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Lee KI, Morita-Ishihara T, Iyoda S, Ogura Y, Hayashi T, Sekizuka T, Kuroda M, Ohnishi M. A Geographically Widespread Outbreak Investigation and Development of a Rapid Screening Method Using Whole Genome Sequences of Enterohemorrhagic Escherichia coli O121. Front Microbiol 2017; 8:701. [PMID: 28473825 PMCID: PMC5397494 DOI: 10.3389/fmicb.2017.00701] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/05/2017] [Indexed: 11/13/2022] Open
Abstract
From 2014 to 2015, we investigated a suspected nationwide outbreak of enterohemorrhagic Escherichia coli serogroup O121. However, similar pulsed field gel electrophoresis (PFGE) profiles and the lack of epidemiological links between the isolates made detection of the outbreak difficult. To elucidate a more precise genetic distance among the isolates, whole genome sequence (WGS) analyses were implemented in the investigation. The WGS-based single nucleotide polymorphism (SNP) analysis showed that 23 out of 44 isolates formed a distinct cluster (the number of intra-cluster SNPs was ≤8). Specific genomic regions in the clustered isolates were used to develop a specific PCR analysis. The PCR analysis detected all the clustered isolates and was suitable for rapid screening during the outbreak investigation. Our results showed that WGS analyses were useful for the detection of a geographically widespread outbreak, especially for isolates showing similar PFGE profiles and for the development of a rapid and cost-effective screening method.
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Affiliation(s)
- Ken-Ichi Lee
- Department of Bacteriology I, National Institute of Infectious DiseasesTokyo, Japan
| | | | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious DiseasesTokyo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu UniversityFukuoka, Japan
| | - Tsuyoshi Sekizuka
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Makoto Kuroda
- Laboratory of Bacterial Genomics, Pathogen Genomics Center, National Institute of Infectious DiseasesTokyo, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious DiseasesTokyo, Japan
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Hajibabaei M, Baird DJ, Fahner NA, Beiko R, Golding GB. A new way to contemplate Darwin's tangled bank: how DNA barcodes are reconnecting biodiversity science and biomonitoring. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150330. [PMID: 27481782 PMCID: PMC4971182 DOI: 10.1098/rstb.2015.0330] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2016] [Indexed: 01/10/2023] Open
Abstract
Encompassing the breadth of biodiversity in biomonitoring programmes has been frustrated by an inability to simultaneously identify large numbers of species accurately and in a timely fashion. Biomonitoring infers the state of an ecosystem from samples collected and identified using the best available taxonomic knowledge. The advent of DNA barcoding has now given way to the extraction of bulk DNA from mixed samples of organisms in environmental samples through the development of high-throughput sequencing (HTS). This DNA metabarcoding approach allows an unprecedented view of the true breadth and depth of biodiversity, but its adoption poses two important challenges. First, bioinformatics techniques must simultaneously perform complex analyses of large datasets and translate the results of these analyses to a range of users. Second, the insights gained from HTS need to be amalgamated with concepts such as Linnaean taxonomy and indicator species, which are less comprehensive but more intuitive. It is clear that we are moving beyond proof-of-concept studies to address the challenge of implementation of this new approach for environmental monitoring and regulation. Interpreting Darwin's 'tangled bank' through a DNA lens is now a reality, but the question remains: how can this information be generated and used reliably, and how does it relate to accepted norms in ecosystem study?This article is part of the themed issue 'From DNA barcodes to biomes'.
