scholarly journals Revisiting the Zingiberales: using multiplexed exon capture to resolve ancient and recent phylogenetic splits in a charismatic plant lineage

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1584 ◽  
Author(s):  
Chodon Sass ◽  
William J.D. Iles ◽  
Craig F. Barrett ◽  
Selena Y. Smith ◽  
Chelsea D. Specht
Keyword(s):  
Family Relationships ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Cost Effective ◽  
Model Systems ◽  
Bootstrap Support ◽  
Exon Capture ◽  
Cost Effective Method ◽  
High Bootstrap ◽  
Phylogenetic Estimation

The Zingiberales are an iconic order of monocotyledonous plants comprising eight families with distinctive and diverse floral morphologies and representing an important ecological element of tropical and subtropical forests. While the eight families are demonstrated to be monophyletic, phylogenetic relationships among these families remain unresolved. Neither combined morphological and molecular studies nor recent attempts to resolve family relationships using sequence data from whole plastomes has resulted in a well-supported, family-level phylogenetic hypothesis of relationships. Here we approach this challenge by leveraging the complete genome of one member of the order,Musa acuminata, together with transcriptome information from each of the other seven families to design a set of nuclear loci that can be enriched from highly divergent taxa with a single array-based capture of indexed genomic DNA. A total of 494 exons from 418 nuclear genes were captured for 53 ingroup taxa. The entire plastid genome was also captured for the same 53 taxa. Of the total genes captured, 308 nuclear and 68 plastid genes were used for phylogenetic estimation. The concatenated plastid and nuclear dataset supports the position of Musaceae as sister to the remaining seven families. Moreover, the combined dataset recovers known intra- and inter-family phylogenetic relationships with generally high bootstrap support. This is a flexible and cost effective method that gives the broader plant biology community a tool for generating phylogenomic scale sequence data in non-model systems at varying evolutionary depths.

Phaeosphaeria chinensis sp. nov. (Phaeosphaeriaceae) with an asexual/sexual morph connection from GuangDong Province, China

Phytotaxa ◽  
2019 ◽  
Vol 419 (1) ◽  
pp. 28-38 ◽  
Author(s):  
KE-KE ZHANG ◽  
SINANG HONGSANAN ◽  
DANUSHKA S. TENNAKOON ◽  
SHENG-LI TIAN ◽  
NING XIE
Keyword(s):  
New Species ◽  
Bayesian Inference ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Guangdong Province ◽  
Distinct Species ◽  
Bootstrap Support ◽  
Comprehensive Description ◽  
High Bootstrap ◽  
Asexual Morphs

Phaeosphaeria chinensis sp. nov. was found on dead leaves, collected from Guangdong Province, China. Morphology of the new species was compared with other Phaeosphaeria species and related genera of Phaeosphaeriaceae. Phylogenetic analyses of combined ITS, LSU, SSU and TEF-1 sequence data based on maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) revealed that P. chinensis as a distinct species within the Phaeosphaeria with high bootstrap support. The comparison of the new species with other Phaeosphaeria species and a comprehensive description and micrographs are provided. The linkage of sexual and asexual morphs of the new species is also showed.

Phylogenetic relationships among Unionicola (Acari: Unionicolidae) mussel-mites of North America based on mitochondrial cytochrome oxidase I sequences

Zootaxa ◽  
2010 ◽  
Vol 2537 (1) ◽  
pp. 47 ◽  
Author(s):  
DALE D. EDWARDS ◽  
MALCOLM F. VIDRINE ◽  
BRIAN R. ERNSTING
Keyword(s):  
North America ◽  
Cytochrome Oxidase ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Bootstrap Support ◽  
Cox1 Gene ◽  
Symbiotic Association ◽  
Gene Trees ◽  
Molecular Sequence Data ◽  
Molecular Sequence

Water mites of the genus Unionicola Haldeman, 1842 are common symbionts of molluscs, living on the gills or mantle and foot of their hosts and using these tissues as sites of oviposition. Phylogenetic relationships among species that comprise the genus are poorly understood and what is known has been based on a limited number of morphological and life history characters or molecular sequence data using closely-related taxa. The present study uses sequence data from the cytochrome oxidase subunit I (cox1) gene (664 bp) to reconstruct evolutionary relationships among representative species of North American Unionicola from eight subgenera that occur in symbiotic association with freshwater mussels. Maximum parsimony and maximum likelihood analysis yielded trees with similar topologies, and most of the branches have moderate to high bootstrap support. The topologies of these gene trees are mostly congruent with a previously published morphologically-derived tree. Specifically, the gene trees support monophyly among mites from subgenera that occur in association with the gill tissues of host mussels. The molecular trees of Unionicola mites generated by this study must, however, be interpreted with caution, given that the analysis is based exclusively on Unionicola subgenera from North America. A more robust phylogeny of Unionicola mussel-mites will require the addition of molecular sequence data from taxa outside of North America.

