Publications
NIBIOs employees contribute to several hundred scientific articles and research reports every year. You can browse or search in our collection which contains references and links to these publications as well as other research and dissemination activities. The collection is continously updated with new and historical material.
2019
Authors
CKM Tsui S Beauseigle Dario Isidro Ojeda Alayon AV Rice JEK Cooke FAH Sperling AD Roe RC HamelinAbstract
No abstract has been registered
Authors
N. Feau Dario Isidro Ojeda Alayon S. Beauseigle G. J. Bilodeau A. Brar S. Cervantes-Arango A. L. Dale B. Dhillon C. Hammett P. Herath S. F. Shamoun C. K. M. Tsui P. Tanguay R. C. HamelinAbstract
Early detection provides the best way to prevent introduction and establishment of alien plant pathogens. Amplification of DNA by PCR has revolutionized the detection and monitoring of plant pathogens. Most of those assays rely on the amplification of a fraction of the genome of the targeted species. With the availability of whole genomes for a growing number of fungi and oomycetes it is becoming possible to compare genomes and discover regions that are unique to a target organism. This study has applied this pipeline to develop a set of hierarchical TaqMan real‐time PCR detection assays targeting DNA of all four Phytophthora ramorum lineages, and a closely related species, P. lateralis. Nine assays were generated: three targeting DNA of all P. ramorum lineages, one for each lineage of P. ramorum, one for P. lateralis and one targeting DNA of P. ramorum and P. lateralis. These assays were very accurate and sensitive, ranging from 98.7% to 100% detection accuracy of 2–10 gene copies of the targeted taxa from pure cultures or inoculated tissues. This level of sensitivity is within the lowest theoretical limit of detection of DNA. It is expected that these assays will be useful because of their high level of specificity and the ease with which they can be multiplexed because of the inherent flexibility in primer and probe design afforded by their lack of conservation in non‐target species.
Authors
Dario Isidro Ojeda Alayon Erik Koenen Sandra Cervantes Manuel de la Estrella Eulalia Banguera-Hinestroza Steven B. Janssens Jérémy Migliore Boris B. Demenou Anne Bruneau Félix Forest Olivier J. HardyAbstract
Detarioideae is well known for its high diversity of floral traits, including flower symmetry, number of organs, and petal size and morphology. This diversity has been characterized and studied at higher taxonomic levels, but limited analyses have been performed among closely related genera with contrasting floral traits due to the lack of fully resolved phylogenetic relationships. Here, we used four representative transcriptomes to develop an exome capture (target enrichment) bait for the entire subfamily and applied it to the Anthonotha clade using a complete data set (61 specimens) representing all extant floral diversity. Our phylogenetic analyses recovered congruent topologies using ML and Bayesian methods. Anthonotha was recovered as monophyletic contrary to the remaining three genera (Englerodendron, Isomacrolobium and Pseudomacrolobium), which form a monophyletic group sister to Anthonotha. We inferred a total of 35 transitions for the seven floral traits (pertaining to flower symmetry, petals, stamens and staminodes) that we analyzed, suggesting that at least 30% of the species in this group display transitions from the ancestral condition reconstructed for the Anthonotha clade. The main transitions were towards a reduction in the number of organs (petals, stamens and staminodes). Despite the high number of transitions, our analyses indicate that the seven characters are evolving independently in these lineages. Petal morphology is the most labile floral trait with a total of seven independent transitions in number and seven independent transitions to modification in petal types. The diverse petal morphology along the dorsoventral axis of symmetry within the flower is not associated with differences at the micromorphology of petal surface, suggesting that in this group all petals within the flower might possess the same petal identity at the molecular level. Our results provide a solid evolutionary framework for further detailed analyses of the molecular basis of petal identity.
