Cost-Effective, Species-Specific Microsatellite Development for the Endangered Dwarf Bulrush (Typha minima) Using Next-Generation Sequencing Technology

The dwarf bulrush (Typha minima Funck ex Hoppe) is an endangered pioneer plant species of riparian flood plains. In Switzerland, only 3 natural populations remain, but reintroductions are planned. To identify suitable source populations for reintroductions, we developed 17 polymorphic microsatellite markers with perfect repeats using the 454 pyrosequencing technique and tested them on 20 individuals with low-cost M13 labeling. We detected 2 to 7 alleles per locus and found expected and observed heterozygosities of 0.05-0.76 and 0.07-1, respectively. The whole process was finished in less than 6 weeks and cost approximately USD 5000. Due to low costs and reduced expenditure of time, the use of next-generation sequencing techniques for microsatellite development represent a powerful tool for population genetic studies in nonmodel species, as we show in this first application of the approach to a plant species of conservation importanc

Characterization of microsatellite loci in Leucorrhinia caudalis , a rare dragonfly endangered throughout Europe

Leucorrhinia caudalis is a rare dragonfly, threatened throughout Europe. It only survived in a single population in Switzerland in the 1980s. However, it recently spread and colonized new ponds. In order to be able to study contemporary migration in this species, eight new microsatellite markers were developed and tested on 24 individuals from six Swiss ponds. We detected three to eleven alleles per polymorphic locus and found observed and expected heterozygosities of 0.250 to 0.875 and 0.215 to 0.840, respectivel

Utility of Multilocus Genotypes for Taxon Assignment in Stands of Closely Related European White Oaks from Switzerland

Background and Aims European white oaks (Quercus petraea, Q. pubescens, Q. robur) have long puzzled plant biologists owing to disputed species differentiation. Extensive hybridization or shared ancestry have been proposed as alternative hypotheses to explain why genetic differentiation between these oak species is low. Species delimitation is usually weak and often shows gradual transitions in leaf morphology. Hence, individual identification may be difficult, but remains a critical step for both scientific work and practical management. Methods Multilocus genotype data (five nuclear microsatellites) were used from ten Swiss oak stands for taxon identification without a priori grouping of individuals or populations, using model-based Bayesian assignment tests. Key Results Three groups best structured the data, indicating that the taxonomical signal was stronger than the spatial signal. Most individuals showed high posterior probabilities for either of three genetic groups that were best circumscribed as taxonomical units. The assignment of a subset of trees, whose taxonomic status had been previously characterized in detail, supported this classification scheme. Conclusions Molecular-genetic assignment tests are useful in the identification of species status in critical taxon complexes such as the European white oaks. Such an approach is of practical importance for forest management, e.g. for stand certification or in seed trade to trace the origin of forest product

BPMN+I to support decision making in innovation management for automated production systems including technological, multi team and organizational aspects

A joined interdisciplinary approach from systems engineering, organizational sociology and psychology is introduced using an enriched Business Process Model and Notation (BPMN+I) based modeling approach to support decision making on a management level for both mid-term decisions such as in-/outsourcing and short-term decisions such as fixing a weakness on site during start-up of a plant abroad or involving the design offices. This approach focusses on the actual collaboration between interdisciplinary teams within an organizational context by enriching BPMN with checklists applicable to all interfaces along the projects’ workflow. Our contribution aims at supporting innovation management for automated Production Systems which depends on successful interdisciplinary collaboration

Genetic underpinning of historical afforestation with allochthonous Pinus cembra in the northwestern Swiss Alps

Throughout the last centuries, the structure and genetic composition of forests have been strongly affected by forest management. Over 30% of European forests are artificially regenerated, very often using translocated forest reproductive material, among these species the Swiss stone pine (Pinus cembra L.). In the late nineteenth and early twentieth centuries, the species was largely used for artificial afforestation in the northern Alps. However, only a few planted trees have survived. Therefore, we aimed to evaluate if the historical afforestation of P. cembra in the northwestern Swiss Alps relied on allochthonous material. We sampled 12 sites, genotyping 11 nuclear microsatellites, to infer the spatial genetic structure of regional populations, to test for genetic differences between natural and planted stands, and to infer potential source regions of planted stands using reference samples covering the entire Alps. Population genetic structure analysis allowed us to distinguish planted from natural stands and to determine that forest reproductive material used for plantations was not of regional origin. We found similar levels of genetic diversity between natural and planted stands. Assignment tests revealed that reproductive material for planting was translocated to the study area from two source regions, i.e., near the border of Switzerland and Austria, and further to the East, between Austria and Italy. Our study shows how genetic tools may inform about historical transfer of forest reproductive material, which still may affect the population genetic make-up of regional occurrences, e.g., because of reduced natural regeneration

