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opencc-by-4.0Jan 2020View details →

Responses of resistant and susceptible hybrid clones of Eucalyptus urophylla × Eucalyptus grandis to infection by Ceratocystis fimbriata

Responses of resistant and susceptible hybrid clones of Eucalyptus urophylla × Eucalyptus grandis to infection by Ceratocystis fimbriata The use of resistant genotypes of eucalypt is widely used to control Ceratocystis wilt caused by Ceratocystis fimbriata. However, little is known regarding the fungal infection process and the host defense responses. Thus, the objective of this study was to compare the histopathological responses of one resistant and one susceptible clone of Eucalyptus urophylla × Eucalyptus grandis to artificial inoculation with C. fimbriata and to identify possible host defense responses against fungal infection. Fungal colonization was analyzed by light and scanning electron microscopy. The host defense responses to artificial fungal inoculation were evaluated through histochemical analysis and determining of the lignin concentration and lesion lengths, whereas the pathogen viability was confirmed by reisolations. This excel file contains the raw data for each data table within a manuscript published  in Annals of Forest Science.

opencc-zeroJun 2020View details →

Variation in susceptibility of Eucalyptus grandis and selected hybrid clones to two termite species Macrotermes bellicosus and M. subhyalinus in Uganda

The maximum productivity of plantation forestry and its role in climate change mitigation, adaptation and resilience cannot be met without proper management. Termites in the genus Macrotermes have been reported as a major challenge to Eucalyptus plantation forestry establishment. The current study evaluated the susceptibility of four Eucalyptus hybrid clones; GU 7, GC 796, GC 550 and GC 796/2 and E. grandis to the most damaging Macrotermes bellicosus (Smeathman) and Macrotermes subhyalinus (Rambur) to identify tolerant material that can be planted in high incidence areas. The study involved exposure of moisture dry pieces of wood from E. grandis and the four hybrid clones to damage by M. bellicosus and M. subhyalinus. Results confirmed that M. bellicosus is the most aggressive. Results further revealed that E. grandis and GC 550 are the most susceptible whereas GC 796 is the most tolerant clone. The findings from the study will contribute to improved management of termites by planting tolerant material in high risk areas.

manual general clone validation results

Manual general clone validation results. These clones are detected from BigCloneBench.

general clones for recall measurement

General type-1, 2, and 3 clones generated automatically by Mutation Framework

large-variance clones for recall measurement

Large-variance clones automatically generated based on mutation techniques

manual large-variance clone validation results

Manual large-variance clone validation results

opencc-zeroDec 2016View details →

Data from: Neutral processes forming large clones during colonization of new areas

In species reproducing both sexually and asexually clones are often more common in recently established populations. Earlier studies have suggested that this pattern arises due to natural selection favouring generally or locally successful genotypes in new environments. Alternatively, as we show here, this pattern may result from neutral processes during species' range expansions. We model a dioecious species expanding into a new area in which all individuals are capable of both sexual and asexual reproduction, and all individuals have equal survival rates and dispersal distances. Even under conditions that favour sexual recruitment in the long run, colonisation starts with an asexual wave. After colonisation is completed, a sexual wave erodes clonal dominance. If individuals reproduce more than one season, and with only local dispersal, a few large clones typically dominate for thousands of reproductive seasons. Adding occasional long-distance dispersal, more dominant clones emerge, but they persist for a shorter period of time. The general mechanism involved is simple: edge effects at the expansion front favour asexual (uniparental) recruitment where potential mates are rare. Specifically, our model shows that neutral processes (with respect to genotype fitness) during the population expansion, such as random dispersal and demographic stochasticity, produce genotype patterns that differ from the patterns arising in a selection model. The comparison with empirical data from a postglacially established seaweed species (Fucus radicans) shows that in this case a neutral mechanism is strongly supported.

opencc-zeroDec 2014View details →

Data from: Offspring provisioning explains clone specific maternal age effects on life history and lifespan in the water flea, Daphnia pulex

Genetic inheritance underpins evolutionary theories of aging, but the role that nongenetic inheritance plays is unclear. Parental age reduces the life span of offspring in a diverse array of taxa but has not been explained from an evolutionary perspective. We quantified the effect that maternal age had on the growth and maturation decisions, life history, rates of senescence, and life span of offspring from three Daphnia pulex clones collected from different populations. We then used those data to test general hypotheses proposed to explain maternal age effects on offspring life span. Three generations of breeding from young or old mothers produced dramatic differences in the life histories of fourth-generation offspring, including significant reductions in life span. The magnitude of the effect differed between clones, which suggests that genetic and nongenetic factors ultimately underpin trait inheritance and shape patterns of aging. Older parents did not transmit a senescent state to their offspring. Instead, offspring from older ancestors had increased early-life reproductive effort, which resulted in an earlier onset of reproductive senescence, and an increased rate of actuarial senescence, which shortened their life span. Our results provide a clear example of the need to consider multiple inheritance mechanisms when studying trait evolution.

