Can the Cambrian explosion be inferred through molecular phylogeny?

Most of the major invertebrate phyla appear in the fossil record during a relatively short time interval, not exceeding 20 million years (Myr), 540-520 Myr ago. This rapid diversification is known as the `Cambrian explosion'. In the present paper, we ask whether molecular phylogenetic reconstruction provides confirmation for such an evolutionary burst. The expectation is that the molecular phylogenetic trees should take the form of a large unresolved multifurcation of the various animal lineages. Complete 18S rRNA sequences of 69 extant representatives of 15 animal phyla were obtained from data banks. After eliminating a major source of artefact leading to lack of resolution in phylogenetic trees (mutational saturation of sequences), we indeed observe that the major lines of triploblast coelomates (arthropods, molluscs, echinoderms, chordates...) are very poorly resolved i.e. the nodes defining the various clades are not supported by high bootstrap values. Using a previously developed procedure consisting of calculating bootstrap proportions of each node of the tree as a function of increasing amount of nucleotides (Lecointre, G., Philippe, H. Le, H. L. V. and Le Guyader, H. (1994) Mol. Phyl. Evol., in press) we obtain a more informative indication of the robustness of each node. In addition, this procedure allows us to estimate the number of additional nucleotides that would be required to resolve confidently the currently uncertain nodes; this number turns out to be extremely high and experimentally unfeasible. We then take this approach one step further: using parameters derived from the above analysis, assuming a molecular clock and using palaeontological dates for calibration, we establish a relationship between the number of sites contained in a given data set and the time interval that this data set can confidently resolve (with 95% bootstrap support). Under these assumptions, the presently available 18S rRNA database cannot confidently resolve cladogenetic events separated by less than about 40 Myr. Thus, at the present time, the potential resolution by the palaeontological approach is higher than that by the molecular one.

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Towards a unified classification for human respiratory syncytial virus genotypes

Virus Evolution ◽

10.1093/ve/veaa052 ◽

2020 ◽

Vol 6 (2) ◽

Cited By ~ 1

Author(s):

Kaat Ramaekers ◽

Annabel Rector ◽

Lize Cuypers ◽

Philippe Lemey ◽

Els Keyaerts ◽

...

Keyword(s):

Respiratory Syncytial Virus ◽

Phylogenetic Trees ◽

Phylogenetic Signal ◽

Phylogenetic Reconstruction ◽

Hypervariable Region ◽

Human Respiratory Syncytial Virus ◽

Bootstrap Support ◽

Whole Genome ◽

Patristic Distance ◽

Syncytial Virus

Abstract Since the first human respiratory syncytial virus (HRSV) genotype classification in 1998, inconsistent conclusions have been drawn regarding the criteria that define HRSV genotypes and their nomenclature, challenging data comparisons between research groups. In this study, we aim to unify the field of HRSV genotype classification by reviewing the different methods that have been used in the past to define HRSV genotypes and by proposing a new classification procedure, based on well-established phylogenetic methods. All available complete HRSV genomes (>12,000 bp) were downloaded from GenBank and divided into the two subgroups: HRSV-A and HRSV-B. From whole-genome alignments, the regions that correspond to the open reading frame of the glycoprotein G and the second hypervariable region (HVR2) of the ectodomain were extracted. In the resulting partial alignments, the phylogenetic signal within each fragment was assessed. Maximum likelihood phylogenetic trees were reconstructed using the complete genome alignments. Patristic distances were calculated between all pairs of tips in the phylogenetic tree and summarized as a density plot in order to determine a cutoff value at the lowest point following the major distance peak. Our data show that neither the HVR2 fragment nor the G gene contains sufficient phylogenetic signal to perform reliable phylogenetic reconstruction. Therefore, whole-genome alignments were used to determine HRSV genotypes. We define a genotype using the following criteria: a bootstrap support of ≥70 per cent for the respective clade and a maximum patristic distance between all members of the clade of ≤0.018 substitutions per site for HRSV-A or ≤0.026 substitutions per site for HRSV-B. By applying this definition, we distinguish twenty-three genotypes within subtype HRSV-A and six genotypes within subtype HRSV-B. Applying the genotype criteria on subsampled data sets confirmed the robustness of the method.