Abstract
On the basis of a new phylogeny of the Detarioideae, with a particular focus on Englerodendron Harms, Anthonotha P.Beauv. and related genera, the possible options for delimiting monophyletic genera are discussed. As a result, Isomacrolobium Aubrév. & Pellegr. and Pseudomacrolobium Hauman are synonymised under Englerodendron. The following 12 new combinations are formed within the expanded Englerodendron: E. brachyrhachis (Breteler) Estrella & Ojeda, E. explicans (Baill.) Estrella & Ojeda, E. graciliflorum (Harms) Estrella & Ojeda, E. hallei (Aubrév.) Estrella & Ojeda, E. isopetalum (Harms) Breteler & Wieringa, E. lebrunii (J.Léonard) Estrella & Ojeda, E. leptorrhachis (Harms) Estrella & Ojeda, E. mengei (De Wild.) Estrella & Ojeda, E. nigericum (Baker f.) Estrella & Ojeda, E. obanense (Baker f.) Estrella & Ojeda, E. triplisomere (Pellegr.) Estrella & Ojeda and E. vignei (Hoyle) Estrella & Ojeda. A key to identification of the 17 species now recognised within Englerodendron is presented.
Authors
Dario Isidro Ojeda Alayon Tiina M. Mattila Tom Ruttink Sonja T. Kujala Katri Kärkkäinen Jukka-Pekka Verta Tanja PyhäjärviAbstract
Compared to angiosperms, gymnosperms lag behind in the availability of assembled and annotated genomes. Most genomic analyses in gymnosperms, especially conifer tree species, rely on the use of de novo assembled transcriptomes. However, the level of allelic redundancy and transcript fragmentation in these assembled transcriptomes, and their effect on downstream applications have not been fully investigated. Here, we assessed three assembly strategies for short-reads data, including the utility of haploid megagametophyte tissue during de novo assembly as single-allele guides, for six individuals and five different tissues in Pinus sylvestris. We then contrasted haploid and diploid tissue genotype calls obtained from the assembled transcriptomes to evaluate the extent of paralog mapping. The use of the haploid tissue during assembly increased its completeness without reducing the number of assembled transcripts. Our results suggest that current strategies that rely on available genomic resources as guidance to minimize allelic redundancy are less effective than the application of strategies that cluster redundant assembled transcripts. The strategy yielding the lowest levels of allelic redundancy among the assembled transcriptomes assessed here was the generation of SuperTranscripts with Lace followed by CD-HIT clustering. However, we still observed some levels of heterozygosity (multiple gene fragments per transcript reflecting allelic redundancy) in this assembled transcriptome on the haploid tissue, indicating that further filtering is required before using these assemblies for downstream applications. We discuss the influence of allelic redundancy when these reference transcriptomes are used to select regions for probe design of exome capture baits and for estimation of population genetic diversity.
Abstract
Despite sophisticated mathematical models, the theory of microevolution is mostly treated as a qualitative rather than a quantitative tool. Numerical measures of selection, constraints, and evolutionary potential are often too loosely connected to theory to provide operational predictions of the response to selection. In this paper, we study the ability of a set of operational measures of evolvability and constraint to predict short‐term selection responses generated by individual‐based simulations. We focus on the effects of selective constraints under which the response in one trait is impeded by stabilizing selection on other traits. The conditional evolvability is a measure of evolutionary potential explicitly developed for this situation. We show that the conditional evolvability successfully predicts rates of evolution in an equilibrium situation, and further that these equilibria are reached with characteristic times that are inversely proportional to the fitness load generated by the constraining characters. Overall, we find that evolvabilities and conditional evolvabilities bracket responses to selection, and that they together can be used to quantify evolutionary potential on time scales where the G‐matrix remains relatively constant.
