المؤلفون: Ovaskainen, Otso, Abrego, Nerea, Furneaux, Brendan, Hardwick, Bess, Somervuo, Panu, Palorinne, Isabella, Andrew, Nigel, Babiy, Ulyana, Bao, Tan, Bazzano, Gisela, Bondarchuk, Svetlana, Bonebrake, Timothy, Brennan, Georgina, Bret-Harte, Syndonia, Bässler, Claus, Cagnolo, Luciano, Cameron, Erin, Chapurlat, Elodie, Creer, Simon, DAcqui, Luigi, de Vere, Natasha, Desprez-Loustau, Marie-Laure, Dongmo, Michel, Dyrholm Jacobsen, Ida, Fisher, Brian, Flores de Jesus, Miguel, Griffith, Gareth, Gritsuk, Anna, Gross, Andrin, Grudd, Håkan, Halme, Panu, Hanna, Rachid, Hansen, Jannik, Hansen, Lars, Hegbe, Apollon, Hill, Sarah, Hogg, Ian, Hultman, Jenni, Hyde, Kevin, Hynson, Nicole, Ivanova, Natalia, Karisto, Petteri, Kerdraon, Deirdre, Knorre, Anastasia, Krisai-Greilhuber, Irmgard, Kurhinen, Juri, Kuzmina, Masha, Lecomte, Nicolas, Lecomte, Erin, Loaiza, Viviana, Lundin, Erik, Meire, Alexander, Mešić, Armin, Miettinen, Otto, Monkhause, Norman, Mortimer, Peter, Müller, Jörg, Nilsson, R, Nonti, Puani, Nordén, Jenni, Nordén, Björn, Paz, Claudia, Pellikka, Petri, Pereira, Danilo, Petch, Geoff, Pitkänen, Juha-Matti, Popa, Flavius, Potter, Caitlin, Purhonen, Jenna, Pätsi, Sanna, Rafiq, Abdullah, Raharinjanahary, Dimby, Rakos, Niklas, Rathnayaka, Achala, Raundrup, Katrine, Rebriev, Yury, Rikkinen, Jouko, Rogers, Hanna, Rogovsky, Andrey, Rozhkov, Yuri, Runnel, Kadri, Saarto, Annika, Savchenko, Anton, Schlegel, Markus, Schmidt, Niels, Seibold, Sebastian, Skjøth, Carsten, Stengel, Elisa, Sutyrina, Svetlana, Syvänperä, Ilkka, Tedersoo, Leho, Timm, Jebidiah, Tipton, Laura, Toju, Hirokazu, Uscka-Perzanowska, Maria, van der Bank, Michelle, Herman van der Bank, F, Vandenbrink, Bryan, Ventura, Stefano, Vignisson, Solvi

المصدر: Scientific Data. 11(1)

مصطلحات موضوعية: Air Microbiology, Spores, Fungal, DNA, Fungal, Fungi, Biodiversity

الوصف: 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 present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/7nc2n2kd
https://escholarship.org/content/qt7nc2n2kd/qt7nc2n2kd.pdf

المؤلفون: Seymour, Mathew, Roslin, Tomas, deWaard, Jeremy R, Perez, Kate HJ, D'Souza, Michelle L, Ratnasingham, Sujeevan, Ashfaq, Muhammad, Levesque-Beaudin, Valerie, Blagoev, Gergin A, Bukowski, Belén, Cale, Peter, Crosbie, Denise, Decaëns, Thibaud, deWaard, Stephanie L, Ekrem, Torbjørn, El-Ansary, Hosam O, Evouna Ondo, Fidèle, Fraser, David, Geiger, Matthias F, Hajibabaei, Mehrdad, Hallwachs, Winnie, Hanisch, Priscila E, Hausmann, Axel, Heath, Mark, Hogg, Ian D, Janzen, Daniel H, Kinnaird, Margaret, Kohn, Joshua R, Larrivée, Maxim, Lees, David C, León-Règagnon, Virginia, Liddell, Michael, Lijtmaer, Darío A, Lipinskaya, Tatsiana, Locke, Sean A, Manjunath, Ramya, Martins, Dino J, Martins, Marlúcia B, Mazumdar, Santosh, McKeown, Jaclyn TA, Anderson-Teixeria, Kristina, Miller, Scott E, Milton, Megan A, Miskie, Renee, Morinière, Jérôme, Mutanen, Marko, Naik, Suresh, Nichols, Becky, Noguera, Felipe A, Novotny, Vojtech, Penev, Lyubomir, Pentinsaari, Mikko, Quinn, Jenna, Ramsay, Leah, Rochefort, Regina, Schmidt, Stefan, Smith, M Alex, Sobel, Crystal N, Somervuo, Panu, Sones, Jayme E, Staude, Hermann S, St Jaques, Brianne, Stur, Elisabeth, Telfer, Angela C, Tubaro, Pablo L, Wardlaw, Tim J, Worcester, Robyn, Yang, Zhaofu, Young, Monica R, Zemlak, Tyler, Zakharov, Evgeny V, Zlotnick, Bradley, Ovaskainen, Otso, Hebert, Paul DN

