Article
Agronomy
Alexandros Dritsoulas, Sheng-Yen Wu, Homan Regmi, Larry W. Duncan
Summary: The study investigated changes in arthropod communities in a citrus orchard following soil inundation with entomopathogenic nematodes (EPNs) and found that certain arthropod taxa declined or increased in response to EPN augmentation, representing potential prey or predators of EPN. The study also revealed that regulation of EPN by various microarthropod species was a cumulative response rather than driven by a few key species.
Article
Biodiversity Conservation
Janina Schenk, Sebastian Hoess, Nils Kleinboelting, Walter Traunspurger
Summary: Assessing the ecological consequences of marine and freshwater contamination is important, and the NemaSPEAR index provides a reliable means of bioindication. This study demonstrated the validity of a molecular-taxonomy-based NemaSPEAR index for evaluating sediment quality. The results showed that the molecular-based index can accurately distinguish between sites of different pollution statuses.
ECOLOGICAL INDICATORS
(2022)
Article
Microbiology
Bingxue Wu, Xiaoyan Jiao, Anqi Sun, Fangfang Li, Ji-Zheng He, Hang-Wei Hu
Summary: Soil invertebrates in agricultural systems are influenced by precipitation seasonality and soil pH, and future climate change and agricultural practices may have significant effects on their distribution.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Multidisciplinary Sciences
Tatiana Murillo, Dominik Schneider, Michael Heistermann, Rolf Daniel, Claudia Fichtel
Summary: The gut microbiome plays a crucial role in the host's health by influencing immunity, development, and metabolism. It is a dynamic community that varies between individuals and within individuals at different time points. This study investigated the factors shaping the gut microbiome and found that host-associated factors, such as physiological stress and dietary changes, have a greater impact on the gut microbiome than interactions within the microbial community. The study also found that social relationships and environmental water sources contribute to the shaping of the gut microbiome.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Kendall V. Morse, Dylan R. Richardson, Teresa L. Brown, Robert D. Vangundy, Aubrey Bruce Cahoon
Summary: The aquatic prokaryotic microbiome in a cave is more similar to surface microbes than to those in speleothems and soils, suggesting microbial movement from epikarst zones into the cave. A bloom of cave microbiome diversity occurred in the fall months, contrasting with the relatively steady biodiversity on the surface.
Article
Biochemistry & Molecular Biology
Emil Ellegaard Thomassen, Eva Egelyng Sigsgaard, Mads Reinholdt Jensen, Kent Olsen, Morten D. D. Hansen, Jens-Christian Svenning, Philip Francis Thomsen
Summary: Trophic rewilding has been increasingly used in restoration efforts to reintroduce large-bodied mammals and promote biodiverse ecosystems. However, empirical evidence on the effects of megafauna introductions on other organisms and the mechanisms involved is still limited. This study used environmental DNA analysis of dung from feral cattle and horses to assess seasonal variations in their plant diet and dung-associated invertebrates. The results showed differences in diet and invertebrate communities between the two herbivores, demonstrating their complementary effects on vegetation and biodiversity. These findings are important for decision-making in rewilding projects.
Article
Zoology
Kaitlin Gattoni, Eli M. S. Gendron, Rebeca Sandoval-Ruiz, Abigail Borgemeier, J. Parr McQueen, Rachel M. Shepherd, Dieter Slos, Thomas O. Powers, Dorota L. Porazinska
Summary: Nematodes lack representation in biodiversity research and there is a need for a reliable reference database for molecular identification and assessment of nematode diversity. The 18S-NemaBase, created and curated for nematodes, outperformed other databases in taxonomic assignments and diversity assessments, providing a simpler workflow.
JOURNAL OF NEMATOLOGY
(2023)
Article
Neurosciences
Paul W. Frazel, David Labib, Theodore Fisher, Ran Brosh, Nicolette Pirianian, Anne Marchildon, Jef D. Boeke, Valentina Fossati, Shane A. Liddelow
Summary: Researchers used single-cell/single-nucleus RNA sequencing to analyze the differentiation of macroglia in the brain and spinal cord. They identified candidate genes involved in glial cell fate specification and observed heterogeneous expression of astrocyte surface markers during differentiation. The researchers also optimized a mouse astrocyte differentiation protocol and explored potential genomic regulatory sites mediating glial differentiation using multi-omic analysis.
