scholarly journals Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: New approaches to long-standing problems

2017 ◽  
Author(s):  
A.M. Quattrini ◽  
B.C. Faircloth ◽  
L.F. Dueñas ◽  
T.C.L. Bridge ◽  
M. Brugler ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Illumina Sequencing ◽  
Phylogenetic Relationships ◽  
Evolutionary Relationships ◽  
Diverse Group ◽  
Target Enrichment ◽  
Library Preparation ◽  
Deep Waters ◽  
The Mean ◽  
Multiple Species

AbstractAnthozoans (e.g., corals, anemones) are an ecologically important and diverse group of marine metazoans that occur from shallow to deep waters worldwide. However, our understanding of the evolutionary relationships among the ∼7500 species within this class is hindered by the lack of phylogenetically informative markers that can be reliably sequenced across a diversity of taxa. We designed and tested 16,308 RNA baits to capture 720 Ultraconserved Element loci and 1,071 exon loci. Library preparation and target enrichment was performed on 33 taxa from all orders within the class Anthozoa. Following Illumina sequencing and Trinity assembly, we recovered 1,774 of 1,791 targeted loci. The mean number of loci recovered from each species was 638 ± 222, with more loci recovered from octocorals (783 ± 138 loci) than hexacorals (475 ±187 loci). Phylogenetically informative sites ranged from 26-49% for alignments at differing hierarchical taxonomic levels (e.g., Anthozoa, Octocorallia, Hexacorallia). The percent of variable sites within each of three genera (Acropora, Alcyonium, andSinularia) for which multiple species were sequenced ranged from 4.7-30%. Maximum likelihood analyses recovered highly resolved trees with topologies matching those supported by other studies, including the monophyly of the order Scleractinia. Our results demonstrate the utility of this target-enrichment approach to resolve phylogenetic relationships from relatively old to recent divergences. Re-designing the baits with improved affinities to capture loci within each sub-class will provide a valuable toolset to address systematic questions and further our understanding of the timing of diversifications in the class Anthozoa.

scholarly journals Métodos de reconstrucción filogenética I: máxima verosimilitud

Tequio ◽  
2021 ◽  
Vol 4 (11) ◽  
pp. 69-79
Author(s):  
Pablo Duchen
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Evolutionary Biology ◽  
Transition Probabilities ◽  
Phylogenetic Reconstruction ◽  
Phylogenetic Inference ◽  
Evolutionary Relationships ◽  
Dna Mutation ◽  
Multiple Species ◽  
The One

Phylogenetic inference is widely used in evolutionary biology, aiming to find evolutionary relationships between different species and report the result in the form of a phylogenetic tree (phylogeny). There are several statistical methods used for phylogenetic inference. In this review, the method of maximum likelihood for phylogenetic reconstruction is presented. This technique consists of finding the likelihood of multiple candidate phylogenies, and report the one with the highest likelihood as a representative of the evolutionary relationships of a group of species. In this paper, the likelihood calculation of a phylogeny from multiple-species DNA sequences is reviewed. Also, some key DNA mutation models to calculate transition probabilities between nucleotides are presented. Such transition probabilities are used in the likelihood calculation of a given phylogeny. A simple example is shown to illustrate the necessary steps to infer a phylogeny, as well as the most common software for maximum likelihood inference for larger DNA alignments.

scholarly journals Phylogenomics of the leaf-footed bug subfamily Coreinae (Hemiptera: Coreidae): applicability of ultraconserved elements at shallower depths

2020 ◽  
Author(s):  
Michael Forthman ◽  
Christine W. Miller ◽  
Rebecca T. Kimball
Keyword(s):  
Maximum Likelihood ◽  
Dna Extraction ◽  
Phylogenetic Relationships ◽  
Target Enrichment ◽  
Ultraconserved Elements ◽  
Phylogenetic Studies ◽  
Phylogenetic Hypotheses

AbstractBaits targeting invertebrate ultraconserved elements (UCEs) are becoming more common for phylogenetic studies. Recent studies have shown that invertebrate UCEs typically encode proteins — and thus, are functionally different from more conserved vertebrate UCEs —can resolve deep divergences (e.g., superorder to family ranks). However, the ability of the invertebrate UCE baits to robustly resolve relationships at shallower phylogenetic scales (i.e., tribes and congeners) has been generally limited to Coleoptera and Hymenoptera. Here, we assessed the ability of a recently designed Hemiptera UCE bait set to reconstruct more recent phylogenetic relationships in the largest leaf-footed bug subfamily, the Coreinae (Hemiptera: Coreidae), using a taxon-rich sample representing 21 of the 32 coreine tribes. Many well-supported, novel relationships were congruent in maximum likelihood and summary coalescent analyses. We also found evidence for the para- and polyphyly of several tribes and genera of Coreinae, as well as the subfamilies Coreinae and Meropachyinae. Our study, along with other recent UCE studies, provides evidence that UCEs can produce robust and novel phylogenetic hypotheses at various scales in invertebrates. Additionally, we used different DNA extraction and target enrichment protocols and recovered more UCE data using a touch-down hybridization approach.