Genetic structure in Pinus cembra from the Carpathian Mountains inferred from nuclear and chloroplast microsatellites confirms post-glacial range contraction and identifies introduced individuals

Genetic differentiation of scattered populations at neutral loci is characterized by genetic drift counteracted by the remaining gene flow. Populations of Pinus cembra in the Carpathian Mountains are isolated and restricted to island-like stands at high-elevation mountain ranges. In contrast, paleobotanical data suggest an extended early Holocene distribution of P. cembra in the Carpathians and its surrounding areas, which has contracted to the currently disjunct occurrences. We analyzed the genetic variation of 11 Carpathian populations of P. cembra at chloroplast and, in part newly developed, nuclear microsatellites. Both marker types revealed low levels of genetic differentiation and a lack of isolation by distance, reflecting the post-glacial retraction of the species to its current distribution. Stronger effects of genetic drift were implied by the higher genetic differentiation found for haploid chloroplast than for diploid nuclear markers. Moreover, we found no association between the values of population genetic differentiation for the two marker types. Several populations indicated recent genetic bottlenecks and inbreeding as a consequence of decline in population sizes. Moreover, we found individuals in two populations from the Rodnei Mountains that strikingly differed in assignment probabilities from the remaining specimens, suggesting that they had been introduced from a provenance outside the studied populations. Comparison with Eastern Alpine P. cembra and individuals of the closely related Pinus sibirica suggests that these individuals presumably are P. sibirica. Our study highlights the importance of the maintenance of sufficiently large local population sizes for conservation due to low connectivity between local occurrences

BPMN++ to support managing organisational, multiteam and systems engineering aspects in cyber physical production systems design and operation

Interdisciplinary engineering of cyber physical production systems (CPPS) are often subject to delay, cost overrun and quality problems or may even fail due to the lack of efficient information exchange between multiple interdisciplinary teams working in complex networks within and across companies. We propose a direct integration of multiteam and organisational aspects into the graphical notation of the systems engineering workflow. BPMN++, with eight new notational elements and two subdiagrams, enables the modelling of the required cooperation aspects. BPMN++ provides an improved overview, uniform notation, more compact presentation and easier modifiability from an engineering point of view. We also included a first set of empirical studies and historical qualitative and quantitative data in addition to subjective expert-based ratings to increase validity. The use case introduced to explain the procedure and the notation is derived from surveys in plant manufacturing focussing on the start-up phase and decision support at site. This, in particular, is one of the most complex and critical phases with potentially high economic impact. For evaluation purposes, we compare two alternative solutions for a short-term management decision in the start-up phase of CPPS using the BPMN++ approach

A range‐wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence

Aim: Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re‐colonisation routes. Location: European Alps and Carpathians. Taxa: Pinus cembra. Methods: We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re‐colonisation of the current range. Results: We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re‐colonisation. Main Conclusions: Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in ‘cold period’ refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene ‘warm period’ refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species

A range‐wide postglacial history of Swiss stone pine based on molecular markers and palaeoecological evidence

Aim Knowing a species' response to historical climate shifts helps understanding its perspectives under global warming. We infer the hitherto unresolved postglacial history of Pinus cembra. Using independent evidence from genetic structure and demographic inference of extant populations, and from palaeoecological findings, we derive putative refugia and re-colonisation routes. Location European Alps and Carpathians. Taxa Pinus cembra. Methods We genotyped nuclear and chloroplast microsatellite markers in nearly 3000 individuals from 147 locations across the entire natural range of P. cembra. Spatial genetic structure (Bayesian modelling) and demographic history (approximate Bayesian computation) were combined with palaeobotanical records (pollen, macrofossils) to infer putative refugial areas during the Last Glacial Maximum (LGM) and re-colonisation of the current range. Results We found distinct spatial genetic structure, despite low genetic differentiation even between the two disjunct mountain ranges. Nuclear markers revealed five genetic clusters aligned East–West across the range, while chloroplast haplotype distribution suggested nine clusters. Spatially congruent separation at both marker types highlighted two main genetic lineages in the East and West of the range. Demographic inference supported early separation of these lineages dating back to a previous interstadial or interglacial c. 210,000 years ago. Differentiation into five biologically meaningful genetic clusters likely established during postglacial re-colonisation. Main Conclusions Combining genetic and palaeoecological evidence suggests that P. cembra primarily survived the LGM in ‘cold period’ refugia south of the Central European Alps and near the Carpathians, from where it expanded during the Late Glacial into its current Holocene ‘warm period’ refugia. This colonisation history has led to the distinct East–West structure of five genetic clusters. The two main genetic lineages likely derived from ancient divergence during an interglacial or interstadial. The respective contact zone (Brenner line) matches a main biogeographical break in the European Alps also found in herbaceous alpine plant species

The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

Background: Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information. Findings: The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients. Conclusion: The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available