Panu Somervuo

• D.Sc. (Tech.)
• Researcher at University of Helsinki

To turn environmentally derived metabarcoding data into community matrices for ecological analysis, sequences must first be clustered into operational taxonomic units (OTUs). This task is particularly complex for data including large numbers of taxa with incomplete reference libraries. OptimOTU offers a taxonomically aware approach to OTU clusterin...

Modern DNA-based biodiversity surveys result in massive-scale data, including up to millions of species, of which most are rare. Making the most of such data for inference and prediction requires modelling approaches that can relate species occurrences to environmental and spatial predictors, while incorporating information about taxonomic or phylo...

Fungi are among the most diverse and ecologically important kingdoms in life. However, the distributional ranges of fungi remain largely unknown as do the ecological mechanisms that shape their distributions1,2. To provide an integrated view of the spatial and seasonal dynamics of fungi, we implemented a globally distributed standardized aerial sam...

Novel methods for sampling and characterizing biodiversity hold great promise for re-evaluating patterns of life across the planet. The sampling of airborne spores with a cyclone sampler, and the sequencing of their DNA, have been suggested as an efficient and well-calibrated tool for surveying fungal diversity across various environments. Here we...

Global biodiversity gradients are generally expected to reflect greater species replacement closer to the equator. However, empirical validation of global biodiversity gradients largely relies on vertebrates, plants, and other less diverse taxa. Here we assess the temporal and spatial dynamics of global arthropod biodiversity dynamics using a beta-...

DNA-based identification is vital for classifying biological specimens, yet methods to quantify the uncertainty of sequence-based taxonomic assignments are scarce. Challenges arise from noisy reference databases, including mislabelled entries and missing taxa. PROTAX addresses these issues with a probabilistic approach to taxonomic classification,...

Unravelling how species communities change along environmental gradients requires a dual understanding: the direct responses of the species to their abiotic surroundings and the indirect variation of these responses through biotic interactions. Here, we focus on the interactive relationships between plants and their symbiotic root‐associated fungi...

Understanding how different taxa respond to abiotic characteristics of the environment is of key interest for understanding the assembly of communities. Yet, whether eDNA data will suffice to accurately capture environmental imprints has been the topic of some debate. In this study, we characterised patterns of species occurrences and co-occurrence...

The present work focuses on how the landscape and distance between a bird and an audio recording unit affect automatic species identification. Moreover, it is shown that automatic species identification can be improved by taking into account the effects of landscape and distance. The proposed method uses measurements of impulse responses between th...

Automated recorders are increasingly used in remote sensing of wildlife, yet automated methods of processing the audio remains challenging. Identifying animal sounds with machine learning provides a solution, but optimizing the models requires annotated training data. Producing such data can require much manual effort, which could be alleviated by...

Theoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumulant models (SCMs), which have arisen from theoretical ecology, describe population dynamics generated by a specific family of IBMs, namely sp...

Global gradients in species biodiversity are expected to reflect tighter packing of species closer to the equator. Yet, empirical validation of these patterns has so far focused on less diverse taxa, with comparable assessments of mega-diverse groups historically constrained by the taxonomic impediment. Here we assess the temporal and spatial turno...

Aim: Global gradients in species biodiversity may or may not be associated with greater species replacement closer to the equator. Yet, empirical validation of these patterns has so far focused on less diverse taxa, with comparable assessments of mega-diverse groups historically constrained by the taxonomic impediment. Location: Global Time period:...

An automatic bird sound recognition system is a useful tool for collecting data of different bird species for ecological analysis. Together with autonomous recording units (ARUs), such a system provides a possibility to collect bird observations on a scale that no human observer could ever match. During the last decades, progress has been made in t...

Theoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumulant models (SCMs), which have arisen from recent advances in theoretical ecology, can be used to describe population dynamics generated by a...

Predicting how climate change affects biotic interactions poses a challenge. Plant‐insect herbivore interactions are particularly sensitive to climate change, as climate‐induced changes in plant quality cascade into the performance of insect herbivores. Whereas the immediate survival of herbivore individuals depends on plastic responses to climate...

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this paper, we 1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), 2) publish this library, and 3) deliver a new identifica...

To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this paper, we 1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), 2) publish this library, and 3) deliver a new identifica...

