group coancesrtry was 0.0096, indicating minimal loss of gene diversity. Status number and genetic gain were higher in good than in poor conelet production years, highlighting the importance of fecundity variation in determining the genetic gain and gene diversity of seed orchard crops.

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Weng, Yuhui, Yill Sung Park, and Dag Lindgren. "Unequal clonal deployment improves genetic gains at constant diversity levels for clonal forestry." Tree Genetics & Genomes 8, no. 1 (August 23, 2011): 77–85. http://dx.doi.org/10.1007/s11295-011-0422-2.

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Weeks, Andrew R., and Ary A. Hoffmann. "Frequency-dependent selection maintains clonal diversity in an asexual organism." Proceedings of the National Academy of Sciences 105, no. 46 (November 12, 2008): 17872–77. http://dx.doi.org/10.1073/pnas.0806039105.

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Asexual organisms can be genetically variable and evolve through time, yet it is not known how genetic diversity is maintained in populations. In sexual organisms, negative frequency-dependent selection plays a role in maintaining diversity at some loci, but in asexual organisms, this mechanism could provide a general explanation for persistent genetic diversity because it acts on the whole genome and not just on some polymorphisms within a genome. Using field manipulations, we show that negative frequency-dependent selection maintains clonal diversity in an asexual mite species, and we link predicted equilibrium clonal frequencies to average frequencies in space and time. Intense frequency-dependent selection is likely to be a general mechanism for persistent genetic diversity in asexual organisms.

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Torres-Dini, Diego, Alexandre Magno Sebbenn, Ananda Virginia de Aguiar, Ana Vargas, Cecilia Rachid-Casnati, and Fernando Resquín. "Progeny Selection and Genetic Diversity in a Pinus taeda Clonal Seed Orchard." Forests 15, no. 10 (September 24, 2024): 1682. http://dx.doi.org/10.3390/f15101682.

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The present article describes the development of an improved Pinus taeda clonal seed orchard adapted to the edaphoclimatic conditions of Uruguay. Initially, 2068 hectares distributed in nine companies were prospected, and 124 plus trees were identified based on growth, straightness, and health traits. These trees were clonally propagated via grafting to establish a clonal seed orchard. For the genetic evaluation of the orchard, two progeny tests were carried out in the Rivera and Paysandú municipalities. Quantitative genetic analyses allowed us to identify a simple genotype–environment interaction and an expected genetic gain for volumes of 17%, 13%, and 8% for selection intensities of 12%, 25%, and 50%, respectively. Moreover, the genetic diversity of the 124 clones of the orchard was assessed using 10 microsatellite markers. The fingerprinting profiles allowed us to identify a total of 224 alleles. The polymorphism information content of the different markers was in the range of 0.594 to 0.895. The combined probability of identity and probability of identity among siblings had a discrimination power of 8.26 × 10–14 and 5.91 × 10–5, respectively. Analysis of the genetic structure demonstrated that the seed orchard population was not structured by the supplier.

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Hanko, Gina Renee, Maria Therese Vogel, Vivian Negrón-Ortiz, and Richard C. Moore. "High Prevalence of Clonal Reproduction and Low Genetic Diversity in Scutellaria floridana, a Federally Threatened Florida-Endemic Mint." Plants 12, no. 4 (February 17, 2023): 919. http://dx.doi.org/10.3390/plants12040919.

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The threatened mint Florida skullcap (Scutellaria floridana) is endemic to four counties in the Florida panhandle. Because development and habitat modification extirpated several historical occurrences, only 19 remain to date. To inform conservation management and delisting decisions, a comprehensive investigation of the genetic diversity and relatedness, population structure, and clonal diversity was conducted using SNP data generated by ddRAD. Compared with other Lamiaceae, we detected low genetic diversity (HE = 0.125–0.145), low to moderate evidence of inbreeding (FIS = −0.02–0.555), and moderate divergence (FST = 0.05–0.15). We identified eight populations with most of the genetic diversity, which should be protected in situ, and four populations with low genetic diversity and high clonality. Clonal reproduction in our circular plots and in 92% of the sites examined was substantial, with average clonal richness of 0.07 and 0.59, respectively. Scutellaria floridana appears to have experienced a continued decline in the number of extant populations since its listing under the Endangered Species Act; still, the combination of sexual and asexual reproduction may be advantageous for maintaining the viability of extant populations. However, the species will likely require ongoing monitoring, management, and increased public awareness to ensure its survival and effectively conserve its genetic diversity.

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Duchosal, M. A., R. Kofler, R. S. Balderas, M. T. Aguado, F. J. Dixon, and A. N. Theofilopoulos. "Genetic diversity of murine rheumatoid factors." Journal of Immunology 142, no. 5 (March 1, 1989): 1737–42. http://dx.doi.org/10.4049/jimmunol.142.5.1737.

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Abstract Anti-Ig autoantibodies (rheumatoid factors, RF) have been implicated in the pathogenesis of human and murine rheumatoid arthritis as well as in the regulation of normal immune responses. Their genetic origin, clonal diversity, and inducing agents, and the relatedness between RF associated with disease and those occurring under physiologic conditions are not well understood. In this study, the genetic and clonotypic origin of 34 monoclonal IgM RF-secreting hybridomas from arthritic MRL-lpr/lpr and nonarthritic MRL-+/+ and C57BL/6-lpr/lpr mice was examined by RNA hybridization. For this purpose, we used probes for 10 VH and 13 Vk gene families as well as all JH and Jk gene segments. The majority of hybridomas expressed distinct Ig gene segment patterns and, hence, were clonally unrelated. Overall, a variety of different V and J gene segments were expressed in the hybridoma panel, suggesting that a large number of distinct genetic elements participates in expression of RF-like activity. RF from arthritic mice expressed Vk messages from the overlapping Vk22 and Vk28 gene families more frequently than did those from nonarthritic mice. RF from autoimmune MRL mice, both arthritic MRL-lpr/lpr and nonarthritic MRL-+/+, showed skewed JH4 segment usage, whereas those from C57BL/6-lpr/lpr preferentially expressed JH2.