المصدر: Commun Biol. 7(1)

مصطلحات موضوعية: Animals, Arthropods, Biodiversity, Geography, Spatio-Temporal Analysis, Biological Sciences, Ecology, Evolutionary Biology, Life Below Water, Biological sciences, Biomedical and clinical sciences

الوصف: 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-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.

وصف الملف: application/pdf

URL الوصول: https://escholarship.org/uc/item/4fx5z9zx

المؤلفون: Otso Ovaskainen, Nerea Abrego, Brendan Furneaux, Bess Hardwick, Panu Somervuo, Isabella Palorinne, Nigel R. Andrew, Ulyana V. Babiy, Tan Bao, Gisela Bazzano, Svetlana N. Bondarchuk, Timothy C. Bonebrake, Georgina L. Brennan, Syndonia Bret-Harte, Claus Bässler, Luciano Cagnolo, Erin K. Cameron, Elodie Chapurlat, Simon Creer, Luigi P. D’Acqui, Natasha de Vere, Marie-Laure Desprez-Loustau, Michel A. K. Dongmo, Ida B. Dyrholm Jacobsen, Brian L. Fisher, Miguel Flores de Jesus, Gregory S. Gilbert, Gareth W. Griffith, Anna A. Gritsuk, Andrin Gross, Håkan Grudd, Panu Halme, Rachid Hanna, Jannik Hansen, Lars Holst Hansen, Apollon D. M. T. Hegbe, Sarah Hill, Ian D. Hogg, Jenni Hultman, Kevin D. Hyde, Nicole A. Hynson, Natalia Ivanova, Petteri Karisto, Deirdre Kerdraon, Anastasia Knorre, Irmgard Krisai-Greilhuber, Juri Kurhinen, Masha Kuzmina, Nicolas Lecomte, Erin Lecomte, Viviana Loaiza, Erik Lundin, Alexander Meire, Armin Mešić, Otto Miettinen, Norman Monkhause, Peter Mortimer, Jörg Müller, R. Henrik Nilsson, Puani Yannick C. Nonti, Jenni Nordén, Björn Nordén, Claudia Paz, Petri Pellikka, Danilo Pereira, Geoff Petch, Juha-Matti Pitkänen, Flavius Popa, Caitlin Potter, Jenna Purhonen, Sanna Pätsi, Abdullah Rafiq, Dimby Raharinjanahary, Niklas Rakos, Achala R. Rathnayaka, Katrine Raundrup, Yury A. Rebriev, Jouko Rikkinen, Hanna M. K. Rogers, Andrey Rogovsky, Yuri Rozhkov, Kadri Runnel, Annika Saarto, Anton Savchenko, Markus Schlegel, Niels Martin Schmidt, Sebastian Seibold, Carsten Skjøth, Elisa Stengel, Svetlana V. Sutyrina, Ilkka Syvänperä, Leho Tedersoo, Jebidiah Timm, Laura Tipton, Hirokazu Toju, Maria Uscka-Perzanowska, Michelle van der Bank, F. Herman van der Bank, Bryan Vandenbrink, Stefano Ventura, Solvi R. Vignisson, Xiaoyang Wang, Wolfgang W. Weisser, Subodini N. Wijesinghe, S. Joseph Wright, Chunyan Yang, Nourou S. Yorou, Amanda Young, Douglas W. Yu, Evgeny V. Zakharov, Paul D. N. Hebert, Tomas Roslin

المصدر: Scientific Data, Vol 11, Iss 1, Pp 1-17 (2024)

مصطلحات موضوعية: Science

الوصف: Abstract 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 present data originating from the Global Spore Sampling Project, comprising 2,768 samples collected during two years at 47 outdoor locations across the world. Each sample represents fungal DNA extracted from 24 m3 of air. We applied a conservative bioinformatics pipeline that filtered out sequences that did not show strong evidence of representing a fungal species. The pipeline yielded 27,954 species-level operational taxonomic units (OTUs). Each OTU is accompanied by a probabilistic taxonomic classification, validated through comparison with expert evaluations. To examine the potential of the data for ecological analyses, we partitioned the variation in species distributions into spatial and seasonal components, showing a strong effect of the annual mean temperature on community composition.

