scholarly journals Phylogenetic analysis of fossil flowers using an angiosperm‐wide data set: proof‐of‐concept and challenges ahead

2020 ◽  
Vol 107 (10) ◽  
pp. 1433-1448
Author(s):  
Jürg Schönenberger ◽  
Maria Balthazar ◽  
Andrea López Martínez ◽  
Béatrice Albert ◽  
Charlotte Prieu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Proof Of Concept ◽  
Data Set ◽  
Fossil Flowers

scholarly journals The Termite Group I Phylum Is Highly Diverse and Widespread in the Environment

2007 ◽  
Vol 73 (20) ◽  
pp. 6682-6685 ◽  
Author(s):  
Daniel P. R. Herlemann ◽  
Oliver Geissinger ◽  
Andreas Brune
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Rrna Gene ◽  
Gene Sequences ◽  
16S Rrna Gene Sequences ◽  
Specific Primers ◽  
Environmental Distribution ◽  
Data Set ◽  
Group I

ABSTRACT The bacterial candidate phylum Termite Group I (TG-1) presently consists mostly of “Endomicrobia,” which are endosymbionts of flagellate protists occurring exclusively in the hindguts of termites and wood-feeding cockroaches. Here, we show that public databases contain many, mostly undocumented 16S rRNA gene sequences from other habitats that are affiliated with the TG-1 phylum but are only distantly related to “Endomicrobia.” Phylogenetic analysis of the expanded data set revealed several diverse and deeply branching lineages comprising clones from many different habitats. In addition, we designed specific primers to explore the diversity and environmental distribution of bacteria in the TG-1 phylum.

scholarly journals One View Per City for Buildings Segmentation in Remote-Sensing Images via Fully Convolutional Networks: A Proof-of-Concept Study

Sensors ◽  
2019 ◽  
Vol 20 (1) ◽  
pp. 141
Author(s):  
Jianguang Li ◽  
Wen Li ◽  
Cong Jin ◽  
Lijuan Yang ◽  
Hui He
Keyword(s):  
Remote Sensing ◽  
Image Analysis ◽  
Environmental Benefits ◽  
Sustainable Urban Development ◽  
Aerial Image ◽  
Proof Of Concept ◽  
Data Set ◽  
Concept Study ◽  
Convolutional Networks ◽  
Fully Convolutional Networks

The segmentation of buildings in remote-sensing (RS) images plays an important role in monitoring landscape changes. Quantification of these changes can be used to balance economic and environmental benefits and most importantly, to support the sustainable urban development. Deep learning has been upgrading the techniques for RS image analysis. However, it requires a large-scale data set for hyper-parameter optimization. To address this issue, the concept of “one view per city” is proposed and it explores the use of one RS image for parameter settings with the purpose of handling the rest images of the same city by the trained model. The proposal of this concept comes from the observation that buildings of a same city in single-source RS images demonstrate similar intensity distributions. To verify the feasibility, a proof-of-concept study is conducted and five fully convolutional networks are evaluated on five cities in the Inria Aerial Image Labeling database. Experimental results suggest that the concept can be explored to decrease the number of images for model training and it enables us to achieve competitive performance in buildings segmentation with decreased time consumption. Based on model optimization and universal image representation, it is full of potential to improve the segmentation performance, to enhance the generalization capacity, and to extend the application of the concept in RS image analysis.

A phylogenetic analysis of New Zealand giant and tree weta (Orthoptera : Anostostomatidae : Deinacrida and Hemideina) using morphological and genetic characters

2001 ◽  
Vol 15 (1) ◽  
pp. 1 ◽  
Author(s):  
Mary Morgan-Richards ◽  
George W. Gibbs
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Sound Production ◽  
Morphological Characters ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Life Styles ◽  
Multiple Origins ◽  
Tree Weta ◽  
Genetic Characters

A phylogenetic analysis of New Zealand weta from the sub-family Deinacridinae is presented. Eighteen species were studied using 27 genetic characters (allozyme and cytogenetic) and 25 morphological characters. The combined data set produced a phylogenetic hypothesis with twelve well-supported nodes. Despite the great diversity of habitats and life styles exhibited by the eleven Deinacrida White species a well-supported bipartition separates them from the seven Hemideina Walker species. Six of the Hemideina species formed a monophyletic clade, with respect to H. broughi (Buller). Evolution of stridulatory ridges used for sound production in both defence and intraspecific communication appears to have occurred at least twice. Adaptation to the recent New Zealand alpine environment has also had multiple origins. Biogeographic interpretations from the phylogenetic hypothesis are discussed.