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Affiliation(s)
- Mehrdad Hajibabaei
- Centre for Biodiversity Genomics @ Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
| | - Donald J Baird
- Environment and Climate Change Canada @ Canadian Rivers Institute, University of New Brunswick, 10 Bailey Drive, PO Box 4400, Fredericton, New Brunswick, Canada E3B 5A3
| | - Nicole A Fahner
- Centre for Biodiversity Genomics @ Biodiversity Institute of Ontario and Department of Integrative Biology, University of Guelph, Ontario, Canada N1G 2W1
| | - Robert Beiko
- Faculty of Computer Science, Dalhousie University, 6050 University Avenue, PO Box 15000, Halifax, Nova Scotia, Canada
| | - G Brian Golding
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4K1
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Wiseman BH, Fountain ED, Bowie MH, He S, Cruickshank RH. Vivid molecular divergence over volcanic remnants: the phylogeography of Megadromus guerinii on Banks Peninsula, New Zealand. NEW ZEALAND JOURNAL OF ZOOLOGY 2016. [DOI: 10.1080/03014223.2016.1167093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- BH Wiseman
- Centre for Wildlife Management and Conservation, Lincoln University, Lincoln, New Zealand
| | - ED Fountain
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, USA
| | - MH Bowie
- Department of Ecology, Lincoln University, Lincoln, New Zealand
| | - S He
- Yunnan Agricultural University, Kunming, Yunnan, People’s Republic of China
| | - RH Cruickshank
- Department of Ecology, Lincoln University, Lincoln, New Zealand
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Ståhls G, Vujić A, Petanidou T, Cardoso P, Radenković S, Ačanski J, Pérez Bañón C, Rojo S. Phylogeographic patterns of Merodon hoverflies in the Eastern Mediterranean region: revealing connections and barriers. Ecol Evol 2016; 6:2226-45. [PMID: 27069578 PMCID: PMC4782255 DOI: 10.1002/ece3.2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 01/28/2016] [Indexed: 11/29/2022] Open
Abstract
We investigated the phylogeographic patterns of Merodon species (Diptera, Syrphidae) in the Eastern Mediterranean. Ten species were sampled on five different islands and mainland sites as a minimum. All samples were screened for their mtDNA COI barcode haplotype diversity, and for some samples, we additionally generated genomic fingerprints. The recently established zoogeographic distribution categories classify these species as having (1) Balkan distribution; (2) Anatolian distribution; (3) continental areas and large islands distribution; and (4) with wide distribution. The ancestral haplotypes and their geographical localities were estimated with statistical parsimony (TCS). TCS networks identified as the ancestral haplotype samples that originated from localities situated within the distributional category of the species in question. Strong geographical haplotype structuring was detected for many Merodon species. We were particularly interested to test the relative importance of current (Aegean Sea) and past Mid-Aegean Trench) barriers to dispersal for Merodon flies in the Aegean. We employed phylogenetic β-diversity (Pβ total) and its partition in replacement (Pβ repl) and richness difference (Pβ rich) to test the importance of each explanatory variable (interisland distance, MAT, and island area) in interisland differences using partial Mantel tests and hierarchical partitioning of variation. β-Analyses confirmed the importance of both current and past barriers to dispersal on the evolution of group. Current interisland distance was particularly important to explain the replacement of haplotypes, while the MAT was driving differences in richness of haplotypes, revealing the MAT as a strong past barrier whose effects are still visible today in the phylogenetic history of the clade in the Aegean. These results support the hypothesis of a highly restricted dispersal and gene flow among Merodon populations between islands since late Pleistocene. Additionally, patterns of phylogeographic structure deduced from haplotype connections and ISSR genome fingerprinting data revealed a few putative cases of human-mediated transfers of Merodon spp.
