Optimization and reconstruction of hv-convex (0,1)-matrices

AbstractWe consider a variant of the NP-hard problem of reconstructing hv-convex (0,1)-matrices from known row and column sums. Instead of requiring the ones to occur consecutively in each row and column, we maximize the number of neighboring ones. This is reformulated as an integer programming problem. A solution method based on variable splitting is proposed and tested with good results on moderately sized test problems

Returtømmer - Effektiv bruk av retursløyfer i tømmertransport

Denne rapporten presenterer resultatene fra arbeidet utført i prosjektet "Returtømmer". Prosjektet har hatt som mål å belyse muligheten for økt bruk av returkjøring i transport av tømmer gjennom bruk av optimeringsbaserte modeller. I prosjektet er det utviklet metoder for automatisk planlegging av tømmertranport slik at transportplanleggere kan få ruteforslag basert på transportklart tømmer, avstander, kvanta med mer. Basert på de foreslåtte metodene er det utviklet en enkel demonstrator for testing og denne er benyttet på et testcase basert på historiske data for hele Midt-Norge. Resultatene viser at en optimeringsbasert tilnærming er teknisk gjennomførbar med betydelig muligheter for økt bruk av returkjøring. Analysene utført på testcaset viser mulige reduksjoner rundt 15 % i total kjøredistanse sammenlignet med å ikke benytte seg av returkjøring.publishedVersio

A framework for significance analysis of gene expression data using dimension reduction methods

<p>Abstract</p> <p>Background</p> <p>The most popular methods for significance analysis on microarray data are well suited to find genes differentially expressed across predefined categories. However, identification of features that correlate with continuous dependent variables is more difficult using these methods, and long lists of significant genes returned are not easily probed for co-regulations and dependencies. Dimension reduction methods are much used in the microarray literature for classification or for obtaining low-dimensional representations of data sets. These methods have an additional interpretation strength that is often not fully exploited when expression data are analysed. In addition, significance analysis may be performed directly on the model parameters to find genes that are important for any number of categorical or continuous responses. We introduce a general scheme for analysis of expression data that combines significance testing with the interpretative advantages of the dimension reduction methods. This approach is applicable both for explorative analysis and for classification and regression problems.</p> <p>Results</p> <p>Three public data sets are analysed. One is used for classification, one contains spiked-in transcripts of known concentrations, and one represents a regression problem with several measured responses. Model-based significance analysis is performed using a modified version of Hotelling's <it>T</it>²-test, and a false discovery rate significance level is estimated by resampling. Our results show that underlying biological phenomena and unknown relationships in the data can be detected by a simple visual interpretation of the model parameters. It is also found that measured phenotypic responses may model the expression data more accurately than if the design-parameters are used as input. For the classification data, our method finds much the same genes as the standard methods, in addition to some extra which are shown to be biologically relevant. The list of spiked-in genes is also reproduced with high accuracy.</p> <p>Conclusion</p> <p>The dimension reduction methods are versatile tools that may also be used for significance testing. Visual inspection of model components is useful for interpretation, and the methodology is the same whether the goal is classification, prediction of responses, feature selection or exploration of a data set. The presented framework is conceptually and algorithmically simple, and a Matlab toolbox (Mathworks Inc, USA) is supplemented.</p

Short stories from Sphagnum of rare species, taxonomy, and speciation

Conserving species and their genetic variation are a global priority to safeguard evolu-tionary potential in a rapidly changing world. Species are fundamental units in research and nature management, but taxonomic work is increasingly undermined. Increasing knowledge on the species genetic diversity would aid in prioritizing conservation ef -forts. Sphagnum is a diverse, well- known bryophyte genus, which makes the genus suited to study speciation and cryptic variation. The species share specific character-istics and can be difficult to separate in the field. By combining molecular data with thorough morphological examination, new species have recently been discovered. Still, there are taxonomic uncertainties, even for species assessed on the IUCN Red List of threatened species. Here, we use molecular data to examine three rare species within the subgenus Acutifolia described based on morphological characters. All spe -cies have narrow distributions and limited dispersability. First, we confirm the genetic origin of S. skyense. Second, we show that S. venustum is a haploid species genetically distinct from morphologically similar species. Lastly, S. nitidulum was found to have a distinct haplotype, but cannot be genetically separated from other red Acutifoliaspecies. We also found high genetic variation within red Acutifolia specimens, indicat -ing the need of further morphological examination and possibly taxonomic revision. Until then, our results have shown that genetic data can aid in prioritizing targets of conservation efforts when taxonomy is unresolved. All three taxa should be further searched for by field biologists to increase knowledge about their distribution ranges. genetic structure, microsatellites, molecular data, morphology, peatmosses, speciation, species identification, TaxonomypublishedVersio