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2052-4463

URL الوصول: https://doaj.org/article/a665cd3f632448dbad13496c3a4720f6

المؤلفون: Mathew Seymour, Tomas Roslin, Jeremy R. deWaard, Kate H. J. Perez, Michelle L. D’Souza, Sujeevan Ratnasingham, Muhammad Ashfaq, Valerie Levesque-Beaudin, Gergin A. Blagoev, Belén Bukowski, Peter Cale, Denise Crosbie, Thibaud Decaëns, Stephanie L. deWaard, Torbjørn Ekrem, Hosam O. El-Ansary, Fidèle Evouna Ondo, David Fraser, Matthias F. Geiger, Mehrdad Hajibabaei, Winnie Hallwachs, Priscila E. Hanisch, Axel Hausmann, Mark Heath, Ian D. Hogg, Daniel H. Janzen, Margaret Kinnaird, Joshua R. Kohn, Maxim Larrivée, David C. Lees, Virginia León-Règagnon, Michael Liddell, Darío A. Lijtmaer, Tatsiana Lipinskaya, Sean A. Locke, Ramya Manjunath, Dino J. Martins, Marlúcia B. Martins, Santosh Mazumdar, Jaclyn T. A. McKeown, Kristina Anderson-Teixeria, Scott E. Miller, Megan A. Milton, Renee Miskie, Jérôme Morinière, Marko Mutanen, Suresh Naik, Becky Nichols, Felipe A. Noguera, Vojtech Novotny, Lyubomir Penev, Mikko Pentinsaari, Jenna Quinn, Leah Ramsay, Regina Rochefort, Stefan Schmidt, M. Alex Smith, Crystal N. Sobel, Panu Somervuo, Jayme E. Sones, Hermann S. Staude, Brianne St. Jaques, Elisabeth Stur, Angela C. Telfer, Pablo L. Tubaro, Tim J. Wardlaw, Robyn Worcester, Zhaofu Yang, Monica R. Young, Tyler Zemlak, Evgeny V. Zakharov, Bradley Zlotnick, Otso Ovaskainen, Paul D. N. Hebert

المصدر: Communications Biology, Vol 7, Iss 1, Pp 1-11 (2024)

مصطلحات موضوعية: Biology (General), QH301-705.5

الوصف: Abstract 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-diversity framework. Sampling includes 129 sampling sites whereby malaise traps are deployed to monitor temporal changes in arthropod communities. Overall, we encountered more than 150,000 unique barcode index numbers (BINs) (i.e. species proxies). We assess between site differences in community diversity using beta-diversity and the partitioned components of species replacement and richness difference. Global total beta-diversity (dissimilarity) increases with decreasing latitude, greater spatial distance and greater temporal distance. Species replacement and richness difference patterns vary across biogeographic regions. Our findings support long-standing, general expectations of global biodiversity patterns. However, we also show that the underlying processes driving patterns may be regionally linked.

وصف الملف: electronic resource

Relation: https://doaj.org/toc/2399-3642

URL الوصول: https://doaj.org/article/27c56008a02543519a9bcd0f9110d003

المؤلفون: Bastien Parisy, Niels M. Schmidt, Helena Wirta, Laerke Stewart, Loic Pellissier, William E. Holben, Sam Pannoni, Panu Somervuo, Mirkka M. Jones, Jukka Siren, Eero Vesterinen, Otso Ovaskainen, Tomas Roslin

المصدر: Metabarcoding and Metagenomics, Vol 7, Iss , Pp 155-193 (2023)

مصطلحات موضوعية: Ecology, QH540-549.5

الوصف: 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-occurrences in Zackenberg in northeast Greenland using environmental DNA. To explore the potential for extracting ecological signals from eDNA data alone, we compared two approaches (visual vegetation surveys and soil eDNA metabarcoding) to describing plant communities and their responses to abiotic conditions. We then examined plant associations with microbes using a joint species distribution model. We found that most (68%) of plant genera were detectable by both vegetation surveys and eDNA signatures. Species-specific occurrence data revealed how plants, bacteria and fungi responded to their abiotic environment – with plants, bacteria and fungi all responding similarly to soil moisture. Nonetheless, a large proportion of fungi decreased in occurrences with increasing soil temperature. Regarding biotic associations, the nature and proportion of the plant-microbe associations detected were consistent between plant data identified via vegetation surveys and eDNA. Of pairs of plants and microbe genera showing statistically supported associations (while accounting for joint responses to the environment), plants and bacteria mainly showed negative associations, whereas plants and fungi mainly showed positive associations. Ample ecological signals detected by both vegetation surveys and by eDNA-based methods and a general correspondence in biotic associations inferred by both methods, suggested that purely eDNA-based approaches constitute a promising and easily applicable tool for studying plant-soil microbial associations in the Arctic and elsewhere.

