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27 results for “multiple introductions”
Multiple Introductions of Mpox virus to Ireland during the 2022-2023 International Outbreak
<p>Supplementary datasets for the study titled: '<strong>Multiple Introductions of Mpox virus to Ireland during the 2022-2023 International Outbreak</strong>'</p> <p>The datasets presented here are the list of publicly available sequences from other geographical locations used as reference for analysis of Irish mpox sequences (Supplementary Table 1), the list of sequenced mpox viruses (MPXV) in the Republic of Ireland during the outbreak 2022-2023 (Supplementary Table 2) and the list of MPXV genes with mutations in our dataset of Irish sequences (Supplementary Table 4).</p> <p><strong>Description of the data and file structure</strong></p> <p>The files in this dataset were formatted in Microsoft Excel 2019 to allow easy access and manipulation of the data. The data corresponds to details on the sequences used in the analysis of the MPXV from the 2022-2023 international outbreak encompassing data between May 2022 and November of 2023. The contents of the files are described below:</p> <ul> <li><strong>Supplementary Table 1</strong>: This file contains the source (database as GenBank or GISAID) of the data, the accession number to allow its downloading, the mpox clade assigned by Nextclade (https://clades.nextstrain.org/), reported collection date of the sample, reported country of origin and the geographical region assigned.</li> <li><strong>Supplementary Table 2</strong>: This file contains details on the sequences generated in our study with the GenBank accession number, the GISAID accession number, reported collection date, Nextclade assigned taxonomical clade and the percentage of the genome covered by the sequence. </li> <li><em>(Supplementary Table 3)</em>: This table was omitted as it is small and summarizes the counts of mutations.</li> <li><strong>Supplementary Table 4</strong>: This file contains a distribution of mutated positions over the annotated MPXV genome relative to the reference Gene ID as provided in the annotation for NC_063383.1, with gene affected, start and end of the gene (relative to the reference genome GenBank:NC_063383.1), number of non-coding, non-synonymous and synonymous mutations in each gene, and the total of mutations per gene.</li> </ul> <p><strong>Sharing/Access information</strong></p> <p>The databases used to extract and deposit the data were:</p> <ul> <li><strong>GenBank</strong>: the North American repository of sequences and publicly available at: <strong><a href="https://www.ncbi.nlm.nih.gov/genbank/">https://www.ncbi.nlm.nih.gov/genbank/</a></strong></li> <li><strong>GISAID</strong>: International consortium of sequences with some metadata and clinical data. It is a semi-public repository with easy access requiring only to create an account. Available at: <strong><a href="https://gisaid.org/">https://gisaid.org/</a></strong></li> </ul>
Unraveling Dengue Serotype 3 Transmission in Brazil: Evidence for Multiple Introductions of the 3III_B.3.2 Lineage
<p>Dengue, caused by DENV 1-4, remains a global public health concern, with Brazil experiencing some of the largest epidemics. The reemergence of DENV-3 in Brazil between 2023 and 2024 has raised concerns about new outbreaks due to the absence of sustained circulation of this serotype in recent years. This study investigates the dynamics of DENV-3 in Brazil, focusing on the spread of the 3III_B.3.2 lineage within genotype 3III and its introduction routes. We analyzed 1,536 DENV-3 genomes, all classified as genotype 3III, the dominant DENV-3 genotype in Brazil since 2001. Phylogenetic analysis identified the 3III_B.3.2 lineage in all recent Brazilian cases, with detections also reported in Central America, the United States, and Europe. At least six independent introduction events of this lineage into Brazil were identified, with the Caribbean region and Costa Rica as the primary sources. The earliest introduction likely occurred in late 2022 in Roraima, followed by introductions in Sao Paulo, Minas Gerais, and Para. While one instance of interstate transmission was detected - from Sao Paulo to Minas Gerais - our findings indicate that external introductions, rather than domestic spread, were the primary drivers of DENV-3 circulation during this period. These results underscore the importance of continued genomic surveillance and coordinated public health strategies to monitor and mitigate future outbreaks</p>
Microsatellite dataset from: The fast invasion of Europe by the box tree moth: An additional example coupling multiple introduction events, bridgehead effects and admixture events.