opencc-zeroDec 2013View details →

Data from: PCR duplication: a one-step cloning-free method to generate duplicated chromosomal loci and interference-free expression reporters in yeast

Here, we report on a novel PCR targeting-based strategy called 'PCR duplication' that enables targeted duplications of genomic regions in the yeast genome using a simple PCR-based approach. To demonstrate its application we first duplicated the promoter of the FAR1 gene in yeast and simultaneously inserted a GFP downstream of it. This created a reporter for promoter activity while leaving the FAR1 gene fully intact. In another experiment, we used PCR duplication to increase the dosage of a gene in a discrete manner, from 1× to 2x. Using TUB4, the gene encoding for the yeast γ-tubulin, we validated that this led to corresponding increases in the levels of mRNA and protein. PCR duplication is an easy one-step procedure that can be adapted in different ways to permit rapid, disturbance-free investigation of various genomic regulatory elements without the need for ex vivo cloning.

opencc-zeroDec 2017View details →

Data from: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.

opencc-zeroOct 2019View details →

The origin and genetic variability of vegetatively propagated clones identified from old planted trees and plantations of Thujopsis dolabrata var. hondae in Ishikawa Prefecture, Japan

<a name="_Hlk10084612">Clonal plantations of Thujopsis dolabrata var. hondae have been established in Ishikawa Prefecture, Japan, since at least the 1800s. Historical planting of the species has led to the development of vegetatively propagated local cultivars, which originated from 'donor' trees that have often been conserved in sacred groves or avenues at shrines and temples. These donor trees must have been selected from natural populations. In this study we estimated the origin and genetic variability of clones identified among old planted trees and clonal plantations of T. dolabrata var. hondae, using 19 microsatellite markers. We discovered 12 clones among old planted trees, including five identical to members of a set of 14 we previously identified in plantations (giving 21 clones in total). Based on analyses combining assignment and exclusion tests, we inferred origins of eight of those 21 clones: six may have originated from a natural population distributed in Ishikawa, one from Hokkaido & Aomori, and the other from Iwate & Yamagata, suggesting the clones constituting cultivars have multiple origins. The clones identified in plantations have significantly lower genetic variability, and higher relatedness, indicating that clones of cultivars have a much narrower genetic base than those of natural populations. We suggest new clones selected from natural populations</a> elsewhere, as well as Ishikawa, are needed for future breeding of T. dolabrata var. hondae to develop clonal forestry for this species.

opencc-zeroDec 2016View details →

Data from: Host species of a sexual-parasite do not differentiate between clones of Amazon mollies

A major mechanism of pre-zygotic isolation is the ability for individuals to recognize conspecifics. In gynogenetic species complexes, the sexual host species occur in syntopy with the unisexual species that relies on the sexuals' sperm for reproduction, which provide an excellent opportunity for the evolution of fine-tuned species recognition capabilities. Here, we examined if males and females from both parental species (sailfin molly, Poecilia latipinna, and Atlantic molly, P. mexicana) can distinguish between different clonal lineages of the hybrid, all-female Amazon molly (P. formosa). Both males and females were presented with the choice of two different pairings of Amazon mollies: 1) a sympatric female and an allopatric female; and 2) two sympatric females. We found that neither males nor females of sailfin or Atlantic mollies show a preference for a clone type. These results suggest that either the parental species do not have the ability to recognize different Amazon molly clones or they recognize but do not have a preference for a specific Amazon molly clone.

opencc-zeroSep 2019View details →

Susceptibility of Eucalyptus hybrid clones to Botryosphaeria canker in Uganda

The study assessed susceptibility of the nine commonly grown Eucalyptus clones to Neofusicoccum species associated with Botryosphaeria canker in Uganda. The inoculation trials indicated that susceptibility of Eucalyptus hybrids differed significantly (p=0.000), clones GU609, GU7, GC578, and GC796 exhibiting a higher tolerance than GC784, GC550, GU8, GC514 and GC540. The results further revealed that N. parvum was more pathogenic than N. kwambonambiense. The generated information can be exploited by expanding the growing of tolerant hybrids in areas with high Botryosphaeria canker disease pressure.