Photosynthesis, growth, and decay traits in Sphagnum - a multispecies comparison

Peat mosses (Sphagnum) largely govern carbon sequestration in Northern Hemisphere peatlands. We investigated functional traits related to growth and decomposition in Sphagnum species. We tested the importance of environment and phylogeny in driving species traits and investigated trade-offs among them. We selected 15 globally important Sphagnum species, representing four sections (subgenera) and a range of peatland habitats. We measured rates of photosynthesis and decomposition in standard laboratory conditions as measures of innate growth and decay potential, and related this to realized growth, production, and decomposition in their natural habitats. In general, we found support for a trade-off between measures of growth and decomposition. However, the relationships are not strong, with r ranging between 0.24 and 0.45 for different measures of growth versus decomposition. Using photosynthetic rate to predict decomposition in standard conditions yielded R-2 = 0.20. Habitat and section (phylogeny) affected the traits and the trade-offs. In a wet year, species from sections Cuspidata and Sphagnum had the highest production, but in a dry year, differences among species, sections, and habitats evened out. Cuspidata species in general produced easily decomposable litter, but their decay in the field was hampered, probably due to near-surface anoxia in their wet habitats. In a principal components analysis, PCA, photosynthetic capacity, production, and laboratory decomposition acted in the same direction. The species were imperfectly clustered according to vegetation type and phylogeny, so that some species clustered with others in the same section, whereas others clustered more clearly with others from similar vegetation types. Our study includes a wider range of species and habitats than previous trait analyses in Sphagnum and shows that while the previously described growth-decay trade-off exists, it is far from perfect. We therefore suggest that our species-specific trait measures offer opportunities for improvements of peatland ecosystem models. Innate qualities measured in laboratory conditions translate differently to field responses. Most dramatically, fast-growing species could only realize their potential in a wet year. The same species decompose fast in laboratory, but their decomposition was more retarded in the field than that of other species. These relationships are crucial for understanding the long-term dynamics of peatland communities

Sphagnum magniporosum (Sphagnaceae, subgenus Subsecunda) a new peatmoss species from Venezuela

Publisher Copyright: © 2022 The Authors. This is an Open Access article.We describe Sphagnum magniporosum sp. nov. in Sphagnum subgen. Subsecunda (Sphagnaceae) Bryophyta. The new species is described and characterized using morphological methods. The description is based on qualitative examination of morphological characters of shoots, stems, branches and leaves. The new peatmoss is known from a single locality at a tabletop (tepui) mountain in the Chimantá Massif, Canima National Park in the state Bolívar of Venezuela. The morphology of the species is compared and evaluated using keys, descriptions and illustrations of ten South American and one African Subsecunda species.Peer reviewe

New Estonian records: mosses

In 2016 four species new to Estonia have been identified, mainly by checking earlier collections in different herbaria. This addition raises the total number of bryophyte species registered in Estonia up to 598. One species, which was evaluated as extinct in Estonia, has been found in a new locality. Also a variety new for Estonia has been found.

Mites (Oribatida and Mesostigmata) and vegetation as complementary bioindicators in peatlands