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Vonlanthen, Beatrix, Ximing Zhang, and Helge Bruelheide. "Clonal structure and genetic diversity of three desert phreatophytes." American Journal of Botany 97, no. 2 (February 2010): 234–42. http://dx.doi.org/10.3732/ajb.0800329.

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Wodkiewicz, Maciej, and Bożenna Gruszczyńska. "Genetic Diversity and Spatial Genetic Structure of Stellaria Holostea Populations from Urban Forest Islands." Acta Biologica Cracoviensia s. Botanica 56, no. 1 (September 12, 2014): 42–53. http://dx.doi.org/10.2478/abcsb-2014-0004.

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Abstract Stellaria holostea is a clonal herb highly confined to well-established deciduous forests. This study examined whether its genetic diversity and spatial genetic organization in urban forest islands is similar to the values from well-established populations outside urban landscape. We studied four populations in Warsaw and two populations from well preserved forests outside the city. Genetic diversity was greater in populations from well-preserved forests than from forests heavily exploited in the past. High clonal diversity indices indicate that the studied populations did not lose the ability to reproduce sexually. The small populations in urban forests differed from the remaining sites in spatial organization. High overall FST (0.24) and the lack of correlation between genetic and geographic distance between the studied populations indicate limited gene flow. Urban forests may be of great value for conservation of S. holostea and other ancient forest species as they may still harbor substantial genetic variability despite their isolation.

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GROVE-WHITE, D. H., A. J. H. LEATHERBARROW, P. J. CRIPPS, P. J. DIGGLE, and N. P. FRENCH. "Molecular epidemiology and genetic diversity ofCampylobacter jejuniin ruminants." Epidemiology and Infection 139, no. 11 (December 7, 2010): 1661–71. http://dx.doi.org/10.1017/s0950268810002736.

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SUMMARYMulti-locus sequence typing was performed on 1003Campylobacter jejuniisolates collected in a 2-year longitudinal study of 15 dairy farms and four sheep farms in Lancashire, UK. There was considerable farm-level variation in occurrence and prevalence of clonal complexes (CC). Clonal complexes ST61, ST21, ST403 and ST45 were most prevalent in cattle while in sheep CC ST42, ST21, ST48 and ST52 were most prevalent. CC ST45, a complex previously shown to be more common in summer months in human cases, was more prevalent in summer in our ruminant samples. Gene flow analysis demonstrated a high level of genetic heterogeneity at the within-farm level. Sequence-type diversity was greater in cattle compared to sheep, in cattle at pasturevs. housed, and in isolates from farms on the Pennines compared to the Southern Fylde. Sequence-type diversity was greatest in isolates belonging to CC ST21, ST45 and ST206.

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Shufran, Kevin A., and Gerald E. Wilde. "Clonal diversity in overwintering populations of Schizaphis graminum (Homoptera: Aphididae)." Bulletin of Entomological Research 84, no. 1 (March 1994): 105–14. http://dx.doi.org/10.1017/s0007485300032272.

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AbstractThe intergenic spacer region of the rRNA cistron was used as a molecular fingerprinting probe to study clonal diversity in Schizaphis graminum (Rondani). A high degree of clonal diversity was found in overwintering populations on wheat from Kansas, Texas and Oklahoma. Out of 184 individuals tested, 132 unique maternal lineages wereidentified. Overall, clonal diversity of overwintering populations was no less than in spring and summer populations. However, in some fields there were more instances where individuals of the same genotype were identified. By partitioning the total population diversity into various sampling components (fields, counties and states), 93.1% of the total diversity was found among individual S. graminum within fields. Overwintering of many genetically distinct clones as parthenogenetic morphs is one mechanism by which clonal diversity is maintained in populations of S. graminum. The incidence of clonal diversity further substantiates the importance of the S. graminum holocycle for generating genetic heterogeneity in the USA.

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Behera, M. K., N. Bhola, A. K. Parida, and T. R. Pradhan. "Assessment of inter-population genetic diversity and preliminary evaluation of suitable clones of teak (Tectona grandis Linn. F.)." Journal of Applied and Natural Science 8, no. 1 (March 1, 2016): 273–78. http://dx.doi.org/10.31018/jans.v8i1.785.

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Productivity, uniformity and sustainability are the three important characters of the clonally propagated plants. With the increased use of clonal technology, the scarcity of wood products evidently decreased which has also led to reduced pressure on natural forests and ecosystem. However, the success of clonal technology rests on wise selection and deployment of suitable clones by studying the inter-population genetic diversity. The present study was conducted in a clonal seed orchard (CSO) of teak (Tectona grandis Linn. F.) comprising of 13 different clones to estimate the inter-clonal variation in terms of growth performance and genetic variability at 32 and 33 years of age. Clone ORANP2 exhibited maximum DBH (26.61cm), height (23.69 m), and stem volume (235.40 m3ha-1) with MAI of 7.133 m3ha-1year-1. The highest CAI of DBH (1.08 cm) and volume (18.558m3/ha) was reported in ORANP5 and ORANR3, respectively. The study found that clone ORANP2 is a superior genotype and thus can be recommended for vegetative multiplication and ex-situ mass planting in reforestation programmes. Both heritability and genetic advance values were low for all the plant traits studied (DBH, height and stem volume) indicating that these traits are of less use for a tree breeder for furthering the selection and breeding process on teak or other tropical hardwood species across globe.

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Carbognani, M., A. Piotti, S. Leonardi, L. Pasini, I. Spanu, G. G. Vendramin, M. Tomaselli, and A. Petraglia. "Reproductive and genetic consequences of extreme isolation in Salix herbacea L. at the rear edge of its distribution." Annals of Botany 124, no. 5 (July 31, 2019): 849–60. http://dx.doi.org/10.1093/aob/mcz129.

