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            "title": "Diversification of the terrestrial frog genus <i>Anomaloglossus</i> (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy",
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                {
                    "creatorType": "author",
                    "firstName": "Jean-Pierre",
                    "lastName": "Vacher"
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                    "creatorType": "author",
                    "firstName": "Philippe J. R.",
                    "lastName": "Kok"
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                    "creatorType": "author",
                    "firstName": "Miguel Trefaut",
                    "lastName": "Rodrigues"
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                    "creatorType": "author",
                    "firstName": "Albertina",
                    "lastName": "Lima"
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                    "creatorType": "author",
                    "firstName": "Tomas",
                    "lastName": "Hrbek"
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                {
                    "creatorType": "author",
                    "firstName": "Fernanda P.",
                    "lastName": "Werneck"
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                    "firstName": "Sophie",
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                    "firstName": "Antoine",
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            "abstractNote": "Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.",
            "publicationTitle": "Molecular Phylogenetics and Evolution",
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            "journalAbbreviation": "Molecular Phylogenetics and Evolution",
            "DOI": "10.1016/j.ympev.2023.108008",
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                    "tag": "Amazonia",
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            "title": "Meta-Embedded Clustering (MEC): A new method for improving clustering quality in unlabeled bird sound datasets",
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                    "firstName": "Joachim",
                    "lastName": "Poutaraud"
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                    "firstName": "Sylvain",
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            "abstractNote": "In recent years, ecoacoustics has offered an alternative to traditional biodiversity monitoring techniques with the development of passive acoustic monitoring (PAM) systems allowing, among others, to detect and identify species that are difficult to detect by human observers, automatically. PAM systems typically generate large audio datasets, but using these monitoring techniques to infer ecologically meaningful information remains challenging. In most cases, several thousand hours of recordings need to be manually labeled by experts limiting the operability of the systems. Based on recent developments of meta-learning algorithms and unsupervised learning techniques, we propose here Meta-Embedded Clustering (MEC), a new method with high potential for improving clustering quality in unlabeled bird sound datasets. MEC method is organized in two main steps, with: (a) fine-tuning of a pretrained convolutional neural network (CNN) backbone with different meta-learning algorithms using pseudo-labeled data, and (b) clustering of manually-labeled bird sounds in the latent space based on vector embeddings extracted from the fine-tuned CNN. The MEC method significantly enhanced average clustering performance from less than 1% to more than 80%, greatly outperforming the traditional approach of relying solely on CNN features extracted from a general neotropical audio database. However, this enhanced performance came with the cost of excluding a portion of the data categorized as noise. By improving the quality of clustering in unlabeled bird sound datasets, the MEC method should facilitate the work of ecoacousticians in managing acoustic units of bird song/call clustered according to their similarities, and in identifying potential clusters of species undetected using traditional approaches.",
            "publicationTitle": "Ecological Informatics",
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            "date": "2024-09-01",
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            "pages": "102687",
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            "DOI": "10.1016/j.ecoinf.2024.102687",
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                    "tag": "Dimensionality reduction",
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                    "firstName": "Jason",
                    "lastName": "Vleminckx"
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                    "firstName": "Oscar Valverde",
                    "lastName": "Barrantes"
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                    "firstName": "Claire",
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                    "firstName": "C. E. Timothy",
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                    "firstName": "David",
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                    "firstName": "Julien",
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                    "firstName": "Pascal",
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                    "creatorType": "author",
                    "firstName": "Elvis Harry",
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                    "firstName": "Italo",
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                    "firstName": "Freddie C.",
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                    "firstName": "Juan Ernesto",
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                    "firstName": "Christopher",
                    "lastName": "Baraloto"
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            ],
