25 Works

Data from: Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

Samuel K. Sheppard, Lu Cheng, Guillaume Méric, Caroline P. A. De Haan, Ann-Katrin Llarena, Pekka Marttinen, Ana Vidal, Anne Ridley, Felicity Clifton-Hadley, Thomas R. Connor, Norval J. C. Strachan, Ken Forbes, Frances M. Colles, Keith A. Jolley, Stephen D. Bentley, Martin C. J. Maiden, Marja-Liisa Hänninen, Julian Parkhill, William P. Hanage & Jukka Corander
Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major...

Data from: Genetic structure of native ant supercolonies varies in space and time

Eva Schultner, Jari Saramäki & Heikki Helanterä
Ant supercolonies are the largest cooperative units known in nature. They consist of networks of interconnected nests with hundreds of reproductive queens, where individuals move freely between nests, cooperate across nest boundaries and show little aggression towards non-nestmates. The combination of high queen numbers and free mixing of workers, queens and brood between nests results in extremely low nestmate relatedness. In such low-relatedness societies, cooperative worker behaviour appears maladaptive because it may aid random individuals...

Data from: Modeling the perception of audiovisual distance: Bayesian causal inference and other models

Catarina Mendonça, Pietro Mandelli & Ville Pulkki
Studies of audiovisual perception of distance are rare. Here, visual and auditory cue interactions in distance are tested against several multisensory models, including a modified causal inference model. In this causal inference model predictions of estimate distributions are included. In our study, the audiovisual perception of distance was overall better explained by Bayesian causal inference than by other traditional models, such as sensory dominance and mandatory integration, and no interaction. Causal inference resolved with probability...

Data from: Two-thirds of global cropland area impacted by climate oscillations

Matias Heino, Michael J. Puma, Philip J. Ward, Dieter Gerten, Vera Heck, Stefan Siebert & Matti Kummu
The El Niño Southern Oscillation (ENSO) peaked strongly during the boreal winter 2015-2016, leading to food insecurity in many parts of Africa, Asia and Latin America. Besides ENSO, the Indian Ocean Dipole (IOD) and the North Atlantic Oscillation (NAO) are known to impact crop yields worldwide. Here, we assess for the first time in a unified framework the relationship between ENSO, IOD and NAO and simulated crop productivity at the sub-country scale. Our findings reveal...

Data from: Increasing dependence of lowland populations on mountain water resources

Daniel Viviroli, Matti Kummu, Michel Meybeck, Marko Kallio & Yoshihide Wada
Mountain areas provide disproportionally high runoff in many parts of the world, and here we quantify for the first time their importance for water resources and food production from the viewpoint of the lowland areas downstream. The dataset maps the degree to which lowland areas potentially depend on runoff contributions from mountain areas (39% of land mass) between the 1960s and the 2040s.

Data from: Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

Marcin J. Skwark, Nicholas J. Croucher, Santeri Puranen, Claire Chewapreecha, Maiju Pesonen, Ying Ying Xu, Paul Turner, Simon R. Harris, Stephen B. Beres, James M. Musser, Julian Parkhill, Stephen D. Bentley, Erik Aurell & Jukka Corander
Recent advances in the scale and diversity of population genomic datasets for bacteria now provide the potential for genome-wide patterns of co-evolution to be studied at the resolution of individual bases. Here we describe a new statistical method, genomeDCA, which uses recent advances in computational structural biology to identify the polymorphic loci under the strongest co-evolutionary pressures. We apply genomeDCA to two large population data sets representing the major human pathogens Streptococcus pneumoniae (pneumococcus) and...

Data from: How close do we live to water? a global analysis of population distance to freshwater bodies

Matti Kummu, Hans De Moel, Philip J. Ward & Olli Varis
Traditionally, people have inhabited places with ready access to fresh water. Today, over 50% of the global population lives in urban areas, and water can be directed via tens of kilometres of pipelines. Still, however, a large part of the world's population is directly dependent on access to natural freshwater sources. So how are inhabited places related to the location of freshwater bodies today? We present a high-resolution global analysis of how close present-day populations...

Data from: Evolution of camouflage drives rapid ecological change in an insect community

Timothy E. Farkas, Tommi Mononen, Aaron A. Comeault, Ilkka Hanski & Patrik Nosil
Evolutionary change in individual species has been hypothesized to have far-reaching consequences for entire ecological communities, and such coupling of ecological and evolutionary dynamics (“eco-evolutionary dynamics”) has been demonstrated for a variety systems. However, the relative importance of evolutionary dynamics for ecological dynamics remains unclear. Here, we investigate how spatial patterns of local adaptation in the stick insect Timema cristinae, driven by natural selection, gene flow and founder effects, structure metapopulations, communities, and multitrophic interactions....