Molecular characterization and phylogenetic analysis of ascarid nematodes from twenty-one species of captive wild mammals based on mitochondrial and nuclear sequences

Parasitology ◽  
2012 ◽  
Vol 139 (10) ◽  
pp. 1329-1338 ◽  
Author(s):  
YAN LI ◽  
LILI NIU ◽  
QIANG WANG ◽  
ZHIHE ZHANG ◽  
ZHIGANG CHEN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Relationships ◽  
Molecular Level ◽  
Single Gene ◽  
Health Concern ◽  
Bootstrap Support ◽  
Wild Animals ◽  
Public Health Concern ◽  
Wild Mammals ◽  
High Bootstrap

SUMMARYAlthough ascarid nematodes are important parasites of wild animals of public health concern, few species of ascarids from wild animals have been studied at the molecular level so far. Here, the classification and phylogenetic relationships of roundworms from 21 species of captive wild animals have been studied by sequencing and analysis of parts of the ribosomal 18S and 28S genes and the mitochondrial (mt) 12S gene. Phylogenetic relationships were inferred by 3 methods (NJ/MP/ML) based on the data of single gene sequences and concatenated sequences. Homology analysis indicated that the 18S sequences were conserved among roundworms from all 21 species and that 28S showed interspecies variability. Divergence levels displayed in 12S suggested that 12S appears to be either intra- or interspecifically variable. Evolutionary trees indicated that the ascarids split into 2 families, 4 genera and 7 species, with high bootstrap support for each clade. Combined trees suggested that Baylisascaris ailuri is more closely related to B. transfuga than to B. schroederi. This study provides useful molecular markers for the classification, phylogenetic analysis and epidemiological investigation of roundworms from wild animals.

Phylogenetic assessment of the monotypic genera Sundacarpus and Manoao (Coniferales: Podocarpaceae) utilising evidence from 18S rDNA sequences

2002 ◽  
Vol 15 (1) ◽  
pp. 29 ◽  
Author(s):  
Dean G. Kelch
Keyword(s):  
Sequence Data ◽  
Morphological Data ◽  
Bootstrap Support ◽  
Conservative Approach ◽  
Parsimony Analysis ◽  
Rdna Sequences ◽  
The Family ◽  
18S Rdna Sequences ◽  
High Bootstrap ◽  
Lagarostrobos Franklinii

The Podocarpaceae are the most morphologically diverse of conifer families. A taxonomic trend has resulted in recognising this diversity via smaller generic groupings, including several monotypes. A phylogenetic assessment of the monotypic genera Sundacarpus and Manoao was conducted employing maximum parsimony the analysis of sequence data from 18S-ribosomal DNA from 34 gymnosperm taxa, including 29 Podocarpaceae. In resulting trees, there is high bootstrap support for Podocarpaceae, including Phyllocladus, but the order of deep branches within the family is equivocal. Prumnopitys (Sundacarpus) amara (Blume) de Laub. and four other Prumnopitys spp. comprise a clade with a bootstrap value of 100%, supporting the retention of Sundacarpus as a section of Prumnopitys. Lagarostrobos franklinii (Hook.f.) Quinn and L. (Manoao) colensoi (Hook.) Quinn comprise a clade with equivocal bootstrap support, echoing previous results from parsimony analysis of morphological data. A conservative approach (i.e. one avoiding unnecessary monotypes) favours the retention of L. colensoi in Lagarostrobos, pending further evidence of relationships within the group.

scholarly journals Additions to Chaetothyriaceae (Chaetothyriales): Longihyalospora gen. nov. and Ceramothyrium longivolcaniforme, a new host record from decaying leaves of Ficus ampelas

MycoKeys ◽  
2019 ◽  
Vol 61 ◽  
pp. 91-109 ◽  
Author(s):  
Danushka S. Tennakoon ◽  
Kasun M. Thambugala ◽  
Rajesh Jeewon ◽  
Sinang Hongsanan ◽  
Chang-Hsin Kuo ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Host Record ◽  
Bootstrap Support ◽  
Similar Species ◽  
New Host ◽  
New Host Record ◽  
Distinct Genus ◽  
High Bootstrap ◽  
First Time