Classification, reconstructed phylogeny and geographical history of genera of Pilipalpinae (Coleoptera : Tenebrionoidea : Pyrochroidae)

1995 ◽  
Vol 9 (4) ◽  
pp. 563 ◽  
Author(s):  
DA Pollock
Keyword(s):  
Phylogenetic Analysis ◽  
New Zealand ◽  
Type Species ◽  
New Genera ◽  
Parsimony Analysis ◽  
Data Set ◽  
Geological Evidence ◽  
Southern South America ◽  
Single Clade ◽  
History Of

The 12 genera of Pilipalpinae are classified on the basis of characters of larvae and adults. Three new genera and six new species are here described: Malagaethes, gen. nov. (type species M. lawrencei, sp. nov.); Ranomafana, gen. nov. (type species R. steineri, sp. nov.); Binburrum, gen. nov. (type species Techmessa ruficollis Champion); Binburrum angusticollis, sp. nov.; Binburrum concavifrons, sp. nov.; Cycloderus immaculicollis, sp. nov. and Cycloderus hirsutus, sp. nov. The following new synonymies of specific names are proposed (with valid names given first): Paromarteon constans Lea, 1917 = Eucistela cyanea Carter, 1922; Paromarteon mutabile Blackburn, 1897 = Paromarteon mutabile var. nigripenne Lea, 1920; Temnopalpus bicolor Blackburn, 1888 = Temnopalpus tricolor Lea, 1920; Pilipalpus dasytoides Fairmaire, 1876 = Copobaenus maculicollis Pic, 1942 and Pilipalpus danvini Abdullah, 19646; Exocalopus pectinatus Broun, 1893 = Exocalopus antennalis Broun, 1903. The following subspecies have been elevated to species rank: Paromarteon apicale Lea, Paromarteon fasciatum Lea and Paromarteon parvum Lea. Phylogenetic analysis of 30 structural characters of larvae and adults yielded the following set of incompletely resolved relationships among genera of Pilipalpinae: (((Paromarteon + ((Temnopalpus + Malagaethes) + Pilipalpus + (Ranomafana + (Incollogenius + ((Exocalopus + (Binburrum + (Cycloderus + Morpholycus)) + Techmessodes) + Techmessa))))). The data set contained much homoplasy and several reversals. The historical geographical relationships inferred from the reconstructed phylogeny were compared with geological evidence for the break-up of Pangaea and Gondwanaland. The ancestral stock of Pilipalpinae was widespread on Gondwanaland, and differentiated through its fragmentation. Remnant relict genera persisted on Madagascar, New Zealand, southern South America (Magellanica), and Australia. Brooks Parsimony Analysis was conducted on the data resulting in the following area relationships: (Holarctic + (Madagascar + (New Zealand + (Australia + Chile)))). This agrees generally with accepted geological evidence and is considered support for they hypothesised phylogeny. A single clade (Temnopalpus + Malagaethes) was in disagreement (homoplasous) with the area cladogram, indicating possible incongruence in the data. The area relationships of other Southern Hemisphere groups were compared with Pilipalpinae.

Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis

Paleobiology ◽  
1997 ◽  
Vol 23 (1) ◽  
pp. 1-19 ◽  
Author(s):  
William C. Clyde ◽  
Daniel C. Fisher
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Ad Hoc ◽  
Retention Indices ◽  
Significant Loss ◽  
Phylogenetic Hypothesis ◽  
Data Set ◽  
Phylogenetic Hypotheses ◽  
Morphologic Data

Stratigraphic data are compared to morphologic data in terms of their fit to phylogenetic hypotheses for 29 data sets taken from the literature. Stratigraphic fit is measured using MacClade's stratigraphic character, which tracks the number of independent discrepancies between observed order and the order of occurrence that would be expected on the basis of a given phylogenetic hypothesis. Acceptance of a phylogenetic hypothesis despite such discrepancies requires ad hoc hypotheses concerning differential probabilities of preservation and recovery. These stratigraphic ad hoc hypotheses are treated as logically equivalent to morphologic ad hoc hypotheses of homoplasy. The retention index is used to compare the number of stratigraphic and morphologic ad hoc hypotheses required by given phylogenetic hypotheses. Each data set is subjected to five analyses, varying in the constraints imposed on the structure of the phylogenetic tree against which fit is measured. Analyses 1–4 compare the stratigraphic and morphologic retention indices using phylogenetic trees consistent with the morphologically most-parsimonious cladogram reported in the original study. Analysis 5 compares retention indices using the overall (stratigraphically and morphologically) most-parsimonious phylogenetic tree, which may be, but is not necessarily, consistent with the reported cladogram. Proceeding from Analysis 1 to Analysis 5, stratigraphic data are allowed greater influence in determining the structure of phylogenetic trees, with the trees in Analysis 1 derived without reference to the stratigraphic character and the trees in Analysis 5 derived from full interaction of stratigraphic and morphologic characters. Morphologic and stratigraphic retention indices for these 29 studies cannot be statistically distinguished in comparisons 3–5, suggesting very similar degrees of fit. The values of these retention indices are high, indicating a generally high level of congruence under these phylogenetic hypotheses. Significant gains (49%) in stratigraphic fit can be realized without significant loss (4%) in morphologic fit as the stratigraphic and morphologic evidence are both allowed to participate in constraining the structure of phylogenetic hypotheses. These results suggest that arguments based on alleged “noisiness” of stratigraphic data offer inadequate grounds for ignoring stratigraphic order in phylogenetic analysis. In terms of congruence, stratigraphic and morphologic data perform about equally well.