<p>Genotypes of native and invasive populations of Cydalima perspectalis for 15 microsatellites generated for our paper "The fast invasion of Europe by the box tree moth: An additional example coupling multiple introduction events, bridgehead effects and admixture events."</p> <p>This folder contains:<br> - ReadMe file giving the following information</p> <p>- "Data_Cydalima_genotype.xlsx” containing populations information and individuals genotype for the 15 microsatellites developed by Bras et al. 2018 (Eur. J. Entomol.)</p> <p> </p> <p>This work was done in the frame of a regional project called INCA (grant from Région Centre Val de Loire).</p>
Data from: Multiple genotypes of Phelipanche ramosa indicate repeated introductions to the Americas: Sequence alignments and phylogenetic trees
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Fig. 1 in Mitochondrial Cytochrome Oxidase I Variation In Asian Tiger Mosquito (Aedes Albopictus): Determination Of The Different And Multiple Introduction Situations In Türkiye
Fig. 1. Collection points of A. albopictus samples used in the study
Dataset to study the population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources
<p>During colonial times, Nile tilapia <em>Oreochromis niloticus</em> (Linnaeus, 1758) was introduced in non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focussing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridisation. Using RAD sequencing (27 611 SNPs), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, stressing their ability to interbreed and the potential threat they cause to the genetic integrity of native tilapias. Populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity with Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge to avoid introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.</p>
ddRAD data for: Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps
<p class="MsoNormal"><em><span>Aedes albopictus</span></em><span> originates from Southeast Asia and is considered one of the most invasive species globally. This mosquito </span><span>is a nuisance and a disease vector of significant public health relevance</span><span>. </span><span>In Europe, <em>Ae. albopictus</em> is firmly established and widespread south of the Alps, a mountain range that forms a formidable biogeographic barrier to many organisms. Recent reports of <em>Ae. albopictus</em> north of the Alps raise questions of 1) the origins of its recent invasion, and 2) if this mosquito has established overwintering populations north of the Alps. To answer these questions, </span><span>we analyzed population genomic data from >4000 genome-wide SNPs obtained through </span><span>double digest restriction-site associated DNA sequencing</span><span>. </span><span>We collected SNPs data from specimens from 6 sites in Switzerland, north and south of the Alps, and analyzed them together with specimens from other 33 European sites, 5 from the Americas, and 5 from its Asian native range. At a global level, we detected 4 genetic clusters with specimens from </span><span>Indonesia, Brazil and Japan as the most differentiated, whereas specimens from Europe, Hong Kong and USA largely overlapped</span><span>. Across the Alps, </span><span>we detected a weak genetic structure and high levels of genetic admixture, supporting a scenario of rapid and human-aided dispersal along transportation routes. While the genetic pattern suggests frequent re-introductions from Italian sources into Switzerland, t</span><span>he recovery of a pair of full siblings in two consecutive years in Strasbourg, France, suggests the presence of an overwintering population north of the Alps. </span><span>The finding of overwintering populations of <em>Ae. albopictus </em>north of the Alps and the expansion patterns points to an increased risk of further northwards expansion and the need for increased surveillance of mosquito populations in northern Europe.</span></p> <p> </p>
Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos
<p><span>Biological invasions in remote</span> <span>areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To </span><span>analyze</span><span> geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance</span> <span>among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which</span> <span>promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.</span></p>
Patterns of genetic variation reflect multiple introductions and pre-admixture sources of common ragweed (Ambrosia artemisiifolia) in China
<p>Informations about the locations and genetic diversity of <em>Ambrosia artemisiifolia</em> populations in published paper "Patterns of genetic variation reflect multiple introductions and pre-admixture sources of common ragweed (Ambrosia artemisiifolia) in China".</p>
ddRAD data for: Multiple introductions and overwintering shape the progressive invasion of Aedes albopictus beyond the Alps
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Dataset to study the population genomics of introduced Nile tilapia (Oreochromis niloticus (Linnaeus, 1758)) in the Democratic Republic of the Congo: repeated introductions since colonial times with multiple sources
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Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos
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Data from: Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps
The Giant Hogweed (Heracleum mantegazzianum) has successfully invaded 19 European countries as well as parts of North America. It has become a problematic species due to its ability to displace native flora and to cause public health hazards. Applying population genetics to species invasion can help reconstruct invasion history and may promote more efficient management practice. We thus analyzed levels of genetic variation and population genetic structure of H. mantegazzianum in an invaded area of the western Swiss Alps as well as in its native range (the Caucasus), using eight nuclear microsatellite loci together with plastid DNA markers and sequences. On both nuclear and plastid genomes, native populations exhibited significantly higher levels of genetic diversity compared to invasive populations, confirming an important founder event during the invasion process. Invasive populations were also significantly more differentiated than native populations. Bayesian clustering analysis identified five clusters in the native range that corresponded to geographically and ecologically separated groups. In the invaded range, ten clusters occurred. Unlike native populations, invasive clusters were characterized by a mosaic pattern in the landscape, possibly caused by anthropogenic dispersal of the species via roads and direct collection for ornamental purposes. Lastly, our analyses revealed four main divergent groups in the western Swiss Alps, likely as a consequence of multiple independent establishments of H. mantegazzianum.