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Affiliation(s)
- Gunilla Ståhls
- Zoology UnitFinnish Museum of Natural HistoryUniversity of HelsinkiPO Box 1700014HelsinkiFinland
| | - Ante Vujić
- Department of Biology and EcologyUniversity of Novi SadTrg Dositeja Obradovića 221000Novi SadSerbia
| | - Theodora Petanidou
- Department of GeographyLaboratory of Biogeography & EcologyUniversity of the Aegean81100MytileneGreece
| | - Pedro Cardoso
- Zoology UnitFinnish Museum of Natural HistoryUniversity of HelsinkiPO Box 1700014HelsinkiFinland
| | - Snezana Radenković
- Department of Biology and EcologyUniversity of Novi SadTrg Dositeja Obradovića 221000Novi SadSerbia
| | - Jelena Ačanski
- BioSense InstituteUniversity of Novi SadDr Zorana Đinđića 121000Novi SadSerbia
| | - Celeste Pérez Bañón
- Department of Environmental Sciences & Natural Resources/Research Institute CIBIOUniversity of AlicanteApdo 99E‐03080AlicanteSpain
| | - Santos Rojo
- Department of Environmental Sciences & Natural Resources/Research Institute CIBIOUniversity of AlicanteApdo 99E‐03080AlicanteSpain
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55
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Wei K, Li Y, Chen H, Zhang Q. Genomic Surveillance Elucidates HCV 1a Phylodynamics and Molecular Evolution. Evol Biol 2016. [DOI: 10.1007/s11692-016-9379-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Yan H, Ji ZJ, Jiao YS, Wang ET, Chen WF, Guo BL, Chen WX. Genetic diversity and distribution of rhizobia associated with the medicinal legumes Astragalus spp. and Hedysarum polybotrys in agricultural soils. Syst Appl Microbiol 2016; 39:141-9. [PMID: 26915496 DOI: 10.1016/j.syapm.2016.01.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2015] [Revised: 01/28/2016] [Accepted: 01/29/2016] [Indexed: 10/22/2022]
Abstract
With the increasing cultivation of medicinal legumes in agricultural fields, the rhizobia associated with these plants are facing new stresses, mainly from fertilization and irrigation. In this study, investigations on the nodulation of three cultivated medicinal legumes, Astragalus mongholicus, Astragalus membranaceus and Hedysarum polybotrys were performed. Bacterial isolates from root nodules of these legumes were subjected to genetic diversity and multilocus sequence analyses. In addition, the distribution of nodule bacteria related to soil factors and host plants was studied. A total 367 bacterial isolates were obtained and 13 genospecies were identified. The predominant microsymbionts were identified as Mesorhizobium septentrionale, Mesorhizobium temperatum, Mesorhizobium tianshanense, Mesorhizobium ciceri and Mesorhizobium muleiense. M. septentrionale was found in most root nodules especially from legumes grown in the barren soils (with low available nitrogen and low organic carbon contents), while M. temperatum was predominant in nodules where the plants were grown in the nitrogen-rich fields. A. mongholicus tended to be associated with M. septentrionale, M. temperatum and M. ciceri in different soils, while A. membranaceus and H. polybotrys tended to be associated with M. tianshanense and M. septentrionale, respectively. This study showed that soil fertility may be the main determinant for the distribution of rhizobia associated with these cultured legume plants.
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Affiliation(s)
- Hui Yan
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Zhao Jun Ji
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - Yin Shan Jiao
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
| | - En Tao Wang
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China; Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 México D.F., Mexico
| | - Wen Feng Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China.