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Abstract Background and Aims At the rear edge of the distribution of species, extreme isolation and small population size influence the genetic diversity and differentiation of plant populations. This may be particularly true for Arctic-alpine species in mid-latitude mountains, but exactly how peripherality has shaped their genetic and reproductive characteristics is poorly investigated. The present study, focused on Salix herbacea, aims at providing new insights into the causes behind ongoing demographic dynamics and their consequences for peripheral populations of Arctic-alpine species. Methods We performed a whole-population, highly detailed sampling of the only two S. herbacea populations in the northern Apennines, comparing their clonal and genetic diversity, sex ratio and spatial genetic structure with a reference population from the Alps. After inspecting ~1800 grid intersections in the three populations, 563 ramets were genotyped at 11 nuclear microsatellite markers (nSSRs). Past demography and mating patterns of Apennine populations were investigated to elucidate the possible causes of altered reproductive dynamics. Key Results Apennine populations, which experienced a Holocene bottleneck and are highly differentiated (FST = 0.15), had lower clonal and genetic diversity compared with the alpine population (RMLG = 1 and HE = 0.71), with the smaller population exhibiting the lowest diversity (RMLG = 0.03 and HE = 0.24). An unbalanced sex ratio was found in the larger (63 F:37 M) and the smaller (99 F:1 M) Apennine population. Both were characterized by the presence of extremely large clones (up to 2500 m2), which, however, did not play a dominant role in local reproductive dynamics. Conclusions Under conditions of extreme isolation and progressive size reduction, S. herbacea has experienced an alteration of genetic characteristics produced by the prevalence of clonal growth over sexual reproduction. However, our results showed that the larger Apennine population has maintained levels of sexual reproduction enough to counteract a dramatic loss of genetic and clonal diversity.

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Beltrán, Pilar, Gabriela Delgado, Armando Navarro, Francisca Trujillo, Robert K. Selander, and Alejandro Cravioto. "Genetic Diversity and Population Structure ofVibrio cholerae." Journal of Clinical Microbiology 37, no. 3 (1999): 581–90. http://dx.doi.org/10.1128/jcm.37.3.581-590.1999.

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Multilocus enzyme electrophoresis (MLEE) of 397 Vibrio cholerae isolates, including 143 serogroup reference strains and 244 strains from Mexico and Guatemala, identified 279 electrophoretic types (ETs) distributed in two major divisions (I and II). Linkage disequilibrium was demonstrated in both divisions and in subdivision Ic of division I but not in subdivision Ia, which includes 76% of the ETs. Despite this evidence of relatively frequent recombination, clonal lineages may persist for periods of time measured in at least decades. In addition to the pandemic clones of serogroups O1 and O139, which form a tight cluster of four ETs in subdivision Ia, MLEE analysis identified numerous apparent clonal lineages of non-O1 strains with intercontinental distributions. A clone of serogroup O37 that demonstrated epidemic potential in the 1960s is closely related to the pandemic O1/O139 clones, but the nontoxigenic O1 Inaba El Tor reference strain is not. A strain of serogroup O22, which has been identified as the most likely donor of exogenous rfb region DNA to the O1 progenitor of the O139 clone, is distantly related to the O1/O139 clones. The close evolutionary relationships of the O1, O139, and O37 epidemic clones indicates that new cholera clones are likely to arise by the modification of a lineage that is already epidemic or is closely related to such a clone.

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Milo, Idan, Marie Bedora-Faure, Zacarias Garcia, Ronan Thibaut, Leïla Périé, Guy Shakhar, Ludovic Deriano, and Philippe Bousso. "The immune system profoundly restricts intratumor genetic heterogeneity." Science Immunology 3, no. 29 (November 23, 2018): eaat1435. http://dx.doi.org/10.1126/sciimmunol.aat1435.

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Tumors develop under the selective pressure of the immune system. However, it remains critical to establish how the immune system affects the clonal heterogeneity of tumors that often display cell-to-cell variation in genetic alterations and antigenic expression. To address these questions, we introduced a multicolor barcoding strategy to study the growth of a MYC-driven B cell lymphoma harboring a large degree of intratumor genetic diversity. Using intravital imaging, we visualized that lymphoma subclones grow as patches of sessile cells in the bone marrow, creating a spatially compartmentalized architecture for tumor diversity. Using multicolor barcoding and whole-exome sequencing, we demonstrated that immune responses strongly restrict intratumor genomic diversity and favor clonal dominance, a process mediated by the selective elimination of more immunogenic cells and amplified by epitope spreading. Anti–PD-1 treatment also narrowed intratumor diversity. Our results provide direct evidence that immune pressure shapes the level of intratumor genetic heterogeneity and have important implications for the design of therapeutic strategies.

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Gurung, S., D. P. G. Short, Z. K. Atallah, and K. V. Subbarao. "Clonal Expansion of Verticillium dahliae in Lettuce." Phytopathology® 104, no. 6 (June 2014): 641–49. http://dx.doi.org/10.1094/phyto-10-13-0282-r.

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Few studies in population biology have documented how structure and diversity of pathogens evolve over time at local scales. With the historical samples of Verticillium dahliae available from lettuce, we investigated the structure and diversity of this pathogen in time and space. Three hundred twenty-nine V. dahliae isolates from lettuce fields collected over 18 years were characterized with polymorphic microsatellite markers and polymerase chain reaction tests for race and mating type. Genetic variation within and among commercial lettuce fields in a single season was also investigated using an additional 146 isolates. Sixty-two haplotypes (HTs) were observed among the 329 isolates. A single HT was frequently observed over multiple years and locations (61.40%). Genetic diversity, allelic richness, and private allelic richness suggested a relatively recent clonal expansion. Race 1 (93.63%) and MAT1-2-1 (99.69%) were overwhelmingly represented among the isolates. Linkage disequilibrium was significant (P < 0.001) for all populations, suggesting limited sexual recombination in the sampled populations from lettuce. Populations from 2006, 2009, and 2010 had higher numbers of unique HTs, implying a recent introduction of novel HTs. We conclude that V. dahliae population from lettuce evaluated in this study is expanding clonally, consistent with an asexually reproducing pathogen, and the movement of clonal genotypes locally occurs over time.

