references.bib

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@ARTICLE{Yu2017-yq,
  title     = "Ggtree: An r package for visualization and annotation of
               phylogenetic trees with their covariates and other associated
               data",
  author    = "Yu, Guangchuang and Smith, David K and Zhu, Huachen and Guan, Yi
               and Lam, Tommy Tsan-Yuk",
  abstract  = "Summary We present an r package, ggtree, which provides
               programmable visualization and annotation of phylogenetic trees.
               ggtree can read more tree file formats than other softwares,
               including newick, nexus, NHX, phylip and jplace formats, and
               support visualization of phylo, multiphylo, phylo4, phylo4d,
               obkdata and phyloseq tree objects defined in other r packages.
               It can also extract the tree/branch/node‐specific and other data
               from the analysis outputs of beast, epa, hyphy, paml, phylodog,
               pplacer, r8s, raxml and revbayes software, and allows using
               these data to annotate the tree. The package allows colouring
               and annotation of a tree by numerical/categorical node
               attributes, manipulating a tree by rotating, collapsing and
               zooming out clades, highlighting user selected clades or
               operational taxonomic units and exploration of a large tree by
               zooming into a selected portion. A two‐dimensional tree can be
               drawn by scaling the tree width based on an attribute of the
               nodes. A tree can be annotated with an associated numerical
               matrix (as a heat map), multiple sequence alignment, subplots or
               silhouette images. The package ggtree is released under the
               artistic‐2.0 license. The source code and documents are freely
               available through bioconductor
               (http://www.bioconductor.org/packages/ggtree).",
  journal   = "Methods Ecol. Evol.",
  publisher = "Wiley",
  volume    =  8,
  number    =  1,
  pages     = "28--36",
  month     =  jan,
  year      =  2017,
  copyright = "http://onlinelibrary.wiley.com/termsAndConditions\#vor",
  language  = "en"
}

@ARTICLE{Perelman2011-jg,
  title     = "A molecular phylogeny of living primates",
  author    = "Perelman, Polina and Johnson, Warren E and Roos, Christian and
               Seu{\'a}nez, Hector N and Horvath, Julie E and Moreira, Miguel A
               M and Kessing, Bailey and Pontius, Joan and Roelke, Melody and
               Rumpler, Yves and Schneider, Maria Paula C and Silva, Artur and
               O'Brien, Stephen J and Pecon-Slattery, Jill",
  abstract  = "Comparative genomic analyses of primates offer considerable
               potential to define and understand the processes that mold,
               shape, and transform the human genome. However, primate taxonomy
               is both complex and controversial, with marginal unifying
               consensus of the evolutionary hierarchy of extant primate
               species. Here we provide new genomic sequence (~8 Mb) from 186
               primates representing 61 (~90\%) of the described genera, and we
               include outgroup species from Dermoptera, Scandentia, and
               Lagomorpha. The resultant phylogeny is exceptionally robust and
               illuminates events in primate evolution from ancient to recent,
               clarifying numerous taxonomic controversies and providing new
               data on human evolution. Ongoing speciation, reticulate
               evolution, ancient relic lineages, unequal rates of evolution,
               and disparate distributions of insertions/deletions among the
               reconstructed primate lineages are uncovered. Our resolution of
               the primate phylogeny provides an essential evolutionary
               framework with far-reaching applications including: human
               selection and adaptation, global emergence of zoonotic diseases,
               mammalian comparative genomics, primate taxonomy, and
               conservation of endangered species.",
  journal   = "PLoS Genet.",
  publisher = "Public Library of Science (PLoS)",
  volume    =  7,
  number    =  3,
  pages     = "e1001342",
  month     =  mar,
  year      =  2011,
  language  = "en"
}

@ARTICLE{Chewapreecha2017-lx,
  title     = "Global and regional dissemination and evolution of Burkholderia
               pseudomallei",
  author    = "Chewapreecha, Claire and Holden, Matthew T G and Vehkala, Minna
               and V{\"a}lim{\"a}ki, Niko and Yang, Zhirong and Harris, Simon R
               and Mather, Alison E and Tuanyok, Apichai and De Smet, Birgit
               and Le Hello, Simon and Bizet, Chantal and Mayo, Mark and
               Wuthiekanun, Vanaporn and Limmathurotsakul, Direk and
               Phetsouvanh, Rattanaphone and Spratt, Brian G and Corander,
               Jukka and Keim, Paul and Dougan, Gordon and Dance, David A B and
               Currie, Bart J and Parkhill, Julian and Peacock, Sharon J",
  journal   = "Nat. Microbiol.",
  publisher = "Springer Science and Business Media LLC",
  volume    =  2,
  number    =  4,
  month     =  jan,
  year      =  2017,
  copyright = "https://www.springernature.com/gp/researchers/text-and-data-mining",
  language  = "en"
}