Data from: Inferring dispersal across a fragmented landscape using reconstructed families in the Glanville fritillary butterfly

Toby Fountain, Arild Husby, Etsuko Nonaka, Michelle F. DiLeo, Janne H. Korhonen, Pasi Rastas, Torsti Schulz, Marjo Saastamoinen & Ilkka Hanski
Dispersal is important for determining both a species ecological processes, such as population viability, and its evolutionary processes, like gene flow and local adaptation. Yet obtaining accurate estimates in the wild through direct observation can be challenging or even impossible, particularly over large spatial and temporal scales. Genotyping many individuals from wild populations can provide detailed inferences about dispersal. We therefore utilized genomewide marker data to estimate dispersal in the classic metapopulation of the Glanville...

Data from: Forest loss in protected areas and intact forest landscapes: a global analysis

Matias Heino, Matti Kummu, Marika Makkonen, Mark Mulligan, Peter H. Verburg, Mika Jalava & Timo A. Räsänen
In spite of the high importance of forests, global forest loss has remained alarmingly high during the last decades. Forest loss at a global scale has been unveiled with increasingly finer spatial resolution, but the forest extent and loss in protected areas (PAs) and in large intact forest landscapes (IFLs) have not so far been systematically assessed. Moreover, the impact of protection on preserving the IFLs is not well understood. In this study we conducted...

How latex film formation and adhesion at the nanoscale correlate to performance of pressure sensitive adhesives with cellulose nanocrystals

Elina Niinivaara, Alexandra Ouzas, Carole Fraschini, Richard M. Berry, Marc A. Dubé & Emily D. Cranston
Emulsion polymerized latex-based pressure sensitive adhesives (PSAs) are more environmentally benign because they are synthesized in water but often underperform compared to their solution polymerized counterparts. Studies have shown a simultaneous improvement in the tack, and peel and shear strength of various acrylic PSAs upon the addition of cellulose nanocrystals (CNCs). This work uses atomic force microscopy (AFM) to examine the role of CNCs in (i) the coalescence of hydrophobic 2‐ethyl hexyl acrylate/n‐butyl acrylate/methyl methacrylate...

Data from: Cross-cultural similarity in relationship-specific social touching

Juulia T. Suvilehto, Lauri Nummenmaa, Tokiko Harada, Robin I. M. Dunbar, Riitta Hari, Robert Turner, Norihiro Sadato & Ryo Kitada
Many species use touching for reinforcing social structures, and particularly non-human primates use social grooming for managing their social networks. However, it is still unclear how social touch contributes to maintenance and reinforcement of human social networks. Human studies in Western cultures suggest that the body locations where touch is allowed are associated with the strength of the emotional bond between the person touched and the toucher. However, it is unknown to what extent this...

Permutation-based significance analysis reduces the type 1 error rate in bisulphite sequencing data analysis of human umbilical cord blood samples

Essi Laajala, Viivi Halla-aho, Toni Grönroos, Ubaid Ullah Kalim, Mari Vähä-Mäkilä, Mirja Nurmio, Henna Kallionpää, Niina Lietzén, Juha Mykkänen, Omid Rasool, Jorma Toppari, Matej Orešič, Mikael Knip, Riikka Lund, Riitta Lahesmaa & Harri Lähdesmäki
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn...

Data from: Climatic effects on planning behavior

Yong Liu, Vassilis Kostakos & Hongxiu Li
What mechanism links climate change and social change? Palaeoanthropological analysis of human remains suggests that abrupt climate change is linked to societal restructuring, but it has been challenging to reliably identify the exact mechanisms underlying this relationship. Here we identify one potential mechanism that can link climate to behavior change, and underpins many of the reported findings on social restructuring. Specifically, we show that daily weather is linked to human planning behavior, and this effect...

LeWoS: A universal leaf‐wood classification method to facilitate the 3D modelling of large tropical trees using terrestrial LiDAR

Di Wang, Stéphane Momo Takoudjou & Eric Casella
1. Leaf-wood separation in terrestrial LiDAR data is a prerequisite for non-destructively estimating biophysical forest properties such as standing wood volumes and leaf area distributions. Current methods have not been extensively applied and tested on tropical trees. Moreover, their impacts on the accuracy of subsequent wood volume retrieval were rarely explored. 2. We present LeWoS, a new fully automatic tool to automate the separation of leaf and wood components, based only on geometric information at...

Data from: High-performance single-walled carbon nanotube transparent conducting film fabricated by using low feeding rate of ethanol solution

Er-Xiong Ding, Qiang Zhang, Nan Wei, Abu Taher Khan & Esko I. Kauppinen
We report floating catalyst chemical vapor deposition synthesis of single-walled carbon nanotubes (SWCNTs) for high performance transparent conducting films (TCFs) using low feeding rate of precursor solution. Herein, ethanol acts as carbon source, ferrocene and thiophene as catalyst precursor and growth promoter, respectively. By adopting a low feeding rate of 4 μl/min, the fabricated TCFs present one of the lowest sheet resistances of ca. 78 ohm/sq. at 90% transmittance. Optical characterizations demonstrate that the mean...