NATURE NEUROSCIENCE
(2023)
Article
Environmental Sciences
Gabriella Panto, Francesca Pasotti, Lara Macheriotou, Ann Vanreusel
Summary: This study investigated meiobenthic and nematode communities in the Prince Gustav Channel and Duse Bay, finding that the availability and freshness of organic matter are the main factors influencing density, with unclear potential factors leading to local and regional variability. Bathymetric transects and environmental variables revealed differences in the basins, with potential implications for biodiversity and functional traits.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Behavioral Sciences
Christoph Abel, Peggy Giertz, Yedidya R. Ratovonamana, Thomas Puettker, S. Jacques Rakotondranary, Bettina M. Scheel, Tobias L. Lenz, Joerg U. Ganzhorn
Summary: Species can either maintain a certain social organization in different habitats or show different social organizations in similar habitats. The reasons underlying this variability are not always clear but might have consequences for population dynamics, especially under changing environmental conditions. Our study revealed that the social organization of mouse lemurs in Madagascar converges towards random spatial distributions with declining food availability, suggesting that social organization is shaped by both phylogenetic origin and ecological conditions.
BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Eglantine Mathieu-Begne, Simon Blanchet, Olivier Rey, Eve Toulza, Charlotte Veyssiere, Sophie Manzi, Maxim Lefort, Orlane Scelsi, Geraldine Loot
Summary: Recent studies have shown that there is a link between diseases and host microbiota. It is difficult to determine whether host microbiota promote infections or whether infections result in changes in host microbiota, especially in natural conditions. However, understanding this is crucial for understanding the role of microbes in disease progression.
Article
Ecology
Veronarindra Ramananjato, Finaritra Randimbiarison, Tanjoniaina Hery Nirina Patrick Rabarijaonina, Onja H. Razafindratsima
Summary: With the help of telemetry technologies, an unprecedented event of rufous mouse lemurs sleeping on the rainforest ground was observed, which has not been seen in any other Microcebus species. This discovery could illustrate an ecophysiological response strategy to habitat changes.
ECOLOGY AND EVOLUTION
(2022)
Article
Soil Science
Masanori Kawanobe, Koki Toyota, Karl Ritz
Summary: This study developed highly sensitive primer sets targeting the 18S rDNA region for soil nematode fauna using NGS technology. The NGS analysis of soil DNA with these primer sets showed a higher diversity and more nematode species detection compared to traditional morphological methods. The results indicate that the developed primer sets and metabarcoding protocol are suitable for comprehensive studies of nematode community structure.
APPLIED SOIL ECOLOGY
(2021)
Article
Parasitology
Tong Wang, Elizabeth M. Redman, Arianna Morosetti, Rebecca Chen, Sarah Kulle, Natasha Morden, Christopher McFarland, Hannah Rose Vineer, Douglas D. Colwell, Eric R. Morgan, John S. Gilleard
Summary: The study in western Canada showed the accumulation of gastrointestinal nematode (GIN) larvae on pasture, with similar dynamics for different GIN species on different farms. Short-term microclimatic conditions were found to impact the population of L3 larvae on the pasture.