| | - Bao Lin Guo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, Beijing 100193, China; College of Biological Sciences and Rhizobia Research Center, China Agricultural University, Beijing 100193, China
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Archaeal community in a human-disturbed watershed in southeast China: diversity, distribution, and responses to environmental changes. Appl Microbiol Biotechnol 2016; 100:4685-98. [PMID: 26810199 DOI: 10.1007/s00253-016-7318-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 01/11/2016] [Accepted: 01/12/2016] [Indexed: 10/22/2022]
Abstract
The response of freshwater bacterial community to anthropogenic disturbance has been well documented, yet the studies of freshwater archaeal community are rare, especially in lotic environments. Here, we investigated planktonic and benthic archaeal communities in a human-perturbed watershed (Jiulong River Watershed, JRW) of southeast China by using Illumina 16S ribosomal RNA gene amplicon sequencing. The results of taxonomic assignments indicated that SAGMGC-1, Methanobacteriaceae, Methanospirillaceae, and Methanoregulaceae were the four most abundant families in surface waters, accounting for 12.65, 23.21, 18.58 and 10.97 % of planktonic communities, whereas Nitrososphaeraceae and Miscellaneous Crenarchaeotic Group occupied more than 49 % of benthic communities. The compositions of archaeal communities and populations in waters and sediments were significantly different from each other. Remarkably, the detection frequencies of families Methanobacteriaceae and Methanospirillaceae, and genera Methanobrevibacter and Methanosphaera in planktonic communities correlated strongly with bacterial fecal indicator, suggesting some parts of methanogenic Archaea may come from fecal contamination. Because soluble reactive phosphorus (SRP) and the ratio of dissolved inorganic nitrogen to SRP instead of nitrogen nutrients showed significant correlation with several planktonic Nitrosopumilus- and Nitrosotalea-like OTUs, Thaumarchaeota may play an unexplored role in biogeochemical cycling of river phosphorus. Multivariate statistical analyses revealed that the variation of α-diversity of planktonic archaeal community was best explained by water temperature, whereas nutrient concentrations and stoichiometry were the significant drivers of β-diversity of planktonic and benthic communities. Taken together, these results demonstrate that the structure of archaeal communities in the JRW is sensitive to anthropogenic disturbances caused by riparian human activities.
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58
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Chen Y, Hou Y, Guo Z, Wang W, Zhong C, Zhou R, Shi S. Applications of Multiple Nuclear Genes to the Molecular Phylogeny, Population Genetics and Hybrid Identification in the Mangrove Genus Rhizophora. PLoS One 2015; 10:e0145058. [PMID: 26674070 PMCID: PMC4682636 DOI: 10.1371/journal.pone.0145058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 11/29/2015] [Indexed: 11/29/2022] Open
Abstract
The genus Rhizophora is one of the most important components of mangrove forests. It is an ideal system for studying biogeography, molecular evolution, population genetics, hybridization and conservation genetics of mangroves. However, there are no sufficient molecular markers to address these topics. Here, we developed 77 pairs of nuclear gene primers, which showed successful PCR amplifications across all five Rhizophora species and sequencing in R. apiculata. Here, we present three tentative applications using a subset of the developed nuclear genes to (I) reconstruct the phylogeny, (II) examine the genetic structure and (III) identify natural hybridization in Rhizophora. Phylogenetic analyses support the hypothesis that Rhizophora had disappeared in the Atlantic-East Pacific (AEP) region and was re-colonized from the IWP region approximately 12.7 Mya. Population genetics analyses in four natural populations of R. apiculata in Hainan, China, revealed extremely low genetic diversity, strong population differentiation and extensive admixture, suggesting that the Pleistocene glaciations, particularly the last glacial maximum, greatly influenced the population dynamics of R. apiculata in Hainan. We also verified the hybrid status of a morphologically intermediate individual between R. apiculata and R. stylosa in Hainan. Based on the sequences of five nuclear genes and one chloroplast intergenic spacer, this individual is likely to be an F1 hybrid, with R. stylosa as its maternal parent. The nuclear gene markers developed in this study should be of great value for characterizing the hybridization and introgression patterns in other cases of this genus and testing the role of natural selection using population genomics approaches.
