Browsing by Subject "BOUNDARIES"

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  • Kekkonen, Mari; Hebert, Paul D. N. (2014)
    The analysis of DNA barcode sequences with varying techniques for cluster recognition provides an efficient approach for recognizing putative species (operational taxonomic units, OTUs). This approach accelerates and improves taxonomic workflows by exposing cryptic species and decreasing the risk of synonymy. This study tested the congruence of OTUs resulting from the application of three analytical methods (ABGD, BIN, GMYC) to sequence data for Australian hypertrophine moths. OTUs supported by all three approaches were viewed as robust, but 20% of the OTUs were only recognized by one or two of the methods. These OTUs were examined for three criteria to clarify their status. Monophyly and diagnostic nucleotides were both uninformative, but information on ranges was useful as sympatric sister OTUs were viewed as distinct, while allopatric OTUs were merged. This approach revealed 124 OTUs of Hypertrophinae, a more than twofold increase from the currently recognized 51 species. Because this analytical protocol is both fast and repeatable, it provides a valuable tool for establishing a basic understanding of species boundaries that can be validated with subsequent studies.
  • Kinnula, Sari; Toivonen, Marjaana; Soinne, Helena; Joona, Juuso; Kivela, Jukka (2020)
    There is a great need for sustainable fertilisers and soil amendments, as current fertilisation practices negatively affect the environment. Pulp mill sludges (PMS) could provide a means to replace fertilisers made using non-renewable resources while adding slowly decomposing organic material to the soil and utilising nutrients from the forest industry. This study tested the effects of composted and lime-stabilised mixed PMS (CPMS and LPMS) on wheat (Triticum aestivum) yields and residual effect on oat (Avena sativa) yields in the boreal region. A two-year field experiment included two CPMS and two LPMS treatments all with additional mineral fertilisation, a mineral fertiliser treatment, and a zero-control treatment. All the fertilisers increased yields. There were no differences in crop yields between CPMS, LPMS and mineral fertiliser treatments. However, some quality characteristics and nitrogen (N) uptake were lower with all or some PMS compared with mineral fertilisation. This result suggests that part of the mineral fertilisation for cereals could be replaced by using PMS, but more information on N mineralisation from sludges is needed.
  • Huang, Bin; Huang, Zhinuo; Ma, Ruifang; Ramakrishnan, Muthusamy; Chen, Jialu; Zhang, Zhijun; Yrjälä, Kim (2021)
    Background Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis). Results In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response-associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT-PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs. Conclusions In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.
  • Lehikoinen, Aleksi; Virkkala, Raimo (2016)
    There is increasing evidence that climate change shifts species distributions towards poles and mountain tops. However, most studies are based on presence-absence data, and either abundance or the observation effort has rarely been measured. In addition, hardly any studies have investigated the direction of shifts and factors affecting them. Here, we show using count data on a 1000km south-north gradient in Finland, that between 1970-1989 and 2000-2012, 128 bird species shifted their densities, on average, 37km towards the north north-east. The species-specific directions of the shifts in density were significantly explained by migration behaviour and habitat type. Although the temperatures have also moved on average towards the north north-east (186km), the species-specific directions of the shifts in density and temperature did not correlate due to high variation in density shifts. Findings highlight that climate change is unlikely the only driver of the direction of species density shifts, but species-specific characteristics and human land-use practices are also influencing the direction. Furthermore, the alarming results show that former climatic conditions in the north-west corner of Finland have already moved out of the country. This highlights the need for an international approach in research and conservation actions to mitigate the impacts of climate change.
  • Pino-Bodas, Raquel; Rosa Burgaz, Ana; Ahti, Teuvo; Stenroos, Soili (2018)
    The lichen species Cladonia angustiloba is characterized by a well-developed primary thallus and narrow squamules which show deep incisions, and the presence of usnic and fumarprotocetraric acids. Morphologically it is similar to C. foliacea and C. convoluta, from which it can be distiguished by the squamule size and morphology. Since similar characters were used to distinguish C. foliacea from C. convoluta which do not represent different lineages, it is necessary to examine the taxonomic status of C. angustiloba by means of DNA sequences. In this study, the species delimitation within the C. foliacea complex was studied by sequencing three loci, ITS rDNA, cox1 and RPB2. The data were analyzed by means of phylogenetic and species delimitation methods (GMYC, PTP, ABGD and BPP). Our results show that none of the three species is monophyletic. Most of the species delimitation methods did not support the current species as evolutionary lineages. Only some of the BPP analyses supported C. angustiloba as a species distinct from C. foliacea and C. convoluta. However, the hypothesis that considers the C. foliacea complex as constituted by a unique species obtained the best Bayes Factor value. Therefore, C. angustiloba and C. convoluta are synonymized with C. foliacea. A new, thoroughly checked synonymy with typifications of the whole C. foliacea complex is presented. An updated survey of the world distribution data is compiled.