PARASITES & VECTORS
(2021)
Article
Evolutionary Biology
Jelmer W. Poelstra, Jordi Salmona, George P. Tiley, Dominik Schussler, Marina B. Blanco, Jean B. Andriambeloson, Olivier Bouchez, C. Ryan Campbell, Paul D. Etter, Paul A. Hohenlohe, Kelsie E. Hunnicutt, Amaia Iribar, Eric A. Johnson, Peter M. Kappeler, Peter A. Larsen, Sophie Manzi, JosE M. Ralison, Blanchard Randrianambinina, Rodin M. Rasoloarison, David W. Rasolofoson, Amanda R. Stahlke, David W. Weisrock, Rachel C. Williams, LounEs Chikhi, Edward E. Louis Jr, Ute Radespiel, Anne D. Yoder
Summary: Mouse lemurs are cryptic primates found throughout Madagascar, with a recent surge in recognized species leading to concerns of oversplitting. Research in northeastern Madagascar with high microendemism and predicted habitat loss revealed marked differences among mouse lemur lineages, supporting the recognition of an undescribed lineage as a separate species. The rapid evolution of reproductive isolation in sympatric lineages suggests a complex evolutionary history in the mouse lemur clade.
SYSTEMATIC BIOLOGY
(2021)
Article
Anatomy & Morphology
Juha Laakkonen, Alixia Vedrines
Summary: The anatomical architecture of the hip and stifle joints of the Saimaa ringed seal is similar to that of the Baltic ringed seal, allowing for more lateral movement during aquatic motion but less adaptation to terrestrial locomotion.
ANATOMIA HISTOLOGIA EMBRYOLOGIA
(2022)
Article
Ecology
Tuomas Aivelo, Melissa Lemoine, Barbara Tschirren
Summary: The study found systematic changes in tick bacterial microbiota diversity along elevational gradients in the Swiss Alps, with a decrease in microbial diversity as elevation increased. Higher microbial diversity was observed later in the season, with adult female ticks showing the lowest microbial alpha diversity.
Article
Biochemistry & Molecular Biology
Ari Loytynoja
Summary: This study reanalyzed genome sequence data from 25 human populations and found thousands of complex mutation clusters caused by template switching mutations in the human genome. Computational tools were developed for detecting template switching mutations, and it was discovered that commonly used analysis pipelines for short-read sequencing data cannot accurately identify these mutations.
Article
Biochemistry & Molecular Biology
Xueyun Feng, Juha Merila, Ari Loytynoja
Summary: Introgressive hybridization is an important process in evolution. The analysis of whole-genome sequences of nine-spined sticklebacks in northern Europe revealed a complex pattern of population ancestry. Freshwater isolates provided insights into the past and intermediate states of evolutionary processes.
Article
Education & Educational Research
Tuomas Aivelo
Summary: This study examined Finnish secondary school students' attitudes towards urban rats and their feelings of disgust. The results showed that older students had a more positive attitude towards the environment and a lower level of disgust. Surprisingly, students with a more positive attitude towards rats also had a higher liking for biology as a school subject and a higher level of general disgust. The findings suggest that disgust in general does not hinder learning and appreciating unloved species as part of biodiversity.
ENVIRONMENTAL EDUCATION RESEARCH
(2023)
Article
Ecology
Mikko Kivikoski, Pasi Rastas, Ari Loeytynoja, Juha Merilae
Summary: Map distance, a measure of the expected number of crossovers between two loci in genetics, is estimated using mapping functions based on observed recombination frequencies. Traditional mapping functions developed when the number of markers was low may underpredict recombination frequencies from map distance in high-density marker data. This study demonstrates that a piecewise function can provide more accurate predictions, highlighting the context-dependent association between map distance and recombination frequency.
Article
Evolutionary Biology
Mikko Kivikoski, Antoine Fraimout, Pasi Rastas, Ari Loytynoja, Juha Merila
Summary: Crossovers in meiosis play a crucial role in ensuring proper segregation and recombination of chromosomes in sexual reproduction. However, little is known about the heritability and repeatability of crossover rates in the wild. This study examined crossover rate variation in outbred stickleback populations and found that repeatability was moderate, with higher values in females than in males. Due to limitations in sample size and parental relatedness, heritability could not be confidently estimated. Overall, the evolvability of crossover rates appears to be low based on our results and comparisons with previous studies.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Biochemistry & Molecular Biology
Ari Loytynoja, Pasi Rastas, Mia Valtonen, Juhana Kammonen, Liisa Holm, Morten Tange Olsen, Lars Paulin, Jukka Jernvall, Petri Auvinen
Summary: In the face of the human-caused biodiversity crisis, it is important to understand the theoretical basis of conservation efforts for endangered species and populations. Population subdivision helps organisms retain genetic diversity crucial for adaptation in a changing environment. This study on the Saimaa ringed seals provides empirical evidence supporting the significance of habitat topography in generating and maintaining population subdivision and highlights the importance of genetic analyses in conservation decisions.