Authors
Lalisa A. Duguma Joanes Atela Peter A. Minang Alemayehu N. Ayana Belachew Gizachew Zeleke Judith M. Nzyoka Florence BernardAbstract
Deforestation and forest degradation (D&D) in the tropics have continued unabated and are posing serious threats to forests and the livelihoods of those who depend on forests and forest resources. Smallholder farmers are often implicated in scientific literature and policy documents as important agents of D&D. However, there is scanty information on why smallholders exploit forests and what the key drivers are. We employed behavioral sciences approaches that capture contextual factors, attitudinal factors, and routine practices that shape decisions by smallholder farmers. Data was collected using household surveys and focus group discussions in two case study forests—Menagesha Suba Forest in Ethiopia and Maasai Mau Forest in Kenya. Our findings indicate that factors that forced farmers to engage in D&D were largely contextual, i.e., sociodemographic, production factors constraint, as well as policies and governance issues with some influences of routine practices such as wood extraction for fuelwood and construction. Those factors can be broadly aggregated as necessity-driven, market-driven, and governance-driven. In the forests studied, D&D are largely due to necessity needs and governance challenges. Though most factors are intrinsic to smallholders’ context, the extent and impact on D&D were largely aggravated by factors outside the forest landscape. Therefore, policy efforts to reduce D&D should carefully scrutinize the context, the factors, and the associated enablers to reduce forest losses under varying socioeconomic, biophysical, and resource governance conditions.
Authors
Bjørn Hallvard Samset Camilla Weum Stjern Marianne Tronstad Lund Christian Wilhelm Mohr Maria Sand Anne Sophie DalozAbstract
The climate is an aggregate of the mean and variability of a range of meteorological variables, notably temperature (T) and precipitation (P). While the impacts of an increase in global mean surface temperature (GMST) are commonly quantified through changes in regional means and extreme value distributions, a concurrent shift in the shapes of the distributions of daily T and P is arguably equally important. Here, we employ a 30‐member ensemble of coupled climate model simulations (CESM1 LENS) to consistently quantify the changes of regionally and seasonally resolved probability density functions of daily T and P as function of GMST. Focusing on aggregate regions covering both populated and rural zones, we identify large regional and seasonal diversity in the probability density functions and quantify where CESM1 projects the most noticeable changes compared to the preindustrial era. As global temperature increases, Europe and the United States are projected to see a rapid reduction in wintertime cold days, and East Asia to experience a strong increase in intense summertime precipitation. Southern Africa may see a shift to a more intrinsically variable climate but with little change in mean properties. The sensitivities of Arctic and African intrinsic variability to GMST are found to be particularly high. Our results highlight the need to further quantify future changes to daily temperature and precipitation distributions as an integral part of preparing for the societal and ecological impacts of climate change and show how large ensemble simulations can be a useful tool for such research.
Authors
Christian Wilhelm MohrAbstract
No abstract has been registered
Abstract
Accurately positioned single-tree data obtained from a cut-to-length harvester were used as training harvester plot data for k-nearest neighbor (k-nn) stem diameter distribution modelling applying airborne laser scanning (ALS) information as predictor variables. Part of the same harvester data were also used for stand-level validation where the validation units were stands including all the harvester plots on a systematic grid located within each individual stand. In the validation all harvester plots within a stand and also the neighboring stands located closer than 200 m were excluded from the training data when predicting for plots of a particular stand. We further compared different training harvester plot sizes, namely 200 m2, 400 m2, 900 m2 and 1600 m2. Due to this setup the number of considered stands and the areas within the stands varied between the different harvester plot sizes. Our data were from final fellings in Akershus County in Norway and consisted of altogether 47 stands dominated by Norway spruce. We also had ALS data from the area. We concentrated on estimating characteristics of Norway spruce but due to the k-nn approach, species-wise estimates and stand totals as a sum over species were considered as well. The results showed that in the most accurate cases stand-level merchantable total volume could be estimated with RMSE values smaller than 9% of the mean. This value can be considered as highly accurate. Also the fit of the stem diameter distribution assessed by a variant of Reynold’s error index showed values smaller than 0.2 which are superior to those found in the previous studies. The differences between harvester plot sizes were generally small, showing most accurate results for the training harvester plot sizes 200 m2 and 400 m2.