Browsing by Subject "TREES"

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  • Ramage, Thibault; Martins-Simoes, Patricia; Mialdea, Gladys; Allemand, Roland; Duplouy, Anne; Rousse, Pascal; Davies, Neil; Roderick, George K.; Charlat, Sylvain (2017)
    We report here on the taxonomic and molecular diversity of 10 929 terrestrial arthropod specimens, collected on four islands of the Society Archipelago, French Polynesia. The survey was part of the 'SymbioCode Project' that aims to establish the Society Islands as a natural laboratory in which to investigate the flux of bacterial symbionts (e.g., Wolbachia) and other genetic material among branches of the arthropod tree. The sample includes an estimated 1127 species, of which 1098 included at least one DNA-barcoded specimen and 29 were identified to species level using morphological traits only. Species counts based on molecular data emphasize that some groups have been understudied in this region and deserve more focused taxonomic effort, notably Diptera, Lepidoptera and Hymenoptera. Some taxa that were also subjected to morphological scrutiny reveal a consistent match between DNA and morphology-based species boundaries in 90% of the cases, with a larger than expected genetic diversity in the remaining 10%. Many species from this sample are new to this region or are undescribed. Some are under description, but many await inspection by motivated experts, who can use the online images or request access to ethanol-stored specimens.
  • Halmeenmäki, Elisa; Heinonsalo, Jussi; Putkinen, Anuliina; Santalahti, Minna; Fritze, Hannu; Pihlatie, Mari (2017)
    The contribution of boreal forest plants to the methane (CH4) cycle is still uncertain. We studied the above and belowground CH4 fluxes of common boreal plants, and assessed the possible contribution of CH4 producing and oxidizing microbes (methanogens and methanotrophs, respectively) to the fluxes. We measured the CH4 fluxes and the amounts of methanogens and methanotrophs in the above- and belowground parts of Vaccinium myrtillus, Vaccinium vitis-idaea, Calluna vulgaris and Pinus sylvestris seedlings and in non-planted soil in a microcosm experiment. The shoots of C. vulgaris and P. sylvestris showed on average emissions of CH4, while the shoots of the Vaccinium species indicated small CH4 uptake. All the root-soil-compartments consumed CH4, however, the non-rooted soils showed on average small CH4 emission. We found methanotrophs from all the rooted and non-rooted soils. Methanogens were not detected in the plant or soil materials. The presence of plant roots seem to increase the amount of methanotrophs and thus CH4 uptake in the soil. The CH4 emissions from the shoots of C. vulgaris and P. sylvestris demonstrate that the plants have an important contribution to the CH4 exchange dynamics in the plant-soil systems.
  • Amara, Edward; Adhikari, Hari; Heiskanen, Janne; Siljander, Mika; Munyao, Martha; Omondi, Patrick; Pellikka, Petri (2020)
    Savannahs provide valuable ecosystem services and contribute to continental and global carbon budgets. In addition, savannahs exhibit multiple land uses, e.g., wildlife conservation, pastoralism, and crop farming. Despite their importance, the effect of land use on woody aboveground biomass (AGB) in savannahs is understudied. Furthermore, fences used to reduce human-wildlife conflicts may affect AGB patterns. We assessed AGB densities and patterns, and the effect of land use and fences on AGB in a multi-use savannah landscape in southeastern Kenya. AGB was assessed with field survey and airborne laser scanning (ALS) data, and a land cover map was developed using Sentinel-2 satellite images in Google Earth Engine. The highest woody AGB was found in riverine forest in a conservation area and in bushland outside the conservation area. The highest mean AGB density occurred in the non-conservation area with mixed bushland and cropland (8.9 Mg center dot ha(-1)), while the lowest AGB density (2.6 Mg center dot ha(-1)) occurred in overgrazed grassland in the conservation area. The largest differences in AGB distributions were observed in the fenced boundaries between the conservation and other land-use types. Our results provide evidence that conservation and fences can create sharp AGB transitions and lead to reduced AGB stocks, which is a vital role of savannahs as part of carbon sequestration.