Article
Biology
Yingying X. G. Wang, Liina Voutilainen, Mahdi Aminikhah, Heikki Helle, Otso Huitu, Juha Laakkonen, Andreas Linden, Jukka Niemimaa, Jussi Sane, Tarja Sironen, Olli Vapalahti, Heikki Henttonen, Eva R. Kallio
Summary: The study shows that certain predators, young bank voles, and diverse rodent communities may reduce the risk of PUUV infection in humans by negatively impacting the abundance of infected bank voles.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Anatomy & Morphology
Janne Granroth, Juha Laakkonen
Summary: This study compared the effects of chemical and enzymatic maceration processes on the removal of soft tissue from skull specimens, and found that the enzymatic maceration process was better for producing specimens that visualize the intracranial arterial arrangement.
ANATOMIA HISTOLOGIA EMBRYOLOGIA
(2023)
Article
Anatomy & Morphology
Juha Laakkonen, Heini Nihtilae, Jukka Jernvall
Summary: The intracranial arterial vascularization of Saimaa and Baltic ringed seals showed similarities to other pinniped species, suggesting little evidence for aquatic adaptation or thermoregulation-related changes.
ANATOMICAL RECORD-ADVANCES IN INTEGRATIVE ANATOMY AND EVOLUTIONARY BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Aqqalu Rosing-Asvid, Ari Loytynoja, Paolo Momigliano, Rikke Guldborg Hansen, Camilla Hjorth Scharff-Olsen, Mia Valtonen, Juhana Kammonen, Rune Dietz, Frank Farso Riget, Steve H. Ferguson, Christian Lydersen, Kit M. Kovacs, David M. Holland, Jukka Jernvall, Petri Auvinen, Morten Tange Olsen
Summary: This study reveals the existence of a unique ringed seal ecotype in the Ilulissat Icefjord, Greenland, through the analysis of genomic, biologging, and survey data. The findings show genetic divergence and phenotypic differences between this ecotype and other Arctic ringed seals. The study highlights the importance of indigenous knowledge in guiding scientific research and calls for further efforts to understand how different populations or ecotypes respond to environmental change.
Article
Education & Educational Research
Anttoni Kervinen, Tuomas Aivelo
Summary: Uncertainty is inherent in scientific research practices and plays a significant role in learning about science. Research has shown that managing uncertainty in epistemic practices of science can aid in learning. This study investigates how Finnish secondary school students respond to epistemic uncertainty during an ecological citizen science inquiry. The findings reveal three responses to uncertainty: envisioning alternative scenarios and hypothesis, accepting and maintaining uncertainty in argumentation practices, and flexibly reframing research activities and goals. It suggests that incorporating shared experiences of uncertainty in pedagogical design can support science learning in different settings.
Article
Biochemical Research Methods
Emmi Olkkonen, Ari Loytynoja
Summary: This protocol demonstrates the efficient utilization of a fragmented reference genome and low-coverage sequencing data for population genetic analyses of a species with highly reduced genetic diversity. By combining genomic and geospatial data, traditional analyses can be extended. Coancestry is introduced as a measure of genetic identity, and tools for quantifying across-genome variation in genetic diversity are described.
Article
Multidisciplinary Sciences
Heli A. M. Monttinen, Ari Loytynoja
Summary: Research has shown that DNA replication-related template switching is an important mechanism in the evolution of RNA genes, explaining mutation patterns, complex sequence changes, and the maintenance of RNA stem structures. This finding provides a solution to understanding the evolution of RNA genes and demonstrates the functionality and significance of template switching.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