  • Brommer, Jon; Lehikoinen, Aleksi; Valkama, Jari (2012)
    Background Climatic warming predicts that species move their entire distribution poleward. Poleward movement of the ‘cold’ side of the distribution of species is empirically supported, but evidence of poleward movement at the ‘warm’ distributional side is relatively scarce. Methodology/Principal Finding Finland has, as the first country in the world, completed three national atlas surveys of breeding birds, which we here use to calculate the sizes and weighted mean latitudes of the national range of 114 southern and 34 northern bird species during three periods (1974–1979; 1986–1989; 2006–2010), each denoting species presence in approximately 3 800 10×10 km2 squares. We find strong evidence that southern species (breeding predominantly in central Europe) showed a latitudinal shift of 1.1–1.3 km/year poleward during all three pairwise comparisons between these atlases (covering 11, 20.5 and 31.5 years respectively). We find evidence of a latitudinal shift of 0.7–0.8 km/year poleward of northern boreal and Arctic species, but this shift was not found in all study periods and may have been influenced by increased effort put into the more recent surveys. Species showed no significant correlation in changes in range size and weighted mean latitude between the first (11 year) and second (20.5 year) period covered by consecutive atlases, suggesting weak phylogenetic signal and little scope of species characteristics in explaining latitudinal avian range changes. Conclusions Extinction-driven avian range changes (at the ‘warm’ side) of a species' distribution occur at approximately half the rate of colonisation-driven range changes (at the ‘cold’ side), and its quantification therefore requires long-term monitoring data, possibly explaining why evidence for such changes is currently rare. A clear latitudinal shift in an assemblage of species may still harbour considerable temporal inconsistency in latitudinal movement on the species level. Understanding this inconsistency is important for predictive modelling of species composition in a changing world.
  • Knickel, Karlheinz; Almeida, Alexandra; Bauchinger, Lisa; Casini, Maria Pia; Gassler, Bernd; Hausegger-Nestelberger, Kerstin; Heley, Jesse; Henke, Reinhard; Knickel, Marina; Oostindie, Henk; Ovaska, Ulla; Pina, Carlos; Rovai, Massimo; Vulto, Hans; Wiskerke, Johannes S. C. (2021)
    Decision-makers, planners and administrators involved in different policy domains at different governance levels face the important challenge of fostering more balanced, sustainable and territorially integrated development. Well-designed, multi-level, multi-sector and multi-actor governance arrangements can play a key role in this process through orchestrating the interplay between different spheres, activities, actors and interests. In this paper, we examine the role of spatial planning in improving the relations between rural, peri-urban and urban areas. We analyse the strengths and limitations of spatial planning and explore the connections with territorial development. The methodology used for this analysis combines regional case studies in seven European locations-Ede, Frankfurt/Rhein-Main, Styria/Graz, Helsinki, Lisbon, Lucca and Mid Wales, with rapid appraisals, the analysis of published data, expert judgement and triangulation. We ask under which conditions spatial planning can induce more balanced, sustainable territorial relations, and look at the contribution planning can make to achieving sustainable development goals. The problem of ineffective (or toothless) plan implementation provides the entry point into the analysis and discussion. We illustrate why mutually beneficial relations between urban, peri-urban and rural communities (and territories) cannot simply be planned. Instead, these relationships need to be supported by strategies, policy instruments and governance arrangements that foster synergies between different actors and activities. The planning process itself needs to become more transparent and participatory. We conclude that the questions addressed in this article in an exploratory fashion merit further research especially as a more sustainable and territorially integrated development is becoming increasingly important in European policy making.