The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we capt...

Predicting how climate change affects biotic interactions and their evolution poses a challenge. Plant-insect herbivore interactions are particularly sensitive to climate change, as climate-induced changes in plant quality cascade into the performance of insect herbivores. Whereas the immediate survival of herbivore individuals depends on plastic r...

Agent-based models are used to study complex phenomena in many fields of science. While simulating agent-based models is often straightforward, predicting their behaviour mathematically has remained a key challenge. Recently developed mathematical methods allow the prediction of the emerging spatial patterns for a general class of agent-based model...

Numerous gene expression and stress adaptation responses in L. monocytogenes are regulated through alternative sigma factors σ B and σ L. Stress response phenotypes and transcriptomes were compared between L. monocytogenes EGD-e and its ΔsigB and ΔsigBL mutants. Targeted growth phenotypic analysis revealed that the ΔsigB and ΔsigBL mutants are impa...

In ecology, one of the most fundamental questions relates to the persistence of populations, or conversely to the probability of their extinction. Deriving extinction thresholds and characterizing other critical phenomena in spatial and stochastic models is highly challenging, with few mathematically rigorous results being available for discrete‐sp...

Inferring interspecific interactions indirectly from community data is of central interest in community ecology. Data on species communities can be surveyed using different methods, each of which may differ in the amount and type of species detected, and thus produce varying information on interaction networks. Since fruit bodies reflect only a fra...

How community‐level specialization differs among groups of organisms, and changes along environmental gradients, is fundamental to understanding the mechanisms influencing ecological communities. In this paper, we investigate the specialization of root‐associated fungi for plant species, asking whether the level of specialization varies with elevat...

Increasing evidence suggests that degradation of biodiversity in human populated areas is a threat for the ecosystem processes that are relevant for human well-being. Fungi are a megadiverse kingdom that plays a key role in ecosystem processes and affects human well-being. How urbanization influences fungi has remained poorly understood, partially...

Understanding the role of interspecific interactions in shaping ecological communities is one of the central goals in community ecology. In fungal communities, measuring interspecific interactions directly is challenging because these communities are composed of large numbers of species, many of which are unculturable. An indirect way of assessing...

The kingdom Fungi is a megadiverse group represented in all ecosystem types. The global diversity and distribution of fungal taxa are poorly known, in part due to the limitations related to traditional fruit-body survey methods. These previous hurdles are now being overcome by rapidly developing DNA-based surveys. Past fungal DNA surveys have predo...

Individual-based models, ‘IBMs’, describe naturally the dynamics of interacting organisms or social or financial agents. They are considered too complex for mathematical analysis, but computer simulations of them cannot give the general insights required. Here, we resolve this problem with a general mathematical framework for IBMs containing intera...

Inbreeding is common in nature, and many laboratory studies have documented that inbreeding depression can reduce the fitness of individuals. Demonstrating the consequences of inbreeding depression on the growth and persistence of populations is more challenging because populations are often regulated by density‐ or frequency‐dependent selection an...

Background Stored potato (Solanum tuberosum L.) tubers are sensitive to wet conditions that can cause rotting in long-term storage. To study the effect of water on the tuber surface during storage, microarray analysis, RNA-Seq profiling, qRT-PCR and phytohormone measurements were performed to study gene expression and hormone content in wet tubers...

Incompleteness of reference sequence databases and unresolved taxonomic relationships complicates taxonomic placement of fungal sequences. We developed Protax ‐fungi, a general tool for taxonomic placement of fungal internal transcribed spacer ( ITS ) sequences, and implemented it into the PlutoF platform of the UNITE database for molecular identif...

Background: Current high-throughput sequencing platforms provide capacity to sequence multiple samples in parallel. Different samples are labeled by attaching a short sample specific nucleotide sequence, barcode, to each DNA molecule prior pooling them into a mix containing a number of libraries to be sequenced simultaneously. After sequencing, th...

Automated audio recording offers a powerful tool for acoustic monitoring schemes of bird, bat, frog and other vocal organisms, but the lack of automated species identification methods has made it difficult to fully utilise such data. We developed Animal Sound Identifier (ASI), a MATLAB software that performs probabilistic classification of species...