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Denoyes-Rothan, Béatrice, Guy Guérin, Christophe Délye, Barbara Smith, Dror Minz, Marcel Maymon, and Stanley Freeman. "Genetic Diversity and Pathogenic Variability Among Isolates of Colletotrichum Species from Strawberry." Phytopathology® 93, no. 2 (February 2003): 219–28. http://dx.doi.org/10.1094/phyto.2003.93.2.219.

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Ninety-five isolates of Colletotrichum including 81 isolates of C. acutatum (62 from strawberry) and 14 isolates of C. gloeosporioides (13 from strawberry) were characterized by various molecular methods and pathogenicity tests. Results based on random amplified polymorphic DNA (RAPD) polymorphism and internal transcribed spacer (ITS) 2 sequence data provided clear genetic evidence of two subgroups in C. acutatum. The first subgroup, characterized as CA-clonal, included only isolates from strawberry and exhibited identical RAPD patterns and nearly identical ITS2 sequence analysis. A larger genetic group, CA-variable, included isolates from various hosts and exhibited variable RAPD patterns and divergent ITS2 sequence analysis. Within the C. acutatum population isolated from strawberry, the CA-clonal group is prevalent in Europe (54 isolates of 62). A subset of European C. acutatum isolates isolated from strawberry and representing the CA-clonal and CA-variable groups was assigned to two pathogenicity groups. No correlation could be drawn between genetic and pathogenicity groups. On the basis of molecular data, it is proposed that the CA-clonal subgroup contains closely related, highly virulent C. acutatum isolates that may have developed host specialization to strawberry. C. gloeosporioides isolates from Europe, which were rarely observed were either slightly or nonpathogenic on strawberry. The absence of correlation between genetic polymorphism and geographical origin in Colletotrichum spp. suggests a worldwide dissemination of isolates, probably through international plant exchanges.

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YANG, Ya-Jun, Ji-Ning LI, Lei GONG, and Jian ZHOU. "Clonal Structure and Genetic Diversity of NaturalSyringa pinnatifoliavar.alanshanicaAssessed by ISSR." Plant Science Journal 31, no. 1 (2013): 85. http://dx.doi.org/10.3724/sp.j.1142.2013.10085.

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Yeeh, Yeehn, Soon Suk Kang, Hye Gi Chung, Mun Su Chung, and Myong Gi Chung. "Genetic and clonal diversity in Korean populations ofVitex rotundifolia (Verbenaceae)." Journal of Plant Research 109, no. 2 (June 1996): 161–68. http://dx.doi.org/10.1007/bf02344541.

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31

Li, Na, Xuesen Liu, Xiaolong Zhang, Chenjie Zhang, Xinyu Lu, Chenyang Sun, Chao Yu, and Le Luo. "Genetic diversity assessment of clonal plant Rosa persica in China." Journal of Genetic Engineering and Biotechnology 22, no. 4 (December 2024): 100405. http://dx.doi.org/10.1016/j.jgeb.2024.100405.

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Colles, F. M., K. Jones, R. M. Harding, and M. C. J. Maiden. "Genetic Diversity of Campylobacter jejuni Isolates from Farm Animals and the Farm Environment." Applied and Environmental Microbiology 69, no. 12 (December 2003): 7409–13. http://dx.doi.org/10.1128/aem.69.12.7409-7413.2003.

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ABSTRACT The genetic diversity of Campylobacter jejuni isolates from farm animals and their environment was investigated by multilocus sequence typing (MLST). A total of 30 genotypes, defined by allelic profiles (assigned to sequence types [STs]), were found in 112 C. jejuni isolates originating in poultry, cattle, sheep, starlings, and slurry. All but two of these genotypes belonged to one of nine C. jejuni clonal complexes previously identified in isolates from human disease and retail food samples and one clonal complex previously associated with an environmental source. There was some evidence for the association of certain clonal complexes with particular farm animals: isolates belonging to the ST-45 complex predominated among poultry isolates but were absent among sheep isolates, while isolates belonging to the ST-61 and ST-42 complexes were predominant among sheep isolates but were absent from the poultry isolates. In contrast, ST-21 complex isolates were distributed among the different isolation sources. Comparison with MLST data from 91 human disease isolates showed small but significant genetic differentiation between the farm and human isolates; however, representatives of six clonal complexes were found in both samples. These data demonstrate that MLST and the clonal complex model can be used to identify and compare the genotypes of C. jejuni isolates from farm animals and the environment with those from retail food and human disease.

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Ertekin, M. "Clone Fertility and Genetic Diversity in a Black Pine Seed Orchard." Silvae Genetica 59, no. 1-6 (December 1, 2010): 145–50. http://dx.doi.org/10.1515/sg-2010-0017.

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AbstractClonal variation in the number of female and male strobili was studied for three consecutive years (2002-2004) in a clonal black pine seed orchard in Turkey. The data showed large differences in female and male fertility among clones in the three years. The correlation between female and male strobilus production was negative and statistically significant in 2004, a good-flowering year. Clonal fertility and fertility variation, expressed by the sibling coefficient and coefficient of variation in strobilus production among 30 clones, were reported. Fertility varied among clones and among years, producing three-year averages of 99.3 and 801.6 for female and male strobili per ramet, respectively. Male fertility variation was higher than was female fertility variation in the three years. The status number, a measure of genetic diversity, was calculated as 26.4 (2002), 23.9 (2003), and 24.0 (2004). On average, the relative status number, estimated based on total fertility, was 86% of the census number. Sexual asymmetry calculations showed that clonal contributions would be balanced between genders. Some management activities such as adjusting ramet number to balance clone contributions and mixing of seeds from consecutive years are suggested for the black pine seed orchard.