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The asymptotic behavior of bootstrap support values in molecular phylogenetics

Systematic Biology ◽

10.1093/sysbio/syaa100 ◽

2020 ◽

Author(s):

Jun Huang ◽

Yuting Liu ◽

Tianqi Zhu ◽

Ziheng Yang

Keyword(s):

Asymptotic Behavior ◽

Phylogenetic Trees ◽

Molecular Phylogenetics ◽

Phylogenetic Reconstruction ◽

Strong Support ◽

Large Datasets ◽

Bootstrap Support ◽

Partial Explanation ◽

Empirical Observation ◽

Statistical Confidence

Abstract The phylogenetic bootstrap is the most commonly used method for assessing statistical confidence in estimated phylogenies by non-Bayesian methods such as maximum parsimony and maximum likelihood (ML). It is observed that bootstrap support tends to be high in large genomic datasets whether or not the inferred trees and clades are correct. Here we study the asymptotic behavior of bootstrap support for the ML tree in large datasets when the competing phylogenetic trees are equally right or equally wrong. We consider phylogenetic reconstruction as a problem of statistical model selection when the compared models are nonnested and misspecified. The bootstrap is found to have qualitatively different dynamics from Bayesian inference, and does not exhibit the polarized behavior of posterior model probabilities, consistent with the empirical observation that the bootstrap is more conservative than Bayesian probabilities. Nevertheless bootstrap support similarly shows fluctuations among large datasets, with no convergence to a point value, when the compared models are equally right or equally wrong. Thus in large datasets strong support for wrong trees or models is likely to occur. Our analysis provides a partial explanation for the high bootstrap support values for incorrect clades observed in empirical data analysis.

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Mitochondrial DNA Sequence Phylogeny of Daucus

Systematic Botany ◽

10.1600/036364420x15862837791311 ◽

2020 ◽

Vol 45 (2) ◽

pp. 403-408 ◽

Cited By ~ 1

Author(s):

David M. Spooner ◽

Holly Ruess ◽

Philipp Simon ◽

Douglas Senalik

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Phylogenetic Trees ◽

Plastid Dna ◽

Nuclear Data ◽

Bootstrap Support ◽

Illumina Hiseq ◽

Data Set ◽

Closely Related Species ◽

Mitochondrial Sequences

Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

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Assessment of the TROPOMI tropospheric NO<sub>2</sub> product based on airborne APEX observations

10.5194/amt-2020-148 ◽

2020 ◽

Cited By ~ 1

Author(s):

Frederik Tack ◽

Alexis Merlaud ◽

Marian-Daniel Iordache ◽

Gaia Pinardi ◽

Ermioni Dimitropoulou ◽

...

Keyword(s):

Remote Sensing ◽

A Priori ◽

Horizontal Distribution ◽

Time Interval ◽

Short Time Interval ◽

Vertical Column ◽

Data Set ◽

Urban Regions ◽

Tropospheric No2 ◽

The Impact

Abstract. Sentinel-5 Precursor (S-5P), launched in October 2017, carrying the TROPOspheric Monitoring Instrument (TROPOMI) nadir-viewing spectrometer, is the first mission of the Copernicus Programme dedicated to the monitoring of air quality, climate, and ozone. In the presented study, the TROPOMI tropospheric nitrogen dioxide (NO2) L2 product (OFFL v1.03.01; 3.5 km × 7 km at nadir observations) has been validated over strongly polluted urban regions by comparison with coincident high-resolution Airborne Prism EXperiment (APEX) remote sensing observations (~75 m × 120 m). Satellite products can be optimally assessed based on (APEX) airborne remote sensing observations as a large amount of satellite pixels can be fully mapped at high accuracy and in a relatively short time interval, reducing the impact of spatio-temporal mismatches. In the framework of the S5PVAL-BE campaign, the APEX imaging spectrometer has been deployed during four mapping flights (26–29 June 2019) over the two largest urban regions in Belgium, i.e. Brussels and Antwerp, in order to map the horizontal distribution of tropospheric NO2. For each flight, 10 to 20 TROPOMI pixels were fully covered by approximately 2800 to 4000 APEX measurements within each TROPOMI pixel. The TROPOMI and APEX NO2 vertical column density (VCD) retrieval schemes are similar in concept. Overall for the ensemble of the four flights, the standard TROPOMI NO2 VCD product is well correlated (R = 0.92) but biased negatively by −1.2 ± 1.2 × 1015 molec cm−2 or −14 % ± 12 %, on average, with respect to coincident APEX NO2 retrievals. When replacing the coarse 1° × 1° TM5-MP a priori NO2 profiles by NO2 profile shapes from the CAMS regional CTM ensemble at 0.1° × 0.1°, the slope increases by 11 % to 0.93, and the bias is reduced to −0.1 ± 1.0 × 1015 molec cm−2 or −1.0 % ± 12 %. When the absolute value of the difference is taken, the bias is 1.3 × 1015 molec cm−2 or 16 %, and 0.7 × 1015 molec cm−2 or 9 % on average, when comparing APEX NO2 VCDs with TM5-MP-based and CAMS-based NO2 VCDs, respectively. Both sets of retrievals are well within the accuracy requirement of a maximum bias of 25–50 % for the TROPOMI tropospheric NO2 product for all individual compared pixels. Additionally, the APEX data set allows the study of TROPOMI subpixel variability and impact of signal smoothing due to its finite satellite pixel size, typically coarser than fine-scale gradients in the urban NO2 field. The amount of underestimation of peak plume values and overestimation of urban background values in the TROPOMI data is in the order of 1–2 × 1015 molec cm−2 on average, or 10 %–20 %, in case of an urban scene.