A novel ascomycete genus, Longihyalospora, occurring on leaf litter of Ficus ampelas in Dahu Forest Area in Chiayi, Taiwan is described and illustrated. Longihyalospora is characterized by dark mycelium covering the upper leaf surface, elongate mycelial pellicle with ring of setae, pale brown to brown peridium, broadly obovoid, short pedicellate asci and hyaline, fusiform, elongated (tapering ends) and multi-septate ascospores with a thin mucilaginous sheath. Phylogenetic analyses of combined ITS, LSU and SSU sequence data revealed Longihyalospora as a distinct genus within the Chaetothyriaceae with high bootstrap support. Moreover, based on morphological similarities, Chaetothyrium vermisporum transferred to the new genus. In addition, Ceramothyrium longivolcaniforme is reported for the first time on Ficus ampelas. Newly added species are compared with other similar species and comprehensive descriptions and micrographs are provided.

scholarly journals Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

2013 ◽  
Author(s):  
Rebecca T Kimball ◽  
Edward L Braun
Keyword(s):  
Japanese Quail ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Model Systems ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Published Data ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Individual Gene

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. Some of the key findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.

scholarly journals Development and evaluation of a custom bait design based on 469 single-copy protein-coding genes for exon capture of isopods (Philosciidae: Haloniscus)

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256861
Author(s):  
Danielle N. Stringer ◽  
Terry Bertozzi ◽  
Karen Meusemann ◽  
Steven Delean ◽  
Michelle T. Guzik ◽  
...  
Keyword(s):  
Sequence Data ◽  
Methodological Approach ◽  
Cost Effective ◽  
Single Copy ◽  
Model Organisms ◽  
Protein Coding ◽  
Genetics Research ◽  
Exon Capture ◽  
High Uniformity ◽  
Multiple Samples

Transcriptome-based exon capture approaches, along with next-generation sequencing, are allowing for the rapid and cost-effective production of extensive and informative phylogenomic datasets from non-model organisms for phylogenetics and population genetics research. These approaches generally employ a reference genome to infer the intron-exon structure of targeted loci and preferentially select longer exons. However, in the absence of an existing and well-annotated genome, we applied this exon capture method directly, without initially identifying intron-exon boundaries for bait design, to a group of highly diverse Haloniscus (Philosciidae), paraplatyarthrid and armadillid isopods, and examined the performance of our methods and bait design for phylogenetic inference. Here, we identified an isopod-specific set of single-copy protein-coding loci, and a custom bait design to capture targeted regions from 469 genes, and analysed the resulting sequence data with a mapping approach and newly-created post-processing scripts. We effectively recovered a large and informative dataset comprising both short (<100 bp) and longer (>300 bp) exons, with high uniformity in sequencing depth. We were also able to successfully capture exon data from up to 16-year-old museum specimens along with more distantly related outgroup taxa, and efficiently pool multiple samples prior to capture. Our well-resolved phylogenies highlight the overall utility of this methodological approach and custom bait design, which offer enormous potential for application to future isopod, as well as broader crustacean, molecular studies.

scholarly journals Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

2013 ◽  
Author(s):  
Rebecca T Kimball ◽  
Edward L Braun
Keyword(s):  
Japanese Quail ◽  
Sequence Data ◽  
Incomplete Lineage Sorting ◽  
Model Systems ◽  
Data Matrix ◽  
Bootstrap Support ◽  
Published Data ◽  
Gene Trees ◽  
Lineage Sorting ◽  
Individual Gene

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. Some of the key findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.

CAD Of Anticorrosive Protection Of Steel Structures

2019 ◽  
pp. 18-23
Keyword(s):  
Protective Coating ◽  
Computer Aided Design ◽  
Steel Structures ◽  
Cost Effective ◽  
Operating Conditions ◽  
Computational Tool ◽  
Protection Method ◽  
Cost Effective Method ◽  
The Cost ◽  
Aided Design

The choice of cost-effective method of anticorrosive protection of steel structures is an urgent and time consuming task, considering the significant number of protection ways, differing from each other in the complex of technological, physical, chemical and economic characteristics. To reduce the complexity of solving this problem, the author proposes a computational tool that can be considered as a subsystem of computer-aided design and used at the stage of variant and detailed design of steel structures. As a criterion of the effectiveness of the anti-corrosion protection method, the cost of the protective coating during the service life is accepted. The analysis of existing methods of steel protection against corrosion is performed, the possibility of their use for the protection of the most common steel structures is established, as well as the estimated period of effective operation of the coating. The developed computational tool makes it possible to choose the best method of protection of steel structures against corrosion, taking into account the operating conditions of the protected structure and the possibility of using a protective coating.

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