            "abstractNote": "Abstract\n            Understanding how biotic interactions and environmental filtering mediated by soil properties shape plant community assembly is a major challenge in ecology, especially when studying complex and hyperdiverse ecosystems like tropical forests. To shed light on the influence of both factors, we examined how the edaphic optimum of species (their niche position) related to their edaphic range (their niche breadth) along different environmental gradients and how this translates into functional strategies. Here we tested four scenarios describing the shape of the niche breadth—niche position relationship, including one neutral scenario and three scenarios proposing different relative influences of abiotic and biotic factors on community assembly along a soil resource gradient. To do so, we used soil concentration data for five key nutrients (N, P, Ca, Mg, and K), along with accurate measurements of 14 leaf, stem, and root traits for 246 tree species inventoried in 101 plots located across Eastern (French Guiana) and Western (Peru) Amazonia. We found that species niche breadth increased linearly with species niche position along each soil nutrient gradient. This increase was associated with more resource acquisitive traits in the leaves and the roots for soil N, Ca, Mg, and K concentration, while it was negatively associated with wood density for soil P concentration. These observations agreed with one of our hypothetical scenarios in which species with resource conservation traits are confined to the most nutrient‐depleted soils (abiotic filter), but they are outperformed by faster‐growing species in more fertile conditions (biotic filter). Our results refine and strengthen support for niche theories of species assembly while providing an integrated approach to improving forest management policies.",
            "publicationTitle": "Ecology",
            "publisher": "",
            "place": "",
            "date": "07/2023",
            "volume": "104",
            "issue": "7",
            "section": "",
            "partNumber": "",
            "partTitle": "",
            "pages": "e4053",
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            "seriesTitle": "",
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            "journalAbbreviation": "Ecology",
            "DOI": "10.1002/ecy.4053",
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                    "lastName": "Allen"
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                    "creatorType": "contributor",
                    "firstName": "Stuart",
                    "lastName": "Grieve"
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            "abstractNote": "Climate change drives complex responses in forest ecosystems, with individual trees responding differently depending on species, size, and local competition. These individual responses to stressors such as drought and temperature can drastically alter forest composition, and cannot be captured through forest-scale assessments. Monitoring forest dynamics at an individual tree scale is therefore essential for accurately assessing ecosystem responses to climate change. Traditional field inventory based on manual measurements is able to provide data at this granularity, but limits the spatial scale and temporal resolution at which forest structure and diversity can be assessed. Aerial data appear to offer a promising solution to this problem by enabling rapid capture of forest data at large scales. However, while deep learning methods have been widely used to process these data, current approaches often rely on labels drawn by eye or other subjective reference data, undermining confidence in the reported accuracy of downstream tasks. In this work, I begin to address the validation gap in deep learning-based forest monitoring methods. By developing validation approaches using high-fidelity reference data, and improving methods to automate the generation of such validation data, my thesis establishes a foundation for reliable validation of airborne or satellite-based forest monitoring. I summarise my contributions as follows: I develop a scalable, airborne approach to measuring tree crown dieback and show that when measured end-to-end, the results correlate with ground-based measurements. I use ultra high-fidelity terrestrial LiDAR to derive ground truth annotations for a common intermediate step in such approaches -- aerial instance segmentation -- and use these labels to show that accuracy is falsely inflated when measured using hand-drawn annotations. I develop a new approach based on self-supervised learning to the semantic segmentation of terrestrial LiDAR, and demonstrate that it massively reduces the need for hand-labelling - a major bottleneck to the scaling of contribution 2.",
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            "abstractNote": "The Neotropical genus of myrmecophilous beetles, Ecitonides Wasmann, 1894 (Staphylinidae: Paederinae: Lathrobiini), currently includes nine valid species distributed in French Guiana, Suriname, Brazil, Peru, Paraguay, and Argentina. Members of this genus are notable for the tuberculate ornamentation on the head, thorax, and abdomen. Although little is known about the biology of these beetles, there are records of association with different species of army ants (Labidus Jurine, 1807 and Nomamyrmex Borgmeier, 1936). In this study, a detailed comparative morphological study of all available species for study was conducted, descriptions of two new species, Ecitonides\ncolossussp. nov. and Ecitonides\nsplendidussp. nov., are provided, and lectotypes for Ecitonides\nbrevicornis Wasmann, 1900 and Ecitonides\nspectabilis Borgmeier, 1932 are designated. Diagnoses, illustrations, and photographs are given; an identification key is provided for all 11 species as well as new geographic distribution data. The aim of this study is to provide morphological data that will serve as a tool for a future investigation of the phylogenetic position of the genus and facilitate species recognition through diagnostic morphological characters and an identification key.",
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            "pages": "283-314",
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            "title": "A taxonomic revision of the <i>Dichotomius bitiensis</i> (Gillet, 1911) species group (Coleoptera: Scarabaeidae: Scarabaeinae) with a description of a new species from Colombia and Venezuela",
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                {
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                    "firstName": "Jorge Armando",