Vegetation is widely used in the assessment of the quality of peatlands, while the invertebrate fauna of peatlands is relatively poorly studied. We compared the bioindicator values of vegetation with two arthropod groups widespread in peatlands, saprophagous Oribatida (Acariformes) and predatory Mesostigmata (Parasitiformes) mites. Samples were collected from ecotones at the edges of peatland ponds in Poland, including four in near-natural condition (i.e., peatlands unaffected by human activity) and three in previously disturbed but now recovering peatlands. A set of abiotic parameters was measured at each site: pond area, mean annual temperature, annual precipitation, and water parameters (pH, conductivity, colour, total nitrogen, phosphorus, calcium, and organic carbon). Overall, 63,635 specimens of Oribatida and 448 of Mesostigmata were recovered in the sampling. Species richness of Oribatida (56 species) was higher than that of flora (46) and Mesostigmata (15). Vegetation was significantly associated with annual precipitation in the years 1998–2007 which accounted for 29.1 % of the variation in vegetation communities. Oribatida variability was significantly associated with the content of organic carbon in water accounting for 32.4 % of variation. In contrast, variation in the Mesostigmata was not significantly associated with any of the abiotic parameters. Vegetation at ponds in previously disturbed and now recovering peatlands had higher bush cover than at near-natural ponds and the pond in the cutaway peat had lowest moss cover and the highest number of associate species (i.e., species with wide tolerance not characteristic of the certain community). Mite communities did not differ consistently between near-natural and recovering peatlands. Sphagnum divinum Flatberg et Hassel was recorded from Poland for the first time.publishedVersio

Combining population genomics and ecological niche modeling to assess taxon limits between Carex jemtlandica and C. lepidocarpa

Carex section Ceratocystis (Cyperaceae) is a group of recently evolved plant species, in which hybridization is frequent, introgression is documented, taxonomy is complex, and morphological boundaries are vague. Within this section, a unified taxonomic treatment of the Carex jemtlandica-Carex lepidocarpa species complex does not exist, and Norway may currently be the sole country accepting species rank for both. Carex jemtlandica is mainly confined to Fennoscandia and is thus a Fennoscandian conservation responsibility. This motivated us to test the principal hypothesis that both C. jemtlandica and C. lepidocarpa represent evolutionary significant units, and that both deserve their current recognition at species level. We investigated their evolutionary distinctiveness in Norway, using restriction site-associated DNA sequencing and ecological niche modeling. Our genomic results reveal two genetic clusters, largely corresponding to C. jemtlandica and C. lepidocarpa that also remain distinct in sympatry, despite clear indications of ongoing hybridization and introgression. The ecological niche modeling suggests that they occupy different environmental niches. Jointly, our results clearly show that C. jemtlandica and C. lepidocarpa represent separately evolving entities that should qualify recognition as evolutionary significant units. Given the high level of introgression compared to other hybridizing species pairs in Carex we recommend treating C. jemtlandica as a subspecies of C. lepidocarpa.Peer reviewe

Inclusion of juvenile stages improves diversity assessment and adds to our understanding of mite ecology – A case study from mires in Norway

Arachnid orders, Mesostigmata, Trombidiformes, and Sarcoptiformes, commonly known as ‘mites’, are abundant in mires, both as adults and as juveniles. However, due to the challenges of identification, the juvenile forms are often excluded from analyses. This is the first study in mires that included all three mite orders identified to the species level, including juvenile instars. We aimed to compare how diversity and the response to ecological variables differed if only the adults (ad) vs. the total number of specimens (ad+juv) are considered. Samples of 20 Sphagnum species (five subgenera) were collected and mites were extracted using Berlese funnels. Overall, nearly 60,000 mites were analyzed; of these Mesostigmata made up 1.87% of the total, Trombidiformes −0.27%, and Sarcoptiformes −97.86%. The study revealed 154 species (33 Mesostigmata, 24 Trombidiformes, and 97 Sarcoptiformes), the highest diversity of mites ever reported from mires. The inclusion of juveniles increased observed species richness by 6%, with 10 species (one Mesostigmata, six Trombidiformes, and three Sarcoptiformes) represented only by juvenile forms. Seventeen species are new to Norway (four Mesostigmata, one Sarcoptiformes, and 12 Trombidiformes, including five undescribed species of Stigmaeidae and Cunaxidae). Four of these were represented in the samples only by juveniles. Including the juveniles explained a greater amount of the variability of Trombidiformes (explanatory variables account for 23.60% for ad, and 73.74% for ad+juv) and Mesostigmata (29.23% − ad, 52.91% − ad+juv), but had less of an impact for Sarcoptiformes (38.48% − ad, 39.26% − ad+juv). Locality, Sphagnum subgenus and species, wetness, and trophic state significantly affected the mite communities and should be taken into consideration when studying mires. Since juvenile stages contribute significantly to mite diversity in mires, they should also be included in mite studies in other habitats.publishedVersio