opencc-zeroDec 2018View details →

Data from: How clonal are clones? A quest for loss of heterozygosity during asexual reproduction in Daphnia magna

Due to the lack of recombination, asexual organisms are predicted to accumulate mutations and show high levels of within-individual allelic divergence (heterozygosity) however, empirical evidence for this prediction is largely missing. Instead, evidence of genome homogenization during asexual reproduction is accumulating. Ameiotic crossover recombination is a mechanism that could lead to long genomic stretches of loss of heterozygosity (LOH) and unmasking of mutations that have little or no effect in heterozygous state. Therefore, LOH might be an important force for inducing variation among asexual offspring and may contribute to the limited longevity of asexual lineages. To investigate the genetic consequences of asexuality, here we used high-throughput sequencing of Daphnia magna for assessing the rate of LOH over a single generation of asexual reproduction. Comparing parthenogenetic daughters with their mothers at several thousand genetic markers generated by Restriction site Associated DNA (RAD) sequencing resulted in high LOH rate estimation that largely overlapped with our estimates for the error rate. To distinguish these two, we Sanger re-sequenced the top 18 candidate RAD-loci for LOH, and all of them proved to be false positives. Hence, even though we cannot exclude the possibility that short stretches of LOH occur in genomic regions not covered by our markers, we conclude that LOH does not occur frequently during asexual reproduction in D. magna and ameiotic crossovers are very rare or absent. This finding suggests that clonal lineages of D. magna will remain genetically homogeneous at least over time periods typically relevant for experimental work.

opencc-zeroDec 2011View details →

Data from: Assessing parameter identifiability in phylogenetic models using Data Cloning

The success of model-based methods in phylogenetics has motivated much research aimed at generating new, biologically informative models. This new computer-intensive approaches to phylogenetics demands validation studies and sound measures of performance. To date such work has consisted only of simulation studies, estimation of known phylogenies and difficult mathematical analyses assessing the estimability of parameters. Little practical guidance has been available to practitioners and theoreticians alike as to when and why the parameters in a particular model can be identified reliably. Here, we illustrate how Data Cloning (DC), a recently developed methodology to compute the Maximum Likelihood estimates along with their asymptotic variance, can be used to diagnose structural parameter non-identifiability (NI) and distinguish it from other parameter estimability problems including the case where parameters are structurally identifiable, but are not estimable in given data set (INE), and the case where parameters are identifiable, and estimable, but only weakly so (WE). The application of the DC theorem uses well-known and widely used Bayesian computational techniques. With the DC approach, practitioners can use any Bayesian phylogenetics software to be able to diagnose non-identifiability. Theoreticians and practitioners alike now have a powerful tool to detect non-identifiability while investigating complex modeling scenarios, where getting closed-form expressions in a probabilistic study is complicated. Furthermore, here we also show how DC can be used as a tool to examine and eliminate the influence of the priors, in particular if the process of prior elicitation is not straightforward. Finally, when applied to phylogenetic inference, DC can be used to study at least two important statistical questions: assessing identifiability of discrete parameters, like the tree topology, and developing efficient sampling methods for computationally expensive posterior densities.

opencc-zeroDec 2014View details →

Data from: Species level phylogeny and polyploid relationships in Hordeum (Poaceae) inferred by next-generation sequencing and in-silico cloning of multiple nuclear loci

Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-group species. Amplicons from each of 96 individuals were pooled, sheared, labeled with individual-specific barcodes and sequenced in a single run on a 454 platform. Reference sequences were obtained by cloning and Sanger sequencing of all loci for nine supplementary individuals. The 454 reads were assembled into contigs representing the 13 loci and, for polyploids, also homoeologues. Phylogenetic analyses were conducted for all loci separately and for a concatenated data matrix of all loci. For diploid taxa, a Bayesian concordance analysis and a coalescent-based dated species tree was inferred from all gene trees. Chloroplast matK was used to determine the maternal parent in allopolyploid taxa. The relative performance of different multilocus analyses in the presence of incomplete lineage sorting and hybridization was also assessed. The resulting multilocus phylogeny reveals for the first time species phylogeny and progenitor-derivative relationships of all di- and polyploid Hordeum taxa within a single analysis. Our study proves that it is possible to obtain a multilocus species-level phylogeny for di- and polyploid taxa by combining PCR with next-generation sequencing, without cloning and without creating a heavy load of sequence data.