وصف الملف: electronic resource

Relation: https://mbmg.pensoft.net/article/99979/download/pdf/; https://mbmg.pensoft.net/article/99979/download/xml/; https://mbmg.pensoft.net/article/99979/; https://doaj.org/toc/2534-9708

URL الوصول: https://doaj.org/article/5d9e852518b34204b0ebbf2772c203e9

المؤلفون: Maria Shumskaya, Nicholas Lorusso, Urvi Patel, Madison Leigh, Panu Somervuo, Dmitry Schigel

المصدر: MycoKeys, Vol 96, Iss , Pp 77-95 (2023)

مصطلحات موضوعية: Botany, QK1-989

الوصف: The MycoPins method described here is a rapid and affordable protocol to monitor early colonization events in communities of wood-inhabiting fungi in fine woody debris. It includes easy to implement field sampling techniques and sample processing, followed by data processing, and analysis of the development of early dead wood fungal communities. The method is based on fieldwork from a time series experiment on standard sterilized colonization targets followed by the metabarcoding analysis and automated molecular identification of species. This new monitoring method through its simplicity, moderate costs, and scalability paves a way for a broader and scalable project pipeline. MycoPins establishes a standard routine for research stations or regularly visited field sites for monitoring of fungal colonization of woody substrates. The routine uses widely available consumables and therefore presents a unifying method for monitoring of fungi of this type.

وصف الملف: electronic resource

Relation: https://mycokeys.pensoft.net/article/101033/download/pdf/; https://mycokeys.pensoft.net/article/101033/download/xml/; https://mycokeys.pensoft.net/article/101033/; https://doaj.org/toc/1314-4049

URL الوصول: https://doaj.org/article/9b534045c4d14821928e7214fc28da1f

المؤلفون: Hamis, Sara^{Aff1, Aff2, IDs0028502301903x_cor1}, Somervuo, Panu, Ågren, J. Arvid^{Aff4, Aff5}, Tadele, Dagim Shiferaw^{Aff5, Aff6}, Kesseli, Juha, Scott, Jacob G.^{Aff5, Aff8, Aff9}, Nykter, Matti^{Aff7, Aff10}, Gerlee, Philip^{Aff11, Aff12}, Finkelshtein, Dmitri, Ovaskainen, Otso^{Aff2, Aff3, Aff14}

المصدر: Journal of Mathematical Biology. 86(5)

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المؤلفون: Petteri Lehikoinen, Meeri Rannisto, Ulisses Camargo, Aki Aintila, Patrik Lauha, Esko Piirainen, Panu Somervuo, Otso Ovaskainen

المصدر: Citizen Science: Theory and Practice, Vol 8, Iss 1 (2023)

مصطلحات موضوعية: citizen science, machine learning, bioacoustics, ornithology, web portal, Science

الوصف: 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 engaging masses to contribute to research and share the workload. Birdwatchers are experts on identifying bird vocalizations and form an ideal focal audience for a citizen science project aiming for the required multitudes of annotated avian audio data. For this purpose, we launched a web portal that was targeted and advertised to Finnish birdwatchers. The users were asked to complete two kinds of tasks: 1) classify if a given bird sound belonged to the focal species and 2) classify all the bird species vocalizing in 10-second audio clips. In less than a year, the portal achieved annotations for 244,300 bird sounds and 5,358 clips, and attracted, on average, 70 visitors on daily basis. More than 200 birdwatchers took part in the classification tasks, of which 17 and 4 most dedicated users produced over half of the sound and clip classifications, respectively. As expected of birder experts, the classifications among users were highly consistent (mean agreement scores between 0.85–0.95, depending on the audio type) and resulted in high-quality training data for parameterizing machine learning models. Feedback about the web portal suggested that additional functionality such as increased freedom of choice would increase user motivation and dedication.

وصف الملف: electronic resource

Relation: https://theoryandpractice.citizenscienceassociation.org/articles/556; https://doaj.org/toc/2057-4991

URL الوصول: https://doaj.org/article/b2ebd51699ef49fdba47db493ce90c24