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Shlush, Liran I. "Age-related clonal hematopoiesis." Blood 131, no. 5 (February 1, 2018): 496–504. http://dx.doi.org/10.1182/blood-2017-07-746453.

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Abstract Age-related alterations in the human blood system occur in B cells, T cells, cells of the innate system, as well as hematopoietic stem and progenitor cells (HSPCs). Interestingly, age-related, reduced genetic diversity can be identified at the stem cell level and also independently in B cells and T cells. This reduced diversity is most probably related to somatic mutations or to changes in the microenvironmental niche. Either process can select for specific clones or cause repeated evolutionary bottlenecks. This review discusses the age-related clonal expansions in the human HSPC pool, which was termed in the past age-related clonal hematopoiesis (ARCH). ARCH is defined as the gradual, clonal expansion of HSPCs carrying specific, disruptive, and recurrent genetic variants, in individuals without clear diagnosis of hematological malignancies. ARCH is associated not just with chronological aging but also with several other, age-related pathological conditions, including inflammation, vascular diseases, cancer mortality, and high risk for hematological malignancies. Although it remains unclear whether ARCH is a marker of aging or plays an active role in these various pathophysiologies, it is suggested here that treating or even preventing ARCH may prove to be beneficial for human health. This review also describes a decision tree for the diagnosis and follow-up for ARCH in a research setting.

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Towill, Leigh E. "Genetic Considerations for Germplasm Preservation of Clonal Materials." HortScience 23, no. 1 (February 1988): 91–95. http://dx.doi.org/10.21273/hortsci.23.1.91.

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Abstract The present diversity of plants used for the needs of society is immense and could expand greatly with the development of new crops and more extensive use of plants producing useful pharmacological compounds. We are relatively familiar with problems associated with germplasm preservation of major food crops, but such information is lacking for many minor crops. Aspects of genetics, physiology, and phenology must be considered to develop a useful and efficient means of germplasm preservation (29).

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LAURENT, J. P., C. BARNABE, V. QUESNEY, S. NOEL, and M. TIBAYRENC. "Impact of clonal evolution on the biological diversity of Trypanosoma cruzi." Parasitology 114, no. 3 (March 1997): 213–18. http://dx.doi.org/10.1017/s0031182096008414.

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Trypanosoma cruzi, the agent of Chagas' disease, exhibits considerable biological variability. Moreover, it has been postulated that populations of this protozoan are subdivided into natural clones, which can be separated from each other by considerable levels of evolutionary divergence. The authors have proposed that this long-term clonal evolution may have a profound impact on Trypanosoma cruzi biological diversity. In order to test this hypothesis, 16 T. cruzi stocks representing 3 major clonal genotypes of the parasite were analysed for 8 different in vitro biological parameters. The overall results show a strong statistical linkage between genetic and biological differences. This is in agreement with the working hypothesis, although a notable biological variability is observable among the stocks of each of the 3 major clonal genotypes. The authors propose that T. cruzi genetic variability must be taken into account in any applied study dealing with this parasite.

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Zhecheva, Keranka, Magdalena Koleva, and Ivan Kiryakov. "Sclerotinia sclerotiorum genetic diversity in Bulgaria." Bulgarian Journal of Crop Science 61, no. 5 (October 28, 2024): 97–104. http://dx.doi.org/10.61308/vcgv9451.

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The mycelial compatibility of 154 isolates of Sclerotinia sclerotiorum, obtained from sunflower and rapeseed plant samples, collected from 2019 - 2021 from 17 locations in Northern and Southern Bulgaria, was studied. The studied isolates were grouped into 108 local MCGs, and 60.1% included only one isolate. The Shannon index (Ho) at the studied locations varied from 0.718 to 1.00. The total diversity in MCG resulting from variation among individuals in the population was 92.2%, and the proportion of total diversity in MCG due to variation among populations was 7.78%. The clonal index for all populations was 0.299. In two of the six compatibility tests between isolates from different locations, 10 additional groups were formed, and one of them (MCGs-1D5x2D4x1SH3x1Y8) included six isolates from four locations (Dropla – Tsaricheno - Rish 1-Straldzha) located in three regions of the country. The results show significant genetic diversity in S. sclerotiorum populations based on mycelial compatibility between isolates.

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CIOCÎRLAN, Elena, Neculae ȘOFLETEA, Georgeta MIHAI, Maria TEODOSIU, and Alexandru L. CURTU. "Comparative analysis of genetic diversity in Norway spruce (Picea abies) clonal seed orchards and seed stands." Notulae Botanicae Horti Agrobotanici Cluj-Napoca 49, no. 4 (December 20, 2021): 12575. http://dx.doi.org/10.15835/nbha49412575.

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Norway spruce, Picea abies (L.) Karst. is the most important conifer species in Romania and the most planted tree species in the Carpathian Mountains. Here we compare the genetic diversity of four Norway spruce clonal seed orchards and two seed stands located in the Eastern Carpathians. A set of highly polymorphic nuclear microsatellite markers was used. The analysis of genotypic identity of ramets for each Norway spruce clone in all seed orchards indicated that nearly all sampled ramets (97%) were genetically identical. The genetic diversity in seed orchards (He=0.700) was slightly smaller compared to the seed stands (He=0.718). Allelic richness was higher in seed stands (10.874), compared to clonal seed orchards (8.941). The Bayesian analysis indicated a genetic structure with two clusters, one corresponding to the clonal seed orchards and a second one consisting of the two seed stands. Our results provide valuable information for the management of Norway spruce seed orchards in Romania.