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                    "firstName": "Fernando Z.",
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            "abstractNote": "The taxonomy of the subgenus Dichotomius sensu stricto was recently updated and divided into twelve species groups and three incertae sedis species. One of these groups is the Dichotomius bitiensis (Gillet, 1911) species group, which is revised in this paper. Based on a revision of all the type material, and the external and male genitalia morphology of other material deposited in fifteen entomological collections, the taxonomic revision of this group is carried out. Seven species are included in the group: D. bitiensis (Argentina, Bolivia, Brazil, and Paraguay); Dichotomius boillyi new name (Brazil, Colombia, French Guiana, and Suriname); Dichotomius costaricensis (Luederwaldt, 1935) (Colombia, Costa Rica, Panama, and Venezuela); Dichotomius medinae sp. nov. (Colombia and Venezuela); Dichotomius motai (Pereira, 1942) (Brazil); Dichotomius missionus (Martínez, 1947) (Argentina) and Dichotomius nitidissimus (Waterhouse, 1891) (Bolivia, Paraguay, and Argentina). The lectotype for Pinotus bitiensis Gillet, 1911 was designated. For each of the species that are included in the group, the following information is presented: Taxonomic history, species' citation in published literature, description or redescription of males and females, list of material examined, photographs of the external morphology, illustrations of the male genital organ and its endophallites, and a distribution map.Keywords: Dichotomius (Dichotomius); Dung beetles; Neotropical; Taxonomy",
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            "date": "2026",
            "volume": "70",
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            "pages": "e20250054",
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                    "firstName": "Eduardo V. P.",
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                    "lastName": "Nunes"
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                    "firstName": "Eric",
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            "title": "Evolutionary persistence of a highly prevalent multicopy mitochondrial-derived nuclear insertion (Mega-NUMT) in Neotropical Drosophila flies",
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                    "firstName": "Merce",
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                    "firstName": "Anton",
                    "lastName": "Strunov"
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                    "firstName": "Eleanor",
                    "lastName": "Heyworth"
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                    "firstName": "Daniela I.",
                    "lastName": "Schneider"
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                    "firstName": "Julia",
                    "lastName": "Thoma"
                },
                {
                    "creatorType": "author",
                    "firstName": "Aurélie",
                    "lastName": "Hua-Van"
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                    "firstName": "Cécile",
                    "lastName": "Courret"
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                    "firstName": "Lisa",
                    "lastName": "Klasson"
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                    "firstName": "Wolfgang J.",
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            "abstractNote": "Background Although strict maternal transmission of mitochondria is a general feature of animals and humans for ensuring homogeneity in mitochondrial DNA (mtDNA) across generations, exceptions were reported in the recent past. For example, some extremely rare but spectacular cases of heteroplasmy and paternal transmission in humans have questioned the universal evolutionary principle. Hence, as an alternative, the Mega-NUMT concept was coined to explain this discovery and was thereafter partly proven to exist. This concept expands on the quite common transfer of mtDNA fragments to the nucleus (NUMTs) by considering the existence of multicopy mitochondrial nuclear insertions. Mega-NUMT reports are currently restricted to a few cases in animals, including humans. However, even in humans, their detailed genomic organization, natural prevalence, and potential biological functions remain unclear.\nMethodology/Principal Findings Here, we discovered that up to 60 full-sized mitochondrial genomes are integrated into the nuclear genome of the neotropical fruit fly Drosophila paulistorum using long-read sequencing and confirmed their presence by in situ hybridization. The copies are organized in one cluster on chromosome 3, which we, due to its similarity with the Mega-NUMT concept, designated the “Dpau Mega-NUMT”. Contrary to the rarity in humans, this Mega-NUMT is found at high prevalence (40%) in both long-term laboratory lines and natural D. paulistorum populations of different semispecies. Additionally, the mitochondrial copies in the Mega-NUMT cluster are phylogenetically separated from the current mitotypes of D. paulistorum. Together, these observations suggest long-term maintenance of the Mega-NUMT in nature. Hence, we propose that the Dpau Mega-NUMT may have been transferred to the nuclear genome before D. paulistorum semispecies radiation and maintained at relatively high prevalence in nature by balancing selection due to yet undetermined functions.\nConclusions/Significance To our knowledge, this is the first verified existence and detailed dissection of a Mega-NUMT outside cats and humans. We show that Mega-NUMTs can be persistent in nature, even at high prevalence, potentially due to balancing selection. Our findings strengthen the importance of high-quality long-read sequencing technologies for deciphering complex repeat-rich genomic regions to deepen our understanding of the dynamics of genome evolution within genomic “dark matter”.",