scholarly journals Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

2021 ◽  
Author(s):  
Jesse D Bloom
Keyword(s):  
Phylogenetic Analysis ◽  
Deep Sequencing ◽  
Sequencing Data ◽  
Data Set ◽  
Deep Sequencing Data ◽  
Sequence Read Archive ◽  
Bat Coronavirus ◽  
Existing Data

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH's Sequence Read Archive. I recover the deleted files from the Google Cloud, and reconstruct partial sequences of 13 early epidemic viruses. Phylogenetic analysis of these sequences in the context of carefully annotated existing data suggests that the Huanan Seafood Market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan early in the epidemic. Instead, the progenitor of known SARS-CoV-2 sequences likely contained three mutations relative to the market viruses that made it more similar to SARS-CoV-2's bat coronavirus relatives.

scholarly journals Compound dataset and custom code for deep generative multi-target compound design

2021 ◽  
pp. FSO715
Author(s):  
Thomas Blaschke ◽  
Jürgen Bajorath
Keyword(s):  
Deep Learning ◽  
Proof Of Concept ◽  
Target Compound ◽  
Software Infrastructure ◽  
Data Set ◽  
Benchmark Data ◽  
Modeling Methodology ◽  
Generative Modeling ◽  
Single Target ◽  
Compound Design

Aim: Generating a data and software infrastructure for evaluating multi-target compound (MT-CPD) design via deep generative modeling. Methodology: The REINVENT 2.0 approach for generative modeling was extended for MT-CPD design and a large benchmark data set was curated. Exemplary results & data: Proof-of-concept for deep generative MT-CPD design was established. Custom code and the benchmark set comprising 2809 MT-CPDs, 61,928 single-target and 295,395 inactive compounds from biological screens are made freely available. Limitations & next steps: MT-CPD design via deep learning is still at its conceptual stages. It will be required to demonstrate experimental impact. The data and software we provide enable further investigation of MT-CPD design and generation of candidate molecules for experimental programs.

scholarly journals Advances in the recovery of haplotypes from the metagenome

2016 ◽  
Author(s):  
Samuel M. Nicholls ◽  
Wayne Aubrey ◽  
Kurt de Grave ◽  
Leander Schietgat ◽  
Christopher J. Creevey ◽  
...  
Keyword(s):  
Sequence Variation ◽  
A Priori ◽  
Region Of Interest ◽  
Genomic Region ◽  
Metagenomic Data ◽  
Proof Of Concept ◽  
Data Set ◽  
Single Organism ◽  
High Throughput Dna Sequencing ◽  
Concept Framework

AbstractHigh-throughput DNA sequencing has enabled us to look beyond consensus reference sequences to the variation observed in sequences within organisms; their haplotypes. Recovery, or assembly of haplotypes has proved computationally difficult and there exist many probabilistic heuristics that attempt to recover the original haplotypes for a single organism of known ploidy. However, existing approaches make simplifications or assumptions that are easily violated when investigating sequence variation within a metagenome.We propose the metahaplome as the set of haplotypes for any particular genomic region of interest within a metagenomic data set and present Hansel and Gretel, a data structure and algorithm that together provide a proof of concept framework for the recovery of true haplotypes from a metagenomic data set. The algorithm performs incremental haplotype recovery, using smoothed Naive Bayes — a simple, efficient and effective method.Hansel and Gretel pose several advantages over existing solutions: the framework is capable of recovering haplotypes from metagenomes, does not require a priori knowledge about the input data, makes no assumptions regarding the distribution of alleles at variant sites, is robust to error, and uses all available evidence from aligned reads, without altering or discarding observed variation. We evaluate our approach using synthetic metahaplomes constructed from sets of real genes and show that up to 99% of SNPs on a haplotype can be correctly recovered from short reads that originate from a metagenomic data set.

scholarly journals Comparative phylogenetic analysis of Dobrava-Belgrade virus L and S genetic segments isolated from an animal reservoir in Serbia

2014 ◽  
Vol 66 (2) ◽  
pp. 497-506 ◽  
Author(s):  
Valentina Nikolic ◽  
N. Stajkovic ◽  
Gorana Stamenkovic ◽  
R. Cekanac ◽  
P. Marusic ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Phylogenetic Tree ◽  
Animal Reservoir ◽  
Data Set ◽  
Bunyaviridae Family ◽  
Mapping Analysis ◽  
Geographical Clustering ◽  
Segment Data ◽  
Comparative Phylogenetic Analysis ◽  
Likelihood Mapping

The Dobrava-Belgrade virus (DOBV) is a member of the Bunyaviridae family, genus Hantavirus, possessing a single-stranded RNA genome consisting of three segments, designated L (large), M (medium) and S (small). In this study, we present phylogenetic analysis of a newly detected DOBV strain isolated from Apodemus agrarius. Analysis was based on partial L and S segment sequences, in comparison to previously published DOBV sequences from Serbia and elsewhere. A phylogenetic tree based on partial S segment revealed local geographical clustering of DOBV sequences from Serbia, unrelated to host (rodent or human). The topology of the phylogenetic tree was confirmed with a high percent of completely or partially resolved quartets in likelihood-mapping analysis, whereas no evidence of possible recombination in the examined S segment data set was found.

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