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Affiliation(s)
- Yongmei Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- School of Chemistry and Pharmaceutical Engineering, University of Sichuan Science and Engineering, Zigong, China
| | - Yansong Hou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenqing Wang
- School of Life Science, Xiamen University, Xiamen, Fujian, China
| | - Cairong Zhong
- Hainan Dongzhai Harbor National Nature Reserve, Haikou, Hainan, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (RZ); (SS)
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- * E-mail: (RZ); (SS)
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59
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Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P. Host ecology determines the dispersal patterns of a plant virus. Virus Evol 2015; 1:vev016. [PMID: 27774287 PMCID: PMC5014491 DOI: 10.1093/ve/vev016] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since its isolation in 1966 in Kenya, rice yellow mottle virus (RYMV) has been reported throughout Africa resulting in one of the economically most important tropical plant emerging diseases. A thorough understanding of RYMV evolution and dispersal is critical to manage viral spread in tropical areas that heavily rely on agriculture for subsistence. Phylogenetic analyses have suggested a relatively recent expansion, perhaps driven by the intensification of agricultural practices, but this has not yet been examined in a coherent statistical framework. To gain insight into the historical spread of RYMV within Africa rice cultivations, we analyse a dataset of 300 coat protein gene sequences, sampled from East to West Africa over a 46-year period, using Bayesian evolutionary inference. Spatiotemporal reconstructions date the origin of RMYV back to 1852 (1791-1903) and confirm Tanzania as the most likely geographic origin. Following a single long-distance transmission event from East to West Africa, separate viral populations have been maintained for about a century. To identify the factors that shaped the RYMV distribution, we apply a generalised linear model (GLM) extension of discrete phylogenetic diffusion and provide strong support for distances measured on a rice connectivity landscape as the major determinant of RYMV spread. Phylogeographic estimates in continuous space further complement this by demonstrating more pronounced expansion dynamics in West Africa that are consistent with agricultural intensification and extensification. Taken together, our principled phylogeographic inference approach shows for the first time that host ecology dynamics have shaped the historical spread of a plant virus.
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Affiliation(s)
- Nídia Sequeira Trovão
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Guy Baele
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Filip Bielejec
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Marc A. Suchard
- Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 0095-1766, USA
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 0095-1766, USA and
| | - Denis Fargette
- Institut de Recherches pour le Développement (IRD), UMR IPME (IRD, CIRAD, Université de Montpellier), 34394 Montpellier, France
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium
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60
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Mortality from contact-related epidemics among indigenous populations in Greater Amazonia. Sci Rep 2015; 5:14032. [PMID: 26354026 PMCID: PMC4564847 DOI: 10.1038/srep14032] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/13/2015] [Indexed: 11/08/2022] Open
Abstract
European expansion and contact with indigenous populations led to catastrophic depopulation primarily through the introduction of novel infectious diseases to which native peoples had limited exposure and immunity. In the Amazon Basin such contacts continue to occur with more than 50 isolated indigenous societies likely to make further contacts with the outside world in the near future. Ethnohistorical accounts are useful for quantifying trends in the severity and frequency of epidemics through time and may provide insight into the likely demographic consequences of future contacts. Here we compile information for 117 epidemics that affected 59 different indigenous societies in Greater Amazonia and caused over 11,000 deaths between 1875 and 2008, mostly (75%) from measles, influenza, and malaria. Results show that mortality rates from epidemics decline exponentially through time and, independently, with time since peaceful contact. The frequency of documented epidemics also decreases with time since contact. While previous work on virgin soil epidemics generally emphasizes the calamity of contacts, we focus instead on improvements through time. The prospects for better survivorship during future contacts are good provided modern health care procedures are implemented immediately.
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Abstract
This article describes a simple tool to display geophylogenies on web maps including Google Maps and OpenStreetMap. The tool reads a NEXUS format file that includes geographic information, and outputs a GeoJSON format file that can be displayed in a web map application.