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Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)

Zootaxa ◽

10.11646/zootaxa.3626.1.3 ◽

2013 ◽

Vol 3626 (1) ◽

pp. 77-93 ◽

Cited By ~ 10

Author(s):

DAVID W. WEISROCK ◽

J. ROBERT MACEY ◽

MASAFUMI MATSUI ◽

DANIEL G. MULCAHY

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Trees ◽

Sequence Data ◽

Bootstrap Support ◽

Phylogenetic Study ◽

Taxon Sampling ◽

12S Rrna ◽

Sister Relationship ◽

Data Set ◽

History Of

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylo-genetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S–16S region (the 3’ end of 12S rRNA, tRNAVAl, and the 5’ end of 16S rRNA), and a ND2–COI region (ND2, tRNATrp, tRNAAla, tRNAAsn, the origin for light strand replication—OL, tRNACys, tRNATyr, and the 5’ end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phy-logenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger Batrachu-perus and Hynobius clades. While the relationships identified in this study do much to clarify the phylogenetic history of the Hynobiidae, the poor resolution among major hynobiid clades, and the contrast of mtDNA-derived relationships with recent phylogenetic results from a small number of nuclear genes, highlights the need for continued phylogenetic study with larger numbers of nuclear loci.

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The analysis of epigenomic evolution

10.1101/2021.03.03.433796 ◽

2021 ◽

Author(s):

Arne Sahm ◽

Philipp Koch ◽

Steve Horvath ◽

Steve Hoffmann

Keyword(s):

Binding Sites ◽

Phylogenetic Trees ◽

Phylogenetic Reconstruction ◽

Systematic Investigation ◽

Data Set ◽

Evolutionarily Conserved ◽

Immune Related Genes ◽

Genomic Regions ◽

Blood Data

While the investigation of the epigenome becomes increasingly important, still little is known about the long-term evolution of epigenetic marks and systematic investigation strategies are still withstanding. Here, we systematically demonstrate the transfer of classic phylogenetic methods such as maximum likelihood based on substitution models, parsimony, and distance-based to interval-scaled epigenetic data (available at Github). Using a great apes blood data set, we demonstrate that DNA methylation is evolutionarily conserved at the level of individual CpGs in promotors, enhancers and genic regions. Our analysis also reveals that this epigenomic conservation is significantly correlated with its transcription factor binding density. Binding sites for transcription factors involved in neuron differentiation and components of AP-1 evolve at a significantly higher rate at methylation than at nucleotide level. Moreover, our models suggest an accelerated epigenomic evolution at binding sites of BRCA1, CBX2, and factors of the polycomb repressor 2 complex in humans. For most genomic regions, the methylation-based reconstruction of phylogenetic trees is at par with sequence-based reconstruction. Most strikingly, phylogenetic reconstruction using methylation rates in enhancer regions was ineffective independently of the chosen model. We identify a set of phylogenetically uninformative CpG sites enriching in enhancers controlling immune-related genes.

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Mitochondrial cob and cox1 Genes and Editing of the Corresponding mRNAs in Dinophysis acuminata from Narragansett Bay, with Special Reference to the Phylogenetic Position of the Genus Dinophysis

Applied and Environmental Microbiology ◽

10.1128/aem.02103-07 ◽

2007 ◽

Vol 74 (5) ◽

pp. 1546-1554 ◽

Cited By ~ 33

Author(s):

Huan Zhang ◽

Debashish Bhattacharya ◽

Lucie Maranda ◽

Senjie Lin

Keyword(s):