Strain diversity and spatial distribution are linked to epidemic dynamics in host populations

Jenalle Eck, Benoit Barrès, Samuel Soubeyrand, Jukka Siren, Elina Numminen & Anna-Liisa Laine
The inherently variable nature of epidemics renders predictions of when and where infection is expected to occur challenging. Differences in pathogen strain composition, diversity, fitness, and spatial distribution are generally ignored in epidemiological modeling and are rarely studied in natural populations, yet they may be important drivers of epidemic trajectories. To examine how these factors are linked to epidemics in natural host populations, we collected epidemiological and genetic data from fifteen populations of the powdery...

Defining and quantifying effective connectivity of landscapes for species' movements

Bram Van Moorter, Ilkka Kivimäki, Manuela Panzacchi & Marco Saerens
Demonstration of the workflow and supplementary information on the randomized shortest paths framework for "Defining and quantifying effective connectivity of landscapes for species’ movements" by Van Moorter B, Kivimäki I, Panzacchi M, Saerens M. (2021) in Ecography 44(6):1–15. Ecosystem functioning depends on multiple successful interactions, many supported by individual movements. The degree to which the landscape allows these interactions to take place has been referred to as ‘effective connectivity' (EC). Many of the cumulative impacts...

Genetic polymorphisms in COMT and BDNF influence synchronization dynamics of human neuronal oscillations

Jaana Simola, Felix Siebenhühner, Vladislav Myrov, Katri Kantojärvi, Tiina Paunio, J. Matias Palva, Elvira Brattico & Satu Palva
Neuronal oscillations, their inter-areal synchronization, and scale-free dynamics constitute fundamental mechanisms for cognition by regulating communication in neuronal networks. These oscillatory dynamics have large inter-individual variability that is partly heritable. We hypothesized that this variability could be partially explained by genetic polymorphism in neuromodulatory genes. We recorded resting-state magnetoencephalography (MEG) from 82 healthy participants and investigated whether oscillation dynamics were influenced by genetic polymorphisms in Catechol-O-methyltransferase (COMT) Val158Met and brain-derived neurotrophic factor (BDNF) Val66Met. Both...

Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples

Essi Laajala, Viivi Halla-aho, Toni Grönroos, Ubaid Ullah Kalim, Mari Vähä-Mäkilä, Mirja Nurmio, Henna Kallionpää, Niina Lietzén, Juha Mykkänen, Omid Rasool, Jorma Toppari, Matej Orešič, Mikael Knip, Riikka Lund, Riitta Lahesmaa & Harri Lähdesmäki
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn...

Data from: Increasing frequency of low summer precipitation synchronizes dynamics and compromises metapopulation stability in the Glanville fritillary butterfly

Ayco J. M. Tack, Tommi Mononen & Ilkka Hanski
Climate change is known to shift species' geographical ranges, phenologies and abundances, but less is known about other population dynamic consequences. Here, we analyse spatio-temporal dynamics of the Glanville fritillary butterfly (Melitaea cinxia) in a network of 4000 dry meadows during 21 years. The results demonstrate two strong, related patterns: the amplitude of year-to-year fluctuations in the size of the metapopulation as a whole has increased, though there is no long-term trend in average abundance;...

Data from: Sex differences in social focus across the lifecycle in humans

Kunal Bhattacharya, Asim Ghosh, Daniel Monsivais, Robin I. M. Dunbar & Kimmo Kaski
Age and gender are two important factors that play crucial roles in the way organisms allocate their social effort. In this study, we analyse a large mobile phone dataset to explore the way life history influences human sociality and the way social networks are structured. Our results indicate that these aspects of human behaviour are strongly related to age and gender such that younger individuals have more contacts and, among them, males more than females....

Data from: Gridded global datasets for Gross Domestic Product and Human Development Index over 1990-2015

Matti Kummu, Maija Taka & Joseph H. A. Guillaume
An increasing amount of high-resolution global spatial data are available, and used for various assessments. However, key economic and human development indicators are still mainly provided only at national level, and downscaled by users for gridded spatial analyses. Instead, it would be beneficial to adopt data for sub-national administrative units where available, supplemented by national data where necessary. To this end, we present gap-filled multiannual datasets in gridded form for Gross Domestic Product (GDP) and...

Data from: Dynamics of investor spanning trees around dot-com bubble

Sindhuja Ranganathan, Mikko Kivelä & Juho Kanniainen
We identify temporal investor networks for Nokia stock by constructing networks from correlations between investor-specific net-volumes and analyze changes in the networks around dot-com bubble. The analysis is conducted separately for households, financial, and non-financial institutions. Our results indicate that spanning tree measures for households reflected the boom and crisis: the maximum spanning tree measures had a clear upward tendency in the bull markets when the bubble was building up, and, even more importantly, the...

Permutation-based significance analysis reduces the type 1 error rate in bisulphite sequencing data analysis of human umbilical cord blood samples

Essi Laajala, Viivi Halla-aho, Toni Grönroos, Ubaid Ullah Kalim, Mari Vähä-Mäkilä, Mirja Nurmio, Henna Kallionpää, Niina Lietzén, Juha Mykkänen, Omid Rasool, Jorma Toppari, Matej Orešič, Mikael Knip, Riikka Lund, Riitta Lahesmaa & Harri Lähdesmäki
DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn...

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