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Affiliation(s)
- Roderic Page
- College of Medical, Veterinary & Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
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62
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Opinion: Conservation and stewardship of the human microbiome. Proc Natl Acad Sci U S A 2015; 111:14312-3. [PMID: 25294925 DOI: 10.1073/pnas.1413200111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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63
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Sork VL, Werth S. Phylogeography of Ramalina menziesii, a widely distributed lichen-forming fungus in western North America. Mol Ecol 2014; 23:2326-39. [PMID: 24673777 DOI: 10.1111/mec.12735] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 03/13/2014] [Indexed: 11/28/2022]
Abstract
The complex topography and climate history of western North America offer a setting where lineage formation, accumulation and migration have led to elevated inter- and intraspecific biodiversity in many taxa. Here, we study Ramalina menziesii, an epiphytic lichenized fungus with a range encompassing major ecosystems from Baja California to Alaska to explore the predictions of two hypotheses: (i) that the widespread distribution of R. menziesii is due to a single migration episode from a single lineage and (ii) that the widespread distribution is due to the formation and persistence of multiple lineages structured throughout the species' range. To obtain evidence for these predictions, we first construct a phylogenetic tree and identify multiple lineages structured throughout the species' range--some ancient ones that are localized and other more recent lineages that are widely distributed. Second, we use an isolation with migration model to show that sets of ecoregion populations diverged from each other at different times, demonstrating the importance of historical and current barriers to gene flow. Third, we estimated migration rates among ecoregions and find that Baja California populations are relatively isolated, that inland California ecoregion populations do not send out emigrants and that migration out of California coastal and Pacific Northwest populations into inland California ecoregions is high. Such intraspecific geographical patterns of population persistence and dispersal both contribute to the wide range of this genetically diverse lichen fungus and provide insight into the evolutionary processes that enhance species diversity of the California Floristic Province.
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Affiliation(s)
- Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA, 90095-7239, USA; Institute of the Environment and Sustainability, University of California, Los Angeles, CA, 90095-1496, USA
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Australian Sphingidae--DNA barcodes challenge current species boundaries and distributions. PLoS One 2014; 9:e101108. [PMID: 24987846 PMCID: PMC4079597 DOI: 10.1371/journal.pone.0101108] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/31/2014] [Indexed: 11/19/2022] Open
Abstract
MAIN OBJECTIVE We examine the extent of taxonomic and biogeographical uncertainty in a well-studied group of Australian Lepidoptera, the hawkmoths (Sphingidae). METHODS We analysed the diversity of Australian sphingids through the comparative analysis of their DNA barcodes, supplemented by morphological re-examinations and sequence information from a nuclear marker in selected cases. The results from the analysis of Australian sphingids were placed in a broader context by including conspecifics and closely related taxa from outside Australia to test taxonomic boundaries. RESULTS Our results led to the discovery of six new species in Australia, one case of erroneously synonymized species, and three cases of synonymy. As a result, we establish the occurrence of 75 species of hawkmoths on the continent. The analysis of records from outside Australia also challenges the validity of current taxonomic boundaries in as many as 18 species, including Agrius convolvuli (Linnaeus, 1758), a common species that has gained adoption as a model system. Our work has revealed a higher level of endemism than previously recognized. Most (90%) Australian sphingids are endemic to the continent (45%) or to Australia, the Pacific Islands and the Papuan and Wallacean regions (45%). Only seven species (10%) have ranges that extend beyond this major biogeographical boundary toward SE Asia and other regions of the Old World. MAIN CONCLUSIONS This study has established that overlooked cryptic diversity and inaccurate species delineation produced significant misconceptions concerning diversity and distribution patterns in a group of insects that is considered well known taxonomically. Because DNA barcoding represents a straightforward way to test taxonomic boundaries, its implementation can improve the accuracy of primary diversity data in biogeography and conservation studies.
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65
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Bokulich NA, Thorngate JH, Richardson PM, Mills DA. Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate. Proc Natl Acad Sci U S A 2014; 111:E139-48. [PMID: 24277822 PMCID: PMC3890796 DOI: 10.1073/pnas.1317377110] [Citation(s) in RCA: 535] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.
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Affiliation(s)
- Nicholas A. Bokulich
- Departments of aViticulture and Enology and
- bFood Science and Technology, and
- cFoods for Health Institute, University of California, Davis, CA 95616
| | | | | | - David A. Mills
- Departments of aViticulture and Enology and
- bFood Science and Technology, and
- cFoods for Health Institute, University of California, Davis, CA 95616
- 1To whom correspondence should be addressed. E-mail:
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