  • Lundell, Robin; Hänninen, Heikki; Saarinen, Timo; Åström, Helena; Zhang, Rui (2020)
    Bud dormancy of plants has traditionally been explained either by physiological growth arresting conditions in the bud or by unfavourable environmental conditions, such as non-growth-promoting low air temperatures. This conceptual dichotomy has provided the framework also for developing process-based plant phenology models. Here, we propose a novel model that in addition to covering the classical dichotomy as a special case also allows the quantification of an interaction of physiological and environmental factors. According to this plant-environment interaction suggested conceptually decades ago, rather than being unambiguous, the concept of "non-growth-promoting low air temperature" depends on the dormancy status of the plant. We parameterized the model with experimental results of growth onset for seven boreal plant species and found that based on the strength of the interaction, the species can be classified into three dormancy types, only one of which represents the traditional dichotomy. We also tested the model with four species in an independent experiment. Our study suggests that interaction of environmental and physiological factors may be involved in many such phenomena that have until now been considered simply as plant traits without any considerations of effects of the environmental factors.
  • Silva, Ximena; Roux, Jolanda; Asiegbu, Fred O. (2020)
    Background and objectives: The global forest economy is threatened by eucalypt pathogens which are often latent or cryptic species that escape common quarantine and detection methods. Plantation forestry using eucalypts is of considerable importance to Paraguay, but knowledge regarding the pests and diseases affecting these plantations is limited. This study identified fungal diseases present in these plantations. Materials and Methods: We surveyed eucalypt plantations in four provinces in Paraguay and collected material from diseased trees for identification of the causal agents. The samples were analyzed using a combination of morphological and molecular methods. Results: Diseases encountered included Botryosphaeria stem canker, Calonectria leaf blight, Chrysoporthe stem canker, myrtle/eucalypt rust, Coniella leaf spot, heartwood rot and Teratosphaeria stem canker. Contrary to expectations, the causal agent of Teratosphaeria stem canker was identified as Teratosphaeria zuluensis (M.J. Wingf., Crous & T.A. Cout.) M.J. Wingf. & Crous and not Teratosphaeria gauchensis (M.-N. Cortinas, Crous & M.J. Wingf.) M.J. Wingf. & Crous, that is commonly documented for the South American region. Conclusions: This study updates the knowledge on forest fungal pathogens in Paraguayan eucalypt plantations and is the first report of T. zuluensis in Paraguay and in South America.
  • Christita, Margaretta; Sipila, Timo P.; Auzane, Agate; Overmyer, Kirk (2022)
    The phyllosphere is an important microbial habitat and reservoir of organisms that modify plant health. Taphrina betulina is the causal agent of birch witches' broom disease. Taphrina species are dimorphic, infecting hosts in the filamentous form and residing in the host phyllosphere as non-infectious yeast. As such, they are expected to be found as resident yeasts on their hosts, even on healthy tissues; however, there is little experimental data supporting this supposition. With the aim of exploring the local infection ecology of T. betulina, we isolated yeasts from the phyllosphere of birch leaves, using three sample classes; infected leaves inside symptom-bearing branches, healthy leaves from symptom-free branches on symptom-bearing trees and leaves from symptom-free branches on symptom-free trees. Isolations yielded 224 yeast strains, representing 11 taxa, including T. betulina, which was the most common isolate and was found in all sample classes, including symptom-free samples. Genotyping revealed genetic diversity among these T. betulina isolates, with seven distinct genotypes differentiated by the markers used. Twenty-two representative T. betulina strains were selected for further study, revealing further phenotypic differences. These findings support that T. betulina is ubiquitous on birch and that individual trees host a diversity of T. betulina strains.
  • Häkkilä, Matti; Savilaakso, Sini; Johansson, Anna; Sandgren, Terhi; Uusitalo, Anne; Mönkkönen, Mikko; Puttonen, Pasi (2019)
    Forest harvesting is the main driver of habitat degradation and biodiversity loss in forests of the boreal zone. To mitigate harmful effects, small-scale habitats with high biodiversity values have been protected within production forests. These include woodland key habitats, and other small-scale habitat patches protected by voluntary conservation action. This article describes a protocol for a systematic review to synthesize the value of small habitat patches left within production landscapes for biodiversity. The topic for this systematic review arose from a discussion with the Finnish forestry sector and was further defined in a stakeholder workshop. Research question: Do small protected habitat patches within production forests provide value for biodiversity conservation in boreal forests? Animal, plant and fungal diversities are addressed as well as the amount of deadwood within the habitat patches as proxy indicators for biodiversity.