Data from: Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source
The introduction of invasive species to new locations (that is, biological invasions) can have major impact on biodiversity, agriculture and public health. As such, determining the routes and modality of introductions with genetic data has become a fundamental goal in molecular ecology. To assist with this goal, new statistical methods and frameworks have been developed, such as approximate Bayesian computation (ABC) for inferring invasion history. Here, we present a model of invasion accounting for multiple introductions from a single source (MISS), a heretofore largely unexplored model. We simulate microsatellite data to evaluate the power of ABC to distinguish between single and multiple introductions from the same source, under a range of demographic parameters. We also apply ABC to microsatellite data from three invasions of bumblebee in New Zealand. In addition, we assess the performance of several methods of summary statistics selection. Our simulated results suggested good ability to distinguish between one- and two-wave models over much but not all of the parameter space tested, independent of summary statistics used. Globally, parameter estimation was good except for bottleneck timing. For one of the bumblebee species, we clearly rejected the MISS model, while for the other two we found inconclusive results. Since a second wave may provide genetic reinforcement to initial colonists, help relieve inbreeding among founders, or increase the hazard of the invasion, its detection may be crucial for managing invasions; we suggest that the MISS model could be considered as a potential model in future theoretical and empirical studies of invasions.
Data from: Historical invasion records can be misleading: genetic evidence for multiple introductions of invasive raccoons (Procyon lotor) in Germany
Biological invasions provide excellent study systems to understand evolutionary, genetic and ecological processes during range expansions. There is strong evidence for positive effects of high propagule pressure and the associated higher genetic diversity on invasion success, but some species have become invasive despite small founder numbers. The raccoon (Procyon lotor) is often considered as a typical example for such a successful invasion resulting from a small number of founders. The species' largest non-native population in Germany is commonly assumed to stem from a small number of founders and two separate founding events in the 1930s and 1940s. In the present study we analyzed 407 raccoons at 20 microsatellite loci sampled from the invasive range in Western Europe to test if these assumptions are correct. Contrary to the expectations, different genetic clustering methods detected evidence for at least four independent introduction events that gave rise to genetically differentiated subpopulations. Further smaller clusters were either artifacts or resulted from founder events at the range margin and recent release of captive individuals. We also found genetic evidence for on-going introductions of individuals. Furthermore a novel randomization process was used to determine the potential range of founder population size that would suffice to capture all the alleles present in a cluster. Our results falsify the assumption that this species has become widespread and abundant despite being genetically depauperate and show that historical records of species introductions may be misleading.
Data from: Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae)
Genetic diversity, and thus the adaptive potential of invasive populations, is largely based on three factors: patterns of genetic diversity in the species' native range, the number and location of introductions, and the number of founding individuals per introduction. Specifically, reductions in genetic diversity ("founder effects") should be stronger for species with low within-population diversity in their native range and few introductions of few individuals to the invasive range. We test these predictions with Geranium carolinianum, a winter annual herb native to North America and invasive in China. We measure the extent of founder effects using allozymes and microsatellites, and ask whether this is consistent with its colonization history and patterns of diversity in the native range. In the native range, genetic diversity is higher and structure is lower than expected based on life-history traits. In China, our results provide evidence for multiple introductions near Nanjing, Jiangsu province, with subsequent range expansion to the west and south. Patterns of genetic diversity across China reveal weak founder effects that are driven largely by low- diversity populations at the expansion front, away from the introduction location. This suggests that reduced diversity in China has resulted from successive founder events during range expansion, and that the loss of genetic diversity in the Nanjing area was mitigated by multiple introductions from diverse source populations. This has implications for the future of G. carolinianum in China, as continued gene flow among populations should eventually increase genetic diversity within the more recently founded populations.
Data from: Reduced genetic diversity, increased isolation and multiple introductions of invasive giant hogweed in the western Swiss Alps
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Data from: Patterns of genetic diversity reveal multiple introductions and recurrent founder effects during range expansion in invasive populations of Geranium carolinianum (Geraniaceae)
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Data from: Using ABC and microsatellite data to detect multiple introductions of invasive species from a single source
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Data from: Historical invasion records can be misleading: genetic evidence for multiple introductions of invasive raccoons (Procyon lotor) in Germany
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