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            "abstractNote": "First catalog of Salticidae (Arachnidae, Araneae) from French Guiana, with the description of one new species. A work of bibliographic synthesis and identification of collected material made possible to complete the knowledge concerning one of the best studied spider families of the neotropical region from a systematic point of view, namely the Salticidae Blackwall, 1841. This catalog lists the presence of 122 species as well as 68 morphospecies, belonging to 36 genera, making a total of 190 potential species. After argument based on the observation of type species or individuals, exchanges with data producers or even verification of data in the bibliography, the following species, 19 in number, are deleted from the list of Salticidae of French Guyana: Amycus ectipus (Simon, 1900), Amycus pertyi Simon, 1900, Anasaitis canosa (Walckenaer, 1837), Chira simoni (Galiano, 1961), Chirothecia crassipes (Taczanowski, 1878), Colonus germaini (Simon, 1900), Corythalia tropica (Mello-Leitão, 1939), Hypaeus miles Simon, 1900, Lyssomanes amazonicus G. W. Peckham, E. G. Peckham & Wheeler, 1889, Lyssomanes elegans (Cambridge, 1900), Lyssomanes parallelus (Peckham & Wheeler, 1889), Matinta fasciata (Mello-Leitão, 1940), Noegus bidens (Simon, 1900), Noegus petrusewiczi Caporiacco, 1947, Psecas bubo (Taczanowski, 1871), Sarinda atrata (Taczanowski, 1871), Scopocira melanops (Taczanowski, 1871), Rudra wagae (Taczanowski, 1871) and Viciria chabanaudi Fage, 1923. The mention of a species in Vedel et al. (2013), not recognized by the World Spider Catalog (2023), is also deleted: Salticus fulvatus (Fabricius, 1896). The following new synonymy is established: Amycus flavolineatus C. L. Koch, 1846 is a junior synonym of Colonus sylvanus (Hentz, 1846), n. syn. Amycus amrishi Makhan, 2006 and Neonella heliophanina (Taczanowski, 1871) are considered as nomina dubia. Pseudopartona ornata Caporiacco, 1954, type species of the genus Pseudopartona Caporiacco, 1954, belongs to the genus Sassacus Sassacus G. W. Peckham & E. G. Peckham, 1895, which results in Pseudopartona being synonymised with Sassacus, and the following new combination Sassacus ornatus (Caporiacco, 1954) n. comb. Finally, 25 species are newly cited, including one newly described species: Eustiromastix agatheae Courtial & Picard n. sp. (male).",
            "publicationTitle": "Zoosystema",
            "publisher": "Muséum national d'Histoire naturelle, Paris",
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            "date": "2026/02",
            "volume": "48",
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            "pages": "75-120",
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            "journalAbbreviation": "zoos",
            "DOI": "10.5252/zoosystema2026v48a4",
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            "title": "Patterns of local, intercontinental and interseasonal variation of soil bacterial and eukaryotic microbial communities",
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                    "creatorType": "author",
                    "firstName": "Johan",
                    "lastName": "De Gruyter"
                },
                {
                    "creatorType": "author",
                    "firstName": "James T.",
                    "lastName": "Weedon"
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                {
                    "creatorType": "author",
                    "firstName": "Stéphane",
                    "lastName": "Bazot"
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                    "firstName": "Steven",
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                    "firstName": "Pere-Roc",
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                    "firstName": "Stefan",
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                    "creatorType": "author",
                    "firstName": "Bernard",
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                    "firstName": "Ivan A.",
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                    "firstName": "Niki",
                    "lastName": "Leblans"
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                    "firstName": "Tanguy",
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                    "creatorType": "author",
                    "firstName": "Romà",
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                    "firstName": "Mikaell Ottosson",
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                    "firstName": "Josep",
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                    "firstName": "Bjarni D.",
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            "abstractNote": "Although ongoing research has revealed some of the main drivers behind global spatial patterns of microbial communities, spatio-temporal dynamics of these communities still remain largely unexplored. Here, we investigate spatio-temporal variability of both bacterial and eukaryotic soil microbial communities at local and intercontinental scales. We compare how temporal variation in community composition scales with spatial variation in community composition, and explore the extent to which bacteria, protists, fungi and metazoa have similar patterns of temporal community dynamics. All soil microbial groups displayed a strong correlation between spatial distance and community dissimilarity, which was related to the ratio of organism to sample size. Temporal changes were variable, ranging from equal to local between-sample variation, to as large as that between communities several thousand kilometers apart. Moreover, significant correlations were found between bacterial and protist communities, as well as between protist and fungal communities, indicating that these microbial groups change in tandem, potentially driven by interactions between them. We conclude that temporal variation can be considerable in soil microbial communities, and that future studies need to consider temporal variation in order to reliably capture all drivers of soil microbiome changes.",
            "publicationTitle": "FEMS microbiology ecology",
            "publisher": "",
            "place": "",
            "date": "2020-03-01",
            "volume": "96",
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            "partNumber": "",
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            "pages": "fiaa018",
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            "citationKey": "degruyterPatternsLocalIntercontinental2020a",
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