  • Hamberg, Leena; Velmala, Sannakajsa M.; Sievänen, Risto; Kalliokoski, Tuomo; Pennanen, Taina (2018)
    The relationship between the growth rate of aboveground parts of trees and fine root development is largely unknown. We investigated the early root development of fast-and slow-growing Norway spruce (Picea abies (L.) H. Karst.) families at a developmental stage when the difference in size is not yet observed. Seedling root architecture data, describing root branching, were collected with the WinRHIZO (TM) image analysis system, and mixed models were used to determine possible differences between the two growth phenotypes. A new approach was used to investigate the spatial extent of root properties along the whole sample root from the base of 1-year-old seedlings to the most distal part of a root. The root architecture of seedlings representing fastgrowing phenotypes showed similar to 30% higher numbers of root branches and tips, which resulted in larger root extensions and potentially a better ability to acquire nutrients. Seedlings of fast-growing phenotypes oriented and allocated root tips and bio-mass further away from the base of the seedling than those growing slowly, a possible advantage in nutrient-limited and heterogeneous boreal forest soils. We conclude that a higher long-term growth rate of the aboveground parts in Norway spruce may relate to greater allocation of resources to explorative roots that confers a competitive edge during early growth phases in forest ecosystems.
  • Deng, Biar; Tammeorg, Priit; Luukkanen, Olavi; Helenius, Juha; Starr, Mike (2017)
    We studied the effects of Acacia seyal Del. intercropping and biochar soil amendment on soil physico-chemical properties and sorghum (Sorghum bicolor L.) yields in a two-year field experiment conducted on a silt loam site near Renk in South Sudan. A split-plot design with three replications was used. The main factor was tree-cropping system (dense acacia + sorghum, scattered acacia + sorghum, and sole sorghum) and biochar (0 and 10 Mg ha(-1)) was the subplot factor. The two acacia systems had lower soil pH, N and higher C/N ratios compared to the sole sorghum system. Biochar significantly increased soil C, exchangeable K+ contents, field capacity and available water content, but reduced soil exchangeable Ca2+ and effective CEC, and had no effect on soil pH. Acacia intercropping significantly reduced sorghum grain yields while biochar had no significant effect on sorghum yields. The land equivalent ratio (LER) for sorghum yield was 0.3 for both acacia systems in 2011, with or without biochar, but increased in 2012 to 0.6 for the scattered acacia system when combined with biochar. The reduction in sorghum yields by the A. seyal trees was probably due to a combination of competition for water and nutrients and shading. The lack of a yield response to biochar maybe due to insufficient time or too low a dosage. Further research is needed to test for the effects of tree intercropping and biochar and their interactions on soil properties and crop yields in drylands.
  • Heikkila, Maria; Mutanen, Marko; Wahlberg, Niklas; Sihvonen, Pasi; Kaila, Lauri (2015)
    Background: Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. Results: Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov. Conclusions: The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.
  • Jucker, Tommaso; Asner, Gregory P.; Dalponte, Michele; Brodrick, Philip G.; Philipson, Christopher D.; Vaughn, Nicholas R.; Teh, Yit Arn; Brelsford, Craig; Burslem, David F. R. P.; Deere, Nicolas J.; Ewers, Robert M.; Kvasnica, Jakub; Lewis, Simon L.; Malhi, Yadvinder; Milne, Sol; Nilus, Reuben; Pfeifer, Marion; Phillips, Oliver L.; Qie, Lan; Renneboog, Nathan; Reynolds, Glen; Riutta, Terhi; Struebig, Matthew J.; Svatek, Martin; Turner, Edgar C.; Coomes, David A. (2018)
    Borneo contains some of the world's most biodiverse and carbon-dense tropical forest, but this 750 000 km(2) island has lost 62% of its old-growth forests within the last 40 years. Efforts to protect and restore the remaining forests of Borneo hinge on recognizing the ecosystem services they provide, including their ability to store and sequester carbon. Airborne laser scanning (ALS) is a remote sensing technology that allows forest structural properties to be captured in great detail across vast geographic areas. In recent years ALS has been integrated into statewide assessments of forest carbon in Neotropical and African regions, but not yet in Asia. For this to happen new regional models need to be developed for estimating carbon stocks from ALS in tropical Asia, as the forests of this region are structurally and composition-ally distinct from those found elsewhere in the tropics. By combining ALS imagery with data from 173 permanent forest plots spanning the lowland rainforests of Sabah on the island of Borneo, we develop a simple yet general model for estimating forest carbon stocks using ALS-derived canopy height and canopy cover as input metrics. An advanced feature of this new model is the propagation of uncertainty in both ALS- and ground-based data, allowing uncertainty in hectare-scale estimates of carbon stocks to be quantified robustly. We show that the model effectively captures variation in aboveground carbon stocks across extreme disturbance gradients spanning tall dipterocarp forests and heavily logged regions and clearly outperforms existing ALS-based models calibrated for the tropics, as well as currently available satellite-derived products. Our model provides a simple, generalized and effective approach for mapping forest carbon stocks in Borneo and underpins ongoing efforts to safeguard and facilitate the restoration of its unique tropical forests.