scholarly journals 423. SARS-CoV-2 NGS Assay Powered by Biotia COVID-DX Software

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S278-S279
Author(s):  
Dorottya Nagy-Szakal ◽  
Mara Couto-Rodriguez ◽  
Joseph Barrows ◽  
Heather L Wells ◽  
Marilyne Debieu ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Viral Genome ◽  
Board Member ◽  
Limit Of Detection ◽  
Clinical Samples ◽  
Analysis Tool ◽  
Viral Titer ◽  
Target Enrichment ◽  
Library Preparation ◽  
Software Analysis

Abstract Background COVID-19 had spread quickly, causing an international public health emergency with an alarming global shortage of COVID-19 diagnostic tests. We developed and clinically validated a next-generation sequencing (NGS)-based target enrichment assay with the COVID-DX Software tailored for the detection, characterization, and surveillance of the SARS-CoV-2 viral genome. Methods The SARS-CoV-2 NGS assay consists of components including library preparation, target enrichment, sequencing, and a COVID-DX Software analysis tool. The NGS library preparation starts with extracted RNA from nasopharyngeal (NP) swabs followed by cDNA synthesis and conversion to Illumina TruSeq-compatible libraries using the Twist Library Preparation Kit via Enzymatic Fragmentation and Unique Dual Indices (UDI). The library is then enriched for SARS-CoV-2 sequences using a panel of dsDNA biotin-labeled probes, specifically designed to target the SARS-CoV-2 genome, then sequenced on an Illumina NextSeq 550 platform. The COVID-DX Software analyzes sequence results and provides a clinically oriented report, including the presence/absence of SARS-CoV-2 for diagnostic use. An additional research use only report describes the assay performance, estimated viral titer, coverage across the viral genome, genetic variants, and phylogenetic analysis. Results The SARS-CoV-2 NGS Assay was validated on 30 positive and 30 negative clinical samples. To measure the sensitivity and specificity of the assay, the positive and negative percent agreement (PPA, NPA) was defined in comparison to an orthogonal EUA RT-PCR assay (PPA [95% CI]: 96.77% [90.56%-100%] and NPA [95% CI]: 100% [100%-100%]). Data reported using our assay defined the limit of detection to be 40 copies/ml using heat-inactivated SARS-CoV-2 viral genome in clinical matrices. In-silico analysis provided >99.9% coverage across the SARS-CoV-2 viral genome and no cross-reactivity with evolutionarily similar respiratory pathogens. Conclusion The SARS-CoV-2 NGS Assay powered by the COVID-DX Software can be used to detect the SARS-CoV-2 virus and provide additional insight into viral titer and genetic variants to track transmission, stratify risk, predict outcome and therapeutic response, and control the spread of infectious disease. Disclosures Dorottya Nagy-Szakal, MD PhD, Biotia (Employee) Mara Couto-Rodriguez, MS, Biotia (Employee) Joseph Barrows, MS, Biotia, Inc. (Employee, Shareholder) Heather L. Wells, MPH, Biotia (Consultant) Marilyne Debieu, PhD, Biotia (Employee) Courteny Hager, BS, Biotia (Employee) Kristin Butcher, MS, Twist Bioscience (Employee) Siyuan Chen, PhD, Twist Bioscience (Employee) Christopher Mason, PhD, Biotia (Board Member, Employee, Shareholder) Niamh B. O’Hara, PhD, Biotia (Board Member, Employee, Shareholder)Twist (Other Financial or Material Support, I am CEO of Biotia and Biotia has business partnership with Twist)

scholarly journals Annelid Diversity: Historical Overview and Future Perspectives

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 129
Author(s):  
María Capa ◽  
Pat Hutchings
Keyword(s):  
State Of The Art ◽  
Molecular Taxonomy ◽  
Evolutionary Relationships ◽  
Diverse Group ◽  
Future Perspectives ◽  
Special Issue ◽  
Species Numbers ◽  
Species Complexes ◽  
Taxonomic Groups ◽  
A New Species

Annelida is a ubiquitous, common and diverse group of organisms, found in terrestrial, fresh waters and marine environments. Despite the large efforts put into resolving the evolutionary relationships of these and other Lophotrochozoa, and the delineation of the basal nodes within the group, these are still unanswered. Annelida holds an enormous diversity of forms and biological strategies alongside a large number of species, following Arthropoda, Mollusca, Vertebrata and perhaps Platyhelminthes, among the species most rich in phyla within Metazoa. The number of currently accepted annelid species changes rapidly when taxonomic groups are revised due to synonymies and descriptions of a new species. The group is also experiencing a recent increase in species numbers as a consequence of the use of molecular taxonomy methods, which allows the delineation of the entities within species complexes. This review aims at succinctly reviewing the state-of-the-art of annelid diversity and summarizing the main systematic revisions carried out in the group. Moreover, it should be considered as the introduction to the papers that form this Special Issue on Systematics and Biodiversity of Annelids.