@ARTICLE{Hall2022-pk,
  title     = "Expanding the Burkholderia pseudomallei Complex with the
               Addition of Two Novel Species: Burkholderia mayonis sp. nov. and
               Burkholderia savannae sp. nov",
  author    = "Hall, Carina M and Baker, Anthony L and Sahl, Jason W and Mayo,
               Mark and Scholz, Holger C and Kaestli, Mirjam and Schupp, James
               and Martz, Madison and Settles, Erik W and Busch, Joseph D and
               Sidak-Loftis, Lindsay and Thomas, Astrid and Kreutzer, Lisa and
               Georgi, Enrico and Schweizer, Herbert P and Warner, Jeffrey M
               and Keim, Paul and Currie, Bart J and Wagner, David M",
  abstract  = "Distinct Burkholderia strains were isolated from soil samples
               collected in tropical northern Australia (Northern Territory and
               the Torres Strait Islands, Queensland). Phylogenetic analysis of
               16S rRNA and whole genome sequences revealed these strains were
               distinct from previously described Burkholderia species and
               assigned them to two novel clades within the B. pseudomallei
               complex (Bpc). Because average nucleotide identity and digital
               DNA-DNA hybridization calculations are consistent with these
               clades representing distinct species, we propose the names
               Burkholderia mayonis sp. nov. and Burkholderia savannae sp. nov.
               Strains assigned to B. mayonis sp. nov. include type strain
               BDU6T (=TSD-80; LMG 29941; ASM152374v2) and BDU8. Strains
               assigned to B. savannae sp. nov. include type strain MSMB266T
               (=TSD-82; LMG 29940; ASM152444v2), MSMB852, BDU18, and BDU19.
               Comparative genomics revealed unique coding regions for both
               putative species, including clusters of orthologous genes
               associated with phage. Type strains of both B. mayonis sp. nov.
               and B. savannae sp. nov. yielded biochemical profiles distinct
               from each other and from other species in the Bpc, and profiles
               also varied among strains within B. mayonis sp. nov. and B.
               savannae sp. nov. Matrix-assisted laser desorption ionization
               time-of-flight (MLST) analysis revealed a B. savannae sp. nov.
               cluster separate from other species, whereas B. mayonis sp. nov.
               strains did not form a distinct cluster. Neither B. mayonis sp.
               nov. nor B. savannae sp. nov. caused mortality in mice when
               delivered via the subcutaneous route. The addition of B. mayonis
               sp. nov. and B. savannae sp. nov. results in a total of eight
               species currently within the Bpc. IMPORTANCE Burkholderia
               species can be important sources of novel natural products, and
               new species are of interest to diverse scientific disciplines.
               Although many Burkholderia species are saprophytic, Burkholderia
               pseudomallei is the causative agent of the disease melioidosis.
               Understanding the genomics and virulence of the closest
               relatives to B. pseudomallei, i.e., the other species within the
               B. pseudomallei complex (Bpc), is important for identifying
               robust diagnostic targets specific to B. pseudomallei and for
               understanding the evolution of virulence in B. pseudomallei. Two
               proposed novel species, B. mayonis sp. nov. and B. savannae sp.
               nov., were isolated from soil samples collected from multiple
               locations in northern Australia. The two proposed species belong
               to the Bpc but are phylogenetically distinct from all other
               members of this complex. The addition of B. mayonis sp. nov. and
               B. savannae sp. nov. results in a total of eight species within
               this significant complex of bacteria that are available for
               future studies.",
  journal   = "Appl. Environ. Microbiol.",
  publisher = "American Society for Microbiology",
  volume    =  88,
  number    =  1,
  pages     = "e0158321",
  month     =  jan,
  year      =  2022,
  keywords  = "BDU6T; Burkholderia; Burkholderia mayonis sp. nov.; Burkholderia
               pseudomallei complex; Burkholderia savannae sp. nov.; MSMB266T;
               novel species",
  copyright = "https://doi.org/10.1128/ASMCopyrightv2",
  language  = "en"
}

@ARTICLE{Janesomboon2021-dd,
  title     = "Detection and differentiation of Burkholderia species with
               pathogenic potential in environmental soil samples",
  author    = "Janesomboon, Sujintana and Muangsombut, Veerachat and Srinon,
               Varintip and Meethai, Chatruthai and Tharinjaroen, Chayada S and
               Amornchai, Premjit and Withatanung, Patoo and Chantratita,
               Narisara and Mayo, Mark and Wuthiekanun, Vanaporn and Currie,
               Bart J and Stevens, Joanne M and Korbsrisate, Sunee",
  abstract  = "The Burkholderia pseudomallei phylogenetic cluster includes B.
               pseudomallei, B. mallei, B. thailandensis, B. oklahomensis, B.
               humptydooensis and B. singularis. Regarded as the only
               pathogenic members of this group, B. pseudomallei and B. mallei
               cause the diseases melioidosis and glanders, respectively.
               Additionally, variant strains of B. pseudomallei and B.
               thailandensis exist that include the geographically restricted
               B. pseudomallei that express a B. mallei-like BimA protein
               (BPBM), and B. thailandensis that express a B. pseudomallei-like
               capsular polysaccharide (BTCV). To establish a PCR-based assay
               for the detection of pathogenic Burkholderia species or their
               variants, five PCR primers were designed to amplify
               species-specific sequences within the bimA (Burkholderia
               intracellular motility A) gene. Our multiplex PCR assay could
               distinguish pathogenic B. pseudomallei and BPBM from the
               non-pathogenic B. thailandensis and the BTCV strains. A second
               singleplex PCR successfully discriminated the BTCV from B.
               thailandensis. Apart from B. humptydooensis, specificity testing
               against other Burkholderia spp., as well as other Gram-negative
               and Gram-positive bacteria produced a negative result. The
               detection limit of the multiplex PCR in soil samples
               artificially spiked with known quantities of B. pseudomallei and
               B. thailandensis were 5 and 6 CFU/g soil, respectively.
               Furthermore, comparison between standard bacterial culture and
               the multiplex PCR to detect B. pseudomallei from 34 soil
               samples, collected from an endemic area of melioidosis, showed
               high sensitivity and specificity. This robust, sensitive, and
               specific PCR assay will be a useful tool for epidemiological
               study of B. pseudomallei and closely related members with
               pathogenic potential in soil.",
  journal   = "PLoS One",
  publisher = "Public Library of Science (PLoS)",
  volume    =  16,
  number    =  1,
  pages     = "e0245175",
  month     =  jan,
  year      =  2021,
  copyright = "http://creativecommons.org/licenses/by/4.0/",
  language  = "en"
}