  • Löytynoja, Ari; Veidenberg, Andres (Humana press, 2021)
    Methods in Molecular Biology
    Wasabi is an open-source, web-based graphical environment for evolutionary sequence analysis and visualization, designed to work with multiple sequence alignments within their phylogenetic context. Its interactive user interface provides convenient access to external data sources and computational tools and is easily extendable with custom tools and pipelines using a plugin system. Wasabi stores intermediate editing and analysis steps as workflow histories and provides direct-access web links to datasets, allowing for reproducible, collaborative research, and easy dissemination of the results. In addition to shared analyses and installation-free usage, the web-based design allows Wasabi to be run as a cross-platform, stand-alone application and makes its integration to other web services straightforward. This chapter gives a detailed description and guidelines for the use of Wasabi's analysis environment. Example use cases will give step-by-step instructions for practical application of the public Wasabi, from quick data visualization to branched analysis pipelines and publishing of results. We end with a brief discussion of advanced usage of Wasabi, including command-line communication, interface extension, offline usage, and integration to local and public web services.
  • Belazzougui, Djamal; Cunial, Fabio; Karkkainen, Juha; Makinen, Veli (2020)
    The field of succinct data structures has flourished over the past 16 years. Starting from the compressed suffix array by Grossi and Vitter (STOC 2000) and the FM-index by Ferragina and Manzini (FOCS 2000), a number of generalizations and applications of string indexes based on the Burrows-Wheeler transform (BWT) have been developed, all taking an amount of space that is close to the input size in bits. In many large-scale applications, the construction of the index and its usage need to be considered as one unit of computation. For example, one can compare two genomes by building a common index for their concatenation and by detecting common substructures by querying the index. Efficient string indexing and analysis in small space lies also at the core of a number of primitives in the data-intensive field of high-throughput DNA sequencing. We report the following advances in string indexing and analysis: We show that the BWT of a string T is an element of {1, . . . , sigma}(n) can be built in deterministic O(n) time using just O(n log sigma) bits of space, where sigma We also show how to build many of the existing indexes based on the BWT, such as the compressed suffix array, the compressed suffix tree, and the bidirectional BWT index, in randomized O(n) time and in O(n log sigma) bits of space. The previously fastest construction algorithms for BWT, compressed suffix array and compressed suffix tree, which used O(n log sigma) bits of space, took O(n log log sigma) time for the first two structures and O(n log(epsilon) n) time for the third, where. is any positive constant smaller than one. Alternatively, the BWT could be previously built in linear time if one was willing to spend O(n log sigma log log(sigma) n) bits of space. Contrary to the state-of-the-art, our bidirectional BWT index supports every operation in constant time per element in its output.
  • Abdi, Omid; Uusitalo, Jori; Kivinen, Veli-Pekka (2022)
    Logging trails are one of the main components of modern forestry. However, spotting the accurate locations of old logging trails through common approaches is challenging and time consuming. This study was established to develop an approach, using cutting-edge deep-learning convolutional neural networks and high-density laser scanning data, to detect logging trails in different stages of commercial thinning, in Southern Finland. We constructed a U-Net architecture, consisting of encoder and decoder paths with several convolutional layers, pooling and non-linear operations. The canopy height model (CHM), digital surface model (DSM), and digital elevation models (DEMs) were derived from the laser scanning data and were used as image datasets for training the model. The labeled dataset for the logging trails was generated from different references as well. Three forest areas were selected to test the efficiency of the algorithm that was developed for detecting logging trails. We designed 21 routes, including 390 samples of the logging trails and non-logging trails, covering all logging trails inside the stands. The results indicated that the trained U-Net using DSM (k = 0.846 and IoU = 0.867) shows superior performance over the trained model using CHM (k = 0.734 and IoU = 0.782), DEMavg (k = 0.542 and IoU = 0.667), and DEMmin (k = 0.136 and IoU = 0.155) in distinguishing logging trails from non-logging trails. Although the efficiency of the developed approach in young and mature stands that had undergone the commercial thinning is approximately perfect, it needs to be improved in old stands that have not received the second or third commercial thinning.