A new method is introduced which tolerates distortions between spectrogram patterns in template matching. Cross-correlation provides a fast method to calculate similarities but it is sensitive to durational and spectral fluctuations. Dynamic time warping tolerates durational differences but requires that frequency components match. An extension to...

Streptomyces spp. are a highly diverse group of bacteria most of which are soil-inhabiting saprophytes. A few are plant pathogens that produce a family of phytotoxins called thaxtomins and cause significant economic losses, e.g., by reducing the marketability of potato tubers (Solanum tuberosum). In northern Europe, S. scabies, S. turgidiscabies an...

Fungi are a megadiverse group of organisms, they play major roles in ecosystem functioning, and are important for human health, food production, and nature conservation. Our knowledge on fungal diversity and fungal ecology is however still very limited, in part because surveying and identifying fungi is time demanding and requires expert knowledge....

Autonomous audio recording is stimulating new field in bioacoustics, with a great promise for conducting cost-effective species surveys. One major current challenge is the lack of reliable classifiers capable of multi-species identification. We present PROTAX-Sound, a statistical framework to perform probabilistic classification of animal sounds. P...

Xeno-Canto ID per sample. 1766 unique identifiers used to locate each of the used audio files in Xeno-Canto database. (TXT)

Species names and IDs. Latin names and 6-letter short names for 200 study species. (TXT)

Methods appendix. Detailed description of audio processing and classification algorithms. (DOCX)

PROTAX-Sound functions. Zip file containing all code necessary to run PROTAX-Sound. (ZIP)

Results appendix. Table containing the 1766 sample-specific full output of PROTAX-Sound classification results. (ZIP)

5-fold data tags. Logical table containing the 5-fold division of the 1766 audio files used for training/test of PROTAX-Sound. (TXT)

Metabarcoding of vertebrate DNA derived from carrion flies has been proposed as a promising tool for biodiversity monitoring. To evaluate its efficacy, we conducted metabarcoding surveys of carrion flies on Barro Colorado Island (BCI), Panama, which has a well-known mammal community, and compared our results against diurnal transect counts and came...

Foodborne pathogenic bacteria are exposed to a number of environmental stresses during food processing, storage, and preparation, and in the human body. In order to improve the safety of food, the understanding of molecular stress response mechanisms foodborne pathogens employ is essential. Many response mechanisms that are activated during heat sh...

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because t...

Aim: To provide pharmacogenomics reporting guidelines, the information and tools required for reporting to public omic databases. Material & methods: For effective DMET data interpretation, sharing, interoperability, reproducibility and reporting, we propose the Minimum Information required for a DMET Experiment (MIDE) reporting. Results: MIDE...

A crucial step in the use of DNA markers for biodiversity surveys is the assignment of Linnaean taxonomies (species, genus, etc.) to sequence reads. This allows the use of all the information known based on the taxonomic names. Taxonomic placement of DNA barcoding sequences is inherently probabilistic because DNA sequences contain errors, because t...

Motivation: When targeted to a barcoding region, high-throughput sequencing can be used to identify species or operational taxonomical units from environmental samples, and thus to study the diversity and structure of species communities. Although there are many methods which provide confidence scores for assigning taxonomic affiliations, it is no...

Potato can be infected with many bacterial pathogens, the detection of which is necessary in seed certification. In this study, a diagnostic microarray previously tested for specificity of probes for detecting the potato bacteria causing blackleg and soft rot (Pectobacterium atrosepticum, Pectobacterium carotovorum, and Dickeya spp.), ring rot (Cla...

Enteropathogenic Yersinia enterocolitica and Yersinia pseudotuberculosis are both etiological agents for intestinal infection known as yersiniosis, but their epidemiology and ecology bear many differences. Swine are the only known reservoir for Y. enterocolitica 4/O:3 strains, which are the most common cause of human disease, while Y. pseudotubercu...

Despite the expression of the mutated gene in all muscles, selective muscles are involved in genetic muscular dystrophies. Different muscular dystrophies show characteristic patterns of fatty degenerative changes by muscle imaging, even to the extent that the patterns have been used for diagnostic purposes. However, the underlying molecular mechani...

Insect flight is one of the most energetically demanding activities in the animal kingdom, yet for many insects flight is necessary for reproduction and foraging. Moreover, dispersal by flight is essential for the viability of species living in fragmented landscapes. Here, working on the Glanville fritillary butterfly (Melitaea cinxia), we use tran...