Whale falls, multiple colonisations of the deep, and the phylogeny of Hesionidae (Annelida)

2015 ◽  
Vol 29 (2) ◽  
pp. 105 ◽  
Author(s):  
Mindi Summers ◽  
Fredrik Pleijel ◽  
Greg W. Rouse
Keyword(s):  
New Species ◽  
Maximum Likelihood ◽  
16S Rrna ◽  
Deep Sea ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
Shallow Waters ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
New Members

Phylogenetic relationships within Hesionidae Grube, 1850 are assessed via maximum parsimony and maximum likelihood analyses of mitochondrial (cytochrome c oxidase subunit I and 16S rRNA) and nuclear (18S rRNA, and 28S rRNA) data. The analyses are based on 42 hesionid species; six of these being new species that are described here. The new species, all from deep (>200 m depth) benthic environments (including whale falls) in the eastern Pacific, are Gyptis shannonae, sp. nov., Neogyptis julii, sp. nov., Sirsoe sirikos, sp. nov., Vrijenhoekia ketea, sp. nov., Vrijenhoekia falenothiras, sp. nov., and Vrijenhoekia ahabi, sp. nov. The molecular divergence among the new members of Vrijenhoekia is pronounced enough to consider them cryptic species, even though we cannot distinguish among them morphologically. Our results also showed that the subfamily Hesioninae Grube, 1850, as traditionally delineated, was paraphyletic. We thus restrict Hesioninae to include only Hesionini Grube, 1850 and refer the remaining members to Psamathinae Pleijel, 1998. The present study increases the number of hesionid species associated with whale falls from one to six and markedly increases the number of described deep-sea hesionid taxa. There appear to have been multiple colonisations of the deep sea from shallow waters by hesionids, though further sampling is warranted.

scholarly journals Evolutionary relationships of completely sequenced Clostridia species and close relatives

2015 ◽  
Vol 65 (Pt_11) ◽  
pp. 4276-4283 ◽  
Author(s):  
Takashi Kunisawa
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Trees ◽  
Gene Arrangement ◽  
Evolutionary Relationships ◽  
Rrna Gene ◽  
Sequence Information ◽  
Bayesian Tree ◽  
Maximum Likelihood Methods ◽  
Genome Sequence Information ◽  
Close Relatives

The class Clostridia in the phylum Firmicutes includes a very heterogeneous assemblage of bacteria. Their evolutionary relationships are not well established; revisions of their phylogenetic placements based on comparative studies of 16S rRNA gene sequences are in progress as genome sequence information accumulates. In this work, phylogenetic trees were reconstructed based on 21 concatenated ribosomal protein sequences using Bayesian and maximum-likelihood methods. Both trees consistently indicate that the Halanaerobiales is a deeply branching order among the class Clostridia. The rest of the Clostridia species are grouped into 10 monophyletic clusters, most of which are comprised of two or three orders and families according to the current Clostridial taxonomy. The maximum-likelihood tree placed Coprothermobacter proteolyticus and Thermodesulfobium narugense in the class Clostridia in accordance with the current taxonomy, in which these two bacteria are assigned to the family Thermodesulfobiaceae. However, the Bayesian tree placed these two bacteria at the boundary between the Firmicutes and Actinobacteria. A gene arrangement that is present uniquely in the Firmicutes species was identified. Both Coprothermobacter proteolyticus and Thermodesulfobium narugense do not have this arrangement characteristic of the Firmicutes. On the basis of the Bayesian tree and gene arrangement comparison, it is suggested that Coprothermobacter proteolyticus and Thermodesulfobium narugense should be placed outside the phylum Firmicutes.

scholarly journals Best estimation for the Reliability of 2-parameter Weibull Distribution

2009 ◽  
Vol 6 (4) ◽  
pp. 705-710
Author(s):  
Baghdad Science Journal
Keyword(s):  
Maximum Likelihood ◽  
Weibull Distribution ◽  
Mean Square Error ◽  
Maximum Likelihood Method ◽  
Likelihood Method ◽  
Statistical Criterion ◽  
Mean Square ◽  
Simulation Process ◽  
The Mean ◽  
Two Parameter

This Research Tries To Investigate The Problem Of Estimating The Reliability Of Two Parameter Weibull Distribution,By Using Maximum Likelihood Method, And White Method. The Comparison Is done Through Simulation Process Depending On Three Choices Of Models (?=0.8 , ß=0.9) , (?=1.2 , ß=1.5) and (?=2.5 , ß=2). And Sample Size n=10 , 70, 150 We Use the Statistical Criterion Based On the Mean Square Error (MSE) For Comparison Amongst The Methods.

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