  • Pensar, Johan; Nyman, Henrik; Niiranen, Juha; Corander, Jukka (2017)
    Markov networks are a popular tool for modeling multivariate distributions over a set of discrete variables. The core of the Markov network representation is an undirected graph which elegantly captures the dependence structure over the variables. Traditionally, the Bayesian approach of learning the graph structure from data has been done under the assumption of chordality since non-chordal graphs are difficult to evaluate for likelihood-based scores. Recently, there has been a surge of interest towards the use of regularized pseudo-likelihood methods as such approaches can avoid the assumption of chordality. Many of the currently available methods necessitate the use of a tuning parameter to adapt the level of regularization for a particular dataset. Here we introduce the marginal pseudo-likelihood which has a built-in regularization through marginalization over the graph-specific nuisance parameters. We prove consistency of the resulting graph estimator via comparison with the pseudo-Bayesian information criterion. To identify high-scoring graph structures in a high-dimensional setting we design a two-step algorithm that exploits the decomposable structure of the score. Using synthetic and existing benchmark networks, the marginal pseudo-likelihood method is shown to perform favorably against recent popular structure learning methods.
  • Levey, Dallas R.; MacGregor-Fors, Ian (2021)
    Agriculture affects biodiversity on a global scale and especially in the Neotropics, leading to land-management challenges in which native wildlife is forced to interact with high-contrast landscape matrices. Further, the direct and indirect effects of hurricanes impacting native habitat in human-modified landscapes increases reliance on agricultural areas and high-contrast matrices. To understand how avian communities in a human-modified landscape respond to hurricane disturbance, we evaluated post-hurricane trends in species richness, density, structure, and functional and taxonomic composition in avian communities at tropical dry forest and in three agricultural habitats using point-count surveys. We compared our results to a similar study that took place years before the hurricanes in the study area. Similar to pre-hurricane trends, tropical dry forest provided key habitat for endemic species relative to agricultural areas, and tree orchards continued to serve as key secondary habitat for a high species richness and community evenness. However, tree orchards, along with cattle pastures and crop fields, failed to serve as successful buffers of hurricane disturbance by supporting half the estimated bird density of tropical dry forest. Cattle pasture and crop fields were both relatively species poor and had low community evenness compared to tropical dry forest and tree orchards after the hurricanes. Tropical dry forest had distinct species and feeding guild compositions compared to the agricultural habitats. All habitat types after the hurricanes had higher numbers of granivores and a reduction of carnivores compared to pre-hurricane levels. Land management in the study landscape needs to incorporate strategies that raise the hurricane resilience of agricultural areas while providing resources to support higher species richness and density in agricultural systems. Such strategies include the preservation of native trees and shrubs and allowing for the natural succession of habitat in unused areas in tree orchards, cattle pasture, and crop fields.
  • Possen, Boy J. H. M.; Rousi, M.; Keski-Saari, Sarita; Silfver, Tarja; Kontunen-Soppela, S.; Oksanen, Elina; Mikola, Juha (2021)
    Strong seasonality in the subarctic causes unfavorable conditions for plant growth driving strong latitudinal clines in growth onset and cessation related to temperature and photoperiodic cues. Results from controlled experiments indeed show such clines, but results from field experiments seem to indicate that such clines may depend on site characteristics, suggesting that environmental variation, other than temperature and photoperiod, is relevant under climate change. Here, we increase our understanding of the effects of climate change on survival, height growth, and the phenological cycle by investigating their inter- and intrapopulation variation using three common gardens and six silver birch (Betula pendula) populations (each represented by up to five cloned genotypes) spanning the Finnish subarctic. We found clinal south-north variation among populations in survival and growth and in spring and autumn phenology to be largely absent. Sapling survival decreased with a transfer of over five degrees of latitude southward, but growth and phenology showed little evidence for adaptation to the local climate. Instead, ample genetic variation and plastic responses were found for all traits studied. Higher soil N availability increased sapling survival and growth, and phenology seemed to be adapted to soil N and day length rather than to temperature. Our results suggest that the climatic conditions predicted for the end of this century may, at least for poor soils, reduce the survival of northern silver birch trees in their early growth. However, those saplings that survive seem to have sufficient phenotypic plasticity to acclimatize to the changing climate. Along with climate, soil fertility plays a significant role and clearly warrants inclusion in the future tests of the effects of climate warming on tree growth and survival.