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Hovens, Christopher, Matthew Hong, Geoff Macintyre, David Wedge, Peter Van Loo, Sebastian LunkePhD, Ludmil Alexandrov, et al. "Tracking clonal diversity in metastatic prostate cancer progression." Journal of Clinical Oncology 33, no. 7_suppl (March 1, 2015): 193. http://dx.doi.org/10.1200/jco.2015.33.7_suppl.193.

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193 Background: Genomic heterogeneity has been observed in a number of tumor types including prostate cancer. However, how subclonal tumor diversity changes during metastasis and progression to lethality remains unexplored. Large scale genomic analyses have reported the most prevalent somatic aberrations associated with the dominant clone of the tumor without permitting an analysis of subclonal complexity or how this complexity impinges on metastatic potential or resistance to treatment. Methods: To understand and track the evolution of lethal prostate cancer from initial therapy to end stage metastases, we performed longitudinal and multiregional sampling of tumors from 7 patients with lethal prostate cancer. We performed whole-genome sequencing, RNA sequencing, and SNP profiling. Computational approaches were used to reconstruct the genetic relationships and evolution of the tumors. These evolutionary tree reconstructions allowed us to observe the dynamics of chromoplexy and mutational processes along specific branches of tumor evolution. To refine the genetic landscape and spatial connections between subclones, we employed deep, targeted re-sequencing of variant loci in the original sequenced samples, in additional FFPE sites sampled from the organ confined tumors, and from blood. Results: We show that while all primary and metastatic prostate tumors share a single ancestral clone, metastases arise from subclones present at minor frequencies in the primary tumor. We reveal that individual metastases comprise mixtures of subclones indicative of intra-metastatic heterogeneity. We provide evidence for cross-metastatic site seeding and dynamic remolding of subclonal mixtures in response to therapy suggesting a distinct metastatic hierarchy. Ultra-deep sequencing of end-stage blood reveals the presence of diverse subclones with metastatic potential derived from various stages in the evolution of the tumor. Conclusions: Our results demonstrate unexpected complexity in the origins of both primary and metastatic prostate cancer, with distinct implications for treatment of advanced disease.

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TAMI, A., H. GRUNDMANN, C. SUTHERLAND, J. S. MCBRIDE, D. R. CAVANAGH, E. CAMPOS, G. SNOUNOU, C. BARNABÉ, M. TIBAYRENC, and D. C. WARHURST. "Restricted genetic and antigenic diversity of Plasmodium falciparum under mesoendemic transmission in the Venezuelan Amazon." Parasitology 124, no. 6 (June 2002): 569–81. http://dx.doi.org/10.1017/s0031182002001713.

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The study of genetic diversity in malaria populations is expected to provide new insights for the deployment of control measures. Plasmodium falciparum diversity in Africa and Asia is thought to reflect endemicity. In comprehensive epidemiological surveys reported here the genetic and antigenic structure of P. falciparum in the Venezuelan Amazon were studied over a 2-year period. DNA polymorphisms in glutamate-rich protein (GLURP), merozoite-surface protein 1 (MSP1) and MSP2 genes, in a multicopy element (PfRRM), all showed low diversity, 1 predominant genotype, and virtually no multi-clonal infections. Moreover, linkage disequilibrium was seen between GLURP, MSP1 and MSP2. Specific antibody responses against MSP1 and MSP2 recombinant antigens reflected the low genetic diversity observed in the parasite population. This is unexpected in a mesoendemic area, and suggests that the low diversity here may not only relate to endemicity but to other influences such as a bottleneck effect. Linkage disequilibrium and a predominant genotype may imply that P. falciparum frequently propagates with an epidemic or clonal population structure in the Venezuelan Amazon.

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Vega, Clara, Victoria Fernández, Luis Gil, and María Valbuena-Carabaña. "Clonal Diversity and Fine-Scale Genetic Structure of a Keystone Species: Ilex aquifolium." Forests 13, no. 9 (September 6, 2022): 1431. http://dx.doi.org/10.3390/f13091431.

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Resprouting species, such as English holly (Ilex aquifolium L.), can be severely affected by long-lasting forest management. In the present study, the clonal and fine-scale spatial genetic structure (FSGS) of English holly are evaluated in a sub-Mediterranean mixed forest of Central Spain, where this species was subjected to different and intense human interventions for centuries, including coppicing in dense structures and in open woody pastures. Using seven microsatellite loci, we assessed the contribution of clonal and sexual reproduction to the diversity of holly in both areas and the fine-scale genetic structure was evaluated. For the dense coppiced area, the results showed high clonal diversity derived mainly from stem resprouting. Stems were separated an average of 3 m and up to 10 m, and dense aggregations of stems sometimes included various genotypes. The results also showed recent seed recruitment leading to small unique and isolated genotypes. Furthermore, FSGS was detected at close distances as being stronger in the coppiced area than in the open woody pasture area, especially for individuals of greater diameter at breast height. The results obtained suggest that current management strategies are not negatively affecting the genetic diversity of this species.

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Sinclair, Elizabeth, Siegfried Krauss, Belinda Cheetham, and Richard Hobbs. "High genetic diversity in a clonal relict Alexgeorgea nitens (Restionaceae): implications for ecological restoration." Australian Journal of Botany 58, no. 3 (2010): 206. http://dx.doi.org/10.1071/bt09193.

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The importance of genetic issues associated with the sourcing of propagules is increasingly recognised for successful ecological restoration. A consideration of life history traits has contributed to ‘best-guess’ scenarios on the appropriate location and desirable properties of local provenance source populations, but these can lack precision. For clonal species, population genetic structure and variation will depend on the balance between the extent and growth rate of asexual clones, sexual reproduction, pollen dispersal, and subsequent seed dispersal and recruitment. We assessed patterns of population genetic structure and variation for Alexgeorgea nitens (Nees) L. Johnston & B. Briggs (Restionaceae), a dioecious, clonal, perennial species, with novel life history traits. Our results show high levels of genetic diversity within populations, and surprisingly low levels of population differentiation (ΦST = 0.17). We suggest that the high genetic diversity observed within these populations reflects extensive pollen dispersal and successful seeding (sexual reproduction) and recruitment events, even though direct observations of seedling recruitment are rare. In this case, a ‘best-guess’ propagule-sourcing scenario based on life-history traits that appear to limit dispersal capability does not predict the extent of high local genetic diversity and weak population genetic structure in A. nitens.