Proteins evolve by mutations and natural selection. The network of sequence similarities is a rich source for mining homologous relationships that inform on protein structure and function. There are many servers available to browse the network of homology relationships but one has to wait up to a minute for results. The SANSparallel webserver provi...

Previous studies have reported that chromosome synteny in Lepidoptera has been well conserved, yet the number of haploid chromosomes varies widely from 5 to 223. Here we report the genome (393 Mb) of the Glanville fritillary butterfly (Melitaea cinxia; Nymphalidae), a widely recognized model species in metapopulation biology and eco-evolutionary re...

Photoassimilates such as sugars are transported through phloem sieve element cells in plants. Adapted for effective transport, sieve elements develop as enucleated living cells. We used electron microscope imaging and three-dimensional reconstruction to follow sieve element morphogenesis in Arabidopsis. We show that sieve element differentiation in...

We characterize allelic and gene expression variation between populations of the Glanville fritillary butterfly (Melitaea cinxia) from two fragmented and two continuous landscapes in northern Europe. The populations exhibit significant differences in their life history traits, e.g. butterflies from fragmented landscapes have higher flight metabolic...

Streptomyces scabies causes yield losses in potato by inducing common scab (CS) symptoms on tubers. Little information is available on global gene expression responses in CS‐causing streptomycetes upon interaction with host plants. In this study, expression of 8746 genes was analysed in the type strain of S. scabies (ATCC49173) using a custom‐desig...

Profound understanding of the mechanisms foodborne pathogenic bacteria utilize in adaptation to the environmental stress they encounter during food processing and storage is of paramount importance in design of control measures. Chill temperature is a central control measure applied in minimally processed foods; however, data on the mechanisms the...

The posttranscriptional regulator RsmA controls the production of plant cell wall degrading enzymes (PCWDE) and cell motility in the Pectobacterium genus of plant pathogens. In this study the physiological role of gene regulation by RsmA is under investigation. Disruption of rsmA gene of the Pectobacterium wasabiae strain, SCC3193 resulted in 3-fol...

Studies on extracellular proteins (ECPs) contribute to understanding of the multifunctional nature of apoplast. Unlike vascular plants (tracheophytes), little information about ECPs is available from non-vascular plants, such as mosses (bryophytes). In this study, moss plants (Physcomitrella patens) were grown in liquid culture and treated with chi...

The two-component system CBO0366/CBO0365 was recently demonstrated to have a role in cold tolerance of group I Clostridium botulinum ATCC 3502. The mechanisms under its control, ultimately resulting in increased sensitivity to low temperature, are unknown. A transcriptomic analysis with DNA microarrays was performed to identify the differences in g...

In this study, we characterized a putative Flp/Tad pilus-encoding gene cluster, and we examined its regulation at the transcriptional level and its role in the virulence of potato pathogenic enterobacteria of the genus Pectobacterium. The Flp/Tad pilus-encoding gene clusters in Pectobacterium atrosepticum, Pectobacterium wasabiae and Pectobacterium...

Yersinia pseudotuberculosis is an important pathogen that probably survives well in the modern food chain. However, little is known about the mechanisms that allow the growth of this pathogen in foods under stress conditions. The expression of rpoE encoding σE was defined by quantitative real-time reverse transcription-PCR. Expression of rpoE was i...

To collect specific information about the genetic mechanisms that Clostridium botulinum strains utilise when adapting to changing environments, 16 C. botulinum genomes were analysed with comparative genome sequence analysis. Particular attention was paid to low temperature adaptation and the presence of cold shock protein coding genes in these geno...

Leuconostoc gasicomitatum is a psychrotrophic lactic acid bacterium (LAB) which causes spoilage in cold-stored modified-atmosphere-packaged (MAP) meat products. In addition to the fermentative metabolism, L. gasicomitatum is able to respire when exogenous heme and oxygen are available. In this study, we investigated the respiration effects on growt...

Abstract Yersinia pseudotuberculosis is a foodborne pathogen often detected and identified using polymerase chain reaction (PCR) with primers targeted to virulence genes. Sequence variability of the virulence genes in strains representing different serotypes is unknown. Sequence variability could hinder the recognition of this pathogen by PCR and a...