  • Hari, Pertti; Aakala, Tuomas; Aalto, Juho; Back, Jaana; Hollmen, Jaakko; Jogiste, Kalev; Koupaei, Kourosh Kabiri; Kahkonen, Mika A.; Korpela, Mikko; Kulmala, Liisa; Nikinmaa, Eero; Pumpanen, Jukka; Salkinoja-Salonen, Mirja; Schiestl-Aalto, Pauliina; Simojoki, Asko; Havimo, Mikko (2017)
    Isaac Newton's approach to developing theories in his book Principia Mathematica proceeds in four steps. First, he defines various concepts, second, he formulates axioms utilising the concepts, third, he mathematically analyses the behaviour of the system defined by the concepts and axioms obtaining predictions and fourth, he tests the predictions with measurements. In this study, we formulated our theory of boreal forest ecosystems, called NewtonForest, following the four steps introduced by Newton. The forest ecosystem is a complicated entity and hence we needed altogether 27 concepts to describe the material and energy flows in the metabolism of trees, ground vegetation and microbes in the soil, and to describe the regularities in tree structure. Thirtyfour axioms described the most important features in the behaviour of the forest ecosystem. We utilised numerical simulations in the analysis of the behaviour of the system resulting in clear predictions that could be tested with field data. We collected retrospective time series of diameters and heights for test material from 6 stands in southern Finland and five stands in Estonia. The numerical simulations succeeded to predict the measured diameters and heights, providing clear corroboration with our theory.
  • Reemer, Menno; Ståhls, Gunilla (2013)
    The intrasubfamilial classification of Microdontinae Rondani (Diptera: Syrphidae) has been a challenge: until recently more than 300 out of more than 400 valid species names were classified in Microdon Meigen. We present phylogenetic analyses of molecular and morphological characters (both separate and combined) of Microdontinae. The morphological dataset contains 174 characters, scored for 189 taxa (9 outgroup), representing all 43 presently recognized genera and several subgenera and species groups. The molecular dataset, representing 90 ingroup species of 28 genera, comprises sequences of five partitions in total from the mitochondrial gene COI and the nuclear ribosomal genes 18S and 28S. We test the sister-group relationship of Spheginobaccha with the other Microdontinae, attempt to elucidate phylogenetic relationships within the Microdontinae and discuss uncertainties in the classification of Microdontinae. Trees based on molecular characters alone are poorly resolved, but combined data are better resolved. Support for many deeper nodes is low, and placement of such nodes differs between parsimony and Bayesian analyses. However, Spheginobaccha is recovered as highly supported sister group in both. Both analyses agree on the early branching of Mixogaster, Schizoceratomyia, Afromicrodon and Paramicrodon. The taxonomical rank in relation to the other Syrphidae is discussed briefly. An additional analysis based on morphological characters only, including all 189 taxa, used implied weighting. A range of weighting strengths (k-values) is applied, chosen such that values of character fit of the resulting trees are divided into regular intervals. Results of this analysis are used for discussing the phylogenetic relationships of genera unrepresented in the molecular dataset.
  • Löytynoja, Ari (Humana press, 2021)
    Methods in Molecular Biology
    Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary homology and proteins' structural similarity are not the same and sequence alignments generated with methods designed for structural matching can be seriously misleading in comparative and phylogenetic analyses. The phylogeny-aware alignment algorithm implemented in the program PRANK has been shown to produce good alignments for evolutionary inferences. Unlike other alignment programs, PRANK makes use of phylogenetic information to distinguish alignment gaps caused by insertions or deletions and, thereafter, handles the two types of events differently. As a by-product of the correct handling of insertions and deletions, PRANK can provide the inferred ancestral sequences as a part of the output and mark the alignment gaps differently depending on their origin in insertion or deletion events. As the algorithm infers the evolutionary history of the sequences, PRANK can be sensitive to errors in the guide phylogeny and violations on the underlying assumptions about the origin and patterns of gaps. To mitigate the effects of such model violations, the phylogeny-aware alignment algorithm has been re-implemented in program PAGAN. By using sequence graphs, PAGAN can model and accumulate evidence from more complex gap structures than PRANK does, and incorporate this uncertainty in the inferred ancestral sequences. These issues are discussed in detail below and practical advice is provided for the use of PRANK and PAGAN in evolutionary analysis. The two software packages can be downloaded from http://wasabiapp.org/software.