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Santos, Ronaldo Carvalho dos, José Luís Pires, Uilson Vanderley Lopes, Karina Peres G. Gramacho, Acassi Batista Flores, Rita de Cássia S. Bahia, Helaine C. Cristine Ramos, Ronan Xavier Corrêa, and Dario Ahnert. "Assessment of genetic diversity on a sample of cocoa accessions resistant to witches' broom disease based on RAPD and pedigree data." Bragantia 64, no. 3 (2005): 361–68. http://dx.doi.org/10.1590/s0006-87052005000300005.

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Genetic diversity in cocoa (Theobroma cacao L.) has been assessed based on morphological and molecular markers for germplasm management and breeding purposes. Pedigree data is available in cocoa but it has not been used for assessing genetic relatedness. The geneitic diversity of 30 clonal cocoa accessions resistant to witche´ broom disease, from the CEPEC series, were studied on the basis of RAPD data and pedigree information. Twenty of these accessions descend from the TSA-644 clone, originated from a cross between the Upper Amazon germplasm called Scavina-6, the main source of resistance to witches' broom disease, and IMC-67. The ten remaining clones come from different sources including Amazon and Trinitario germplasm. RAPD data was collected using 16 primers and pedigree information was obtained from the International Cocoa Germplasm Database. Genetic similarities, genetic distances and coefficient of parentage were calculated using available software. Relatively low genetic diversity was observed in this germplasm set, probably because of great genetic relatedness amongst accessions studied and the poor representation of the germplasm. The TSA-644 descendants were more diverse than the other accessions used in the study. This might be due to the origin of the TSA clone, which was derived from highly divergent genotypes. Association between genetic similarities based on RAPD data and coefficient of parentage, based on pedigree data, was very low, probably due to the homogeneity of the breeding stocks and poor pedigree information. These findings are useful to cocoa breeders in planning crosses for the development of hybrid and clonal cultivars.

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Silva, Vanessa, Sara Araújo, Andreia Monteiro, José Eira, José Eduardo Pereira, Luís Maltez, Gilberto Igrejas, Teresa Semedo Lemsaddek, and Patricia Poeta. "Staphylococcus aureus and MRSA in Livestock: Antimicrobial Resistance and Genetic Lineages." Microorganisms 11, no. 1 (January 3, 2023): 124. http://dx.doi.org/10.3390/microorganisms11010124.

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Animal production is associated with the frequent use of antimicrobial agents for growth promotion and for the prevention, treatment, and control of animal diseases, thus maintaining animal health and productivity. Staphylococcus aureus, in particular methicillin-resistant S. aureus (MRSA), can cause a variety of infections from superficial skin and soft tissue infections to life-threatening septicaemia. S. aureus represents a serious public health problem in hospital and community settings, as well as an economic and animal welfare problem. Livestock-associated MRSA (LA-MRSA) was first described associated with the sequence (ST) 398 that was grouped within the clonal complex (CC) 398. Initially, LA-MRSA strains were restricted to CC398, but over the years it has become clear that its diversity is much greater and that it is constantly changing, a trend increasingly associated with multidrug resistance. Therefore, in this review, we aimed to describe the main clonal lineages associated with different production animals, such as swine, cattle, rabbits, and poultry, as well as verify the multidrug resistance associated with each animal species and clonal lineage. Overall, S. aureus ST398 still remains the most common clone among livestock and was reported in rabbits, goats, cattle, pigs, and birds, often together with spa-type t011. Nevertheless, a wide diversity of clonal lineages was reported worldwide in livestock.

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Everhart, S. E., and H. Scherm. "Fine-Scale Genetic Structure of Monilinia fructicola During Brown Rot Epidemics Within Individual Peach Tree Canopies." Phytopathology® 105, no. 4 (April 2015): 542–49. http://dx.doi.org/10.1094/phyto-03-14-0088-r.

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The purpose of this study was to determine the fine-scale genetic structure of populations of the brown rot pathogen Monilinia fructicola within individual peach tree canopies to better understand within-tree plant pathogen diversity and to complement previous work on spatiotemporal development of brown rot disease at the canopy level. Across 3 years in a total of six trees, we monitored disease development, collected isolates from every M. fructicola symptom during the course of the season, and created high-resolution three-dimensional maps of all symptom and isolate locations within individual canopies using an electromagnetic digitizer. Each canopy population (65 to 173 isolates per tree) was characterized using a set of 13 microsatellite markers and analyzed for evidence of spatial genetic autocorrelation among isolates during the epidemic phase of the disease. Results showed high genetic diversity (average uh = 0.529) and high genotypic diversity (average D = 0.928) within canopies. The percentage of unique multilocus genotypes within trees was greater for blossom blight isolates (78.2%) than for fruit rot isolates (51.3%), indicating a greater contribution of clonal reproduction during the preharvest epidemic. For fruit rot isolates, between 54.2 and 81.7% of isolates were contained in one to four dominant clonal genotypes per tree having at least 10 members. All six fruit rot populations showed positive and significant spatial genetic autocorrelation for distance classes between 0.37 and 1.48 m. Despite high levels of within-tree pathogen diversity, the contribution of locally available inoculum combined with short-distance dispersal is likely the main factor generating clonal population foci and associated spatial genetic clustering within trees.