Nebulin is a large actin-binding protein of the skeletal muscle sarcomere. Multiple isoforms of nebulin are produced from the 183-exon-containing nebulin gene (NEB). Mutations in NEB cause nemaline myopathy, distal myopathy, and core-rod myopathy. Nebulin mRNA expression was assessed by microarrays and RT-PCR in 21 human leg muscle and 2 brain samp...

Clostridium perfringens, one of the most common causes of food poisonings, can carry the enterotoxin gene, cpe, in its chromosome or on a plasmid. C. perfringens food poisonings are more frequently caused by the chromosomal cpe-carrying strains, while the plasmid-borne cpe-positive genotypes are more commonly found in the human feces and environmen...

The role of the two-component system (TCS) CBO0366/CBO0365 in the cold shock response and growth of the mesophilic Clostridium botulinum ATCC 3502 at 15°C was demonstrated by induced expression of the TCS genes upon cold shock and impaired growth of the TCS mutants at 15°C.

The expression of csdA, encoding an RNA helicase, was induced at 3°C in Yersinia pseudotuberculosis. The role of CsdA in Y. pseudotuberculosis under cold conditions was confirmed by impaired growth of insertional csdA mutants at 3°C. The results suggest that CsdA is crucial for Y. pseudotuberculosis survival in the chilled food chain.

Yersinia pseudotuberculosis is a significant psychrotrophic food pathogen whose cold tolerance mechanisms are poorly understood. Signal transduction systems serve to monitor the environment, but no systematic investigation of their role at cold temperatures in Y. pseudotuberculosis has yet been undertaken. The relative expression levels of 54 genes...

Streptomyces strains were isolated from scab lesions on potatoes collected from different parts of Norway. Twenty-eight plant-pathogenic strains, as tested on seedlings of radish and on potato, were identified on the basis of physiological and molecular criteria. Polymerase chain reaction (PCR) analysis, using species-specific primers, and sequenci...

Class I heat shock genes (HSGs) code for molecular chaperones which play a major role in the bacterial response to sudden increases of environmental temperature by assisting protein folding. Quantitative reverse transcriptase real-time PCR gene expression analysis of the food-borne pathogen Clostridium botulinum grown at 37°C showed that the class...

The areas of the pathogenicity island (PAI) designated as 'colonization region' (CR) and 'toxicogenic region' (TR) [Lerat et al. (2009) Mol. Plant Pathol. 10, 579-585] contain genes required for virulence and phytoxin production, respectively, in Streptomyces spp. causing common scab on potatoes. The PAI was tested for genetic variability by microa...

Responses to Potato virus A (PVA, genus Potyvirus) segregate to three phenotypic groups in a diploid cross between Solanum tuberosum subsp. andigena and a highly interspecific potato hybrid. The aim of this study was to compare gene expression between the progeny genotypes which react with hypersensitive response (HR) to PVA, allow PVA accumulation...

Long-term effects of elevated CO(2) and O(3) concentrations on gene expression in silver birch (Betula pendula Roth) leaves were studied during the end of the growing season. Two birch genotypes, clones 4 and 80, with different ozone growth responses, were exposed to 2x ambient CO(2) and/or O(3) in open-top chambers (OTCs). Microarray analyses were...

Mosses (Bryophyta) are nonvascular plants that constitute a large part of the photosynthesizing biomass and carbon storage on Earth. Little is known about how this important portion of flora maintains its health status. This study assessed whether the moss, Physcomitrella patens, responds to treatment with chitosan, a fungal cell wall-derived compo...

Electronic nose presents a rapid method to determine quality characteristics of foodstuffs. Ion mobility spectrometry allows rapid and simple on-site determination of gaseous compounds. Ion mobility based electronic nose system “MGD-1” was used to determine the separation of various hard and extra-hard cheese samples via headspace analysis. The ver...

Comparative genomic hybridization analysis of 32 Nordic group I Clostridium botulinum type B strains isolated from various sources revealed two homogeneous clusters, clusters BI and BII. The type B strains differed from reference strain ATCC 3502 by 413 coding sequence (CDS) probes, sharing 88% of all the ATCC 3502 genes represented on the microarr...