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Loxdale, H. D., B. Massonnet, G. Schöfl, and W. W. Weisser. "Evidence for a quiet revolution: seasonal variation in colonies of the specialist tansy aphid, Macrosiphoniella tanacetaria (Kaltenbach) (Hemiptera: Aphididae) studied using microsatellite markers." Bulletin of Entomological Research 101, no. 2 (November 10, 2010): 221–39. http://dx.doi.org/10.1017/s0007485310000477.

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AbstractIn cyclical parthenogens, clonal diversity is expected to decrease due to selection and drift during the asexual phase per number of asexual generations. The decrease in diversity may be counteracted by immigration of new genotypes. We analysed temporal variation in clonal diversity in colonies of the monophagous tansy aphid, Macrosiphoniella tanacetaria (Kaltenbach), sampled four times over the course of a growing season. In a related field study, we recorded aphid colony sizes and the occurrence of winged dispersers throughout the season. The number of colonies increased from April, when asexual stem mothers hatched from the sexually produced eggs, to the end of June. The proportion of colonies with winged individuals also increased over this period. After a severe reduction in colony sizes in late summer, a second expansion phase occurred in October when sexuals were produced. At the season's end, the only winged forms were males. A linked genetic study showed that the number of microsatellite multilocus genotypes and genetic variability assessed at three polymorphic loci per colony decreased from June to October. Overall, the relatedness of wingless to winged individuals within colonies was lower than average relatedness among wingless individuals, suggesting that winged forms mainly originated in different colonies. The results demonstrate that patterns of genetic diversity within colonies can be explained by the antagonistic forces of clonal selection, migration and genetic drift (largely due to midsummer population bottlenecks). We further suggest that the males emigrate over comparatively longer distances than winged asexual females.

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Stenstrom, Anna, B. Olle Jonsson, Ingibjorg S. jonsdottir, Torbjorn Fagerstrom, and Magnus Augner. "Genetic variation and clonal diversity in four clonal sedges (Carex) along the Arctic coast of Eurasia." Molecular Ecology 10, no. 2 (February 2001): 497–513. http://dx.doi.org/10.1046/j.1365-294x.2001.01238.x.

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De Ryck, Sander De, Dirk Reheul, Jan De De Riek, Ellen De De Keyser, and Benny De De Cauwer. "Genetic and Morphological Variation of Belgian Cyperus esculentus L. Clonal Populations and Their Significance for Integrated Management." Agronomy 13, no. 2 (February 16, 2023): 572. http://dx.doi.org/10.3390/agronomy13020572.

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Cyperus esculentus is an invasive troublesome neophyte in many arable crops across the globe. Analysis of the genetic and morphological profile of local C. esculentus clonal populations may be useful in explaining differential herbicide sensitivity found among distinct clonal populations and spatial distribution patterns. In this study, 35 Belgian C. esculentus clonal populations, evenly spread across the entire infestation area (30,689 km2) and covering a great diversity of farm and soil types, and hydrological and environmental conditions, were genetically characterized using amplified fragment length polymorphism (AFLP) profiling. These clonal populations were also grouped into different morphological clusters using data from shoot, tuber, and inflorescence number, fresh tuber biomass, individual fresh tuber weight, and number of germinable seeds collected in three consecutive years. Of the 271 AFLP markers, 207 were polymorphic. The gene diversity among clonal populations was 0.331 and three genetically distinct clusters were identified. Depending on observation year, clonal populations were grouped in four to five morphologically distinct clusters that closely aligned with the genetic clusters. The genetically distinct clusters differed in their geographical distribution pattern and range as well as in their morphological characteristics. Clonal populations belonging to clusters with broad distribution ranges produced numerous viable seeds. Clusters with clonal populations that produced large tubers were less widespread than the cluster with clonal populations producing many small tubers. The results suggest that tuber size, tuber number, and fecundity may all play an important role in the spread of C. esculentus. Morphotyping may be very useful in designing effective preventive and curative C. esculentus management strategies.

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Barrett, Spencer C. H. "Influences of clonality on plant sexual reproduction." Proceedings of the National Academy of Sciences 112, no. 29 (July 20, 2015): 8859–66. http://dx.doi.org/10.1073/pnas.1501712112.

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Flowering plants possess an unrivaled diversity of mechanisms for achieving sexual and asexual reproduction, often simultaneously. The commonest type of asexual reproduction is clonal growth (vegetative propagation) in which parental genotypes (genets) produce vegetative modules (ramets) that are capable of independent growth, reproduction, and often dispersal. Clonal growth leads to an expansion in the size of genets and increased fitness because large floral displays increase fertility and opportunities for outcrossing. Moreover, the clonal dispersal of vegetative propagules can assist “mate finding,” particularly in aquatic plants. However, there are ecological circumstances in which functional antagonism between sexual and asexual reproductive modes can negatively affect the fitness of clonal plants. Populations of heterostylous and dioecious species have a small number of mating groups (two or three), which should occur at equal frequency in equilibrium populations. Extensive clonal growth and vegetative dispersal can disrupt the functioning of these sexual polymorphisms, resulting in biased morph ratios and populations with a single mating group, with consequences for fertility and mating. In populations in which clonal propagation predominates, mutations reducing fertility may lead to sexual dysfunction and even the loss of sex. Recent evidence suggests that somatic mutations can play a significant role in influencing fitness in clonal plants and may also help explain the occurrence of genetic diversity in sterile clonal populations. Highly polymorphic genetic markers offer outstanding opportunities for gaining novel insights into functional interactions between sexual and clonal reproduction in flowering plants.

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Grimsby, J. L., D. Tsirelson, M. A. Gammon, and R. Kesseli. "Genetic diversity and clonal vs. sexual reproduction in Fallopia spp. (Polygonaceae)." American Journal of Botany 94, no. 6 (June 1, 2007): 957–64. http://dx.doi.org/10.3732/ajb.94.6.957.

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Journal articles on the topic 'Clonal and genetic diversity'

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