Flow Cytometry ◽

Phylogenetic Trees ◽

Gene Tree ◽

Narragansett Bay ◽

Bootstrap Support ◽

Phylogenetic Position ◽

Data Set ◽

Specific Pcr ◽

Dinophysis Acuminata ◽

Unbiased Test

ABSTRACT Dinophysis acuminata cells were isolated from Narragansett Bay water samples in June 2005 using flow cytometry. Dinoflagellate-specific PCR primers were used to isolate small-subunit rRNA (18S rRNA), mitochondrial cytochrome b (cob), and cytochrome c oxidase I (cox1) genes and the encoded cDNAs. Maximum-likelihood analysis of a concatenated data set of ribosomal DNA and cDNA sequences of cob and cox1 showed that D. acuminata was sister to Gonyaulacoids, but without strong bootstrap support. The approximately unbiased test could not reject alternative positions of D. acuminata. To gain better resolution, mRNA editing of cob and cox1 was inferred for D. acuminata and 13 other dinoflagellate species. The location and type of editing as well as the distribution pattern in D. acuminata were generally similar to those in other dinoflagellates except for two edited sites that are unique to this species. Bayesian analyses of a matrix that recorded the location and type of editing, and of a matrix that included the protein sequences of COB and COX1 with the editing data yielded tree topologies similar to the three-gene tree but again failed to resolve the phylogenetic position of D. acuminata. However, the density of edited sites in the D. acuminata mitochondrial genes, consistent with phylogenetic trees, indicated that Dinophysis is a derived dinoflagellate lineage, diverging after other lineages such as Oxyrrhis, Amphidinium, and Symbiodinium. We demonstrate that dinoflagellate-specific PCR coupled with flow cytometry can be a useful tool to analyze genes and their transcripts from a natural dinoflagellate population.

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Assessment of the TROPOMI tropospheric NO<sub>2</sub> product based on airborne APEX observations

Atmospheric Measurement Techniques ◽

10.5194/amt-14-615-2021 ◽

2021 ◽

Vol 14 (1) ◽

pp. 615-646

Author(s):

Frederik Tack ◽

Alexis Merlaud ◽

Marian-Daniel Iordache ◽

Gaia Pinardi ◽

Ermioni Dimitropoulou ◽

...

Keyword(s):

Remote Sensing ◽

Transport Model ◽

Absolute Difference ◽

Time Interval ◽

Short Time Interval ◽

Vertical Column ◽

Data Set ◽

Urban Regions ◽

Tropospheric No2 ◽

The Impact

Abstract. Sentinel-5 Precursor (S-5P), launched in October 2017, carrying the TROPOspheric Monitoring Instrument (TROPOMI) nadir-viewing spectrometer, is the first mission of the Copernicus Programme dedicated to the monitoring of air quality, climate, and ozone. In the presented study, the TROPOMI tropospheric nitrogen dioxide (NO2) level-2 (L2) product (OFFL v1.03.01; 3.5 km × 7 km at nadir observations) has been validated over strongly polluted urban regions by comparison with coincident high-resolution Airborne Prism EXperiment (APEX) remote sensing observations (∼ 75 m × 120 m). Satellite products can be optimally assessed based on (APEX) airborne remote sensing observations, as a large amount of satellite pixels can be fully mapped at high accuracy and in a relatively short time interval, reducing the impact of spatiotemporal mismatches. In the framework of the S-5P validation campaign over Belgium (S5PVAL-BE), the APEX imaging spectrometer has been deployed during four mapping flights (26–29 June 2019) over the two largest urban regions in Belgium, i.e. Brussels and Antwerp, in order to map the horizontal distribution of tropospheric NO2. For each flight, 10 to 20 TROPOMI pixels were fully covered by approximately 2700 to 4000 APEX measurements within each TROPOMI pixel. The TROPOMI and APEX NO2 vertical column density (VCD) retrieval schemes are similar in concept. Overall, for the ensemble of the four flights, the standard TROPOMI NO2 VCD product is well correlated (R = 0.92) but biased negatively by −1.2 ± 1.2 × 1015 molec cm−2 or −14 ± 12 %, on average, with respect to coincident APEX NO2 retrievals. When replacing the coarse 1∘ × 1∘ the massively parallel (MP) version of the Tracer Model version 5 (TM5) a priori NO2 profiles by NO2 profile shapes from the Copernicus Atmospheric Monitoring Service (CAMS) regional chemistry transport model (CTM) ensemble at 0.1∘ × 0.1∘, R is 0.94 and the slope increases from 0.82 to 0.93. The bias is reduced to −0.1 ± 1.0 × 1015 molec cm−2 or −1.0 ± 12 %. The absolute difference is on average 1.3 × 1015 molec cm−2 (16 %) and 0.7 × 1015 molec cm−2 (9 %), when comparing APEX NO2 VCDs with TM5-MP-based and CAMS-based NO2 VCDs, respectively. Both sets of retrievals are well within the mission accuracy requirement of a maximum bias of 25 %–50 % for the TROPOMI tropospheric NO2 product for all individual compared pixels. Additionally, the APEX data set allows the study of TROPOMI subpixel variability and impact of signal smoothing due to its finite satellite pixel size, typically coarser than fine-scale gradients in the urban NO2 field. For a case study in the Antwerp region, the current TROPOMI data underestimate localized enhancements and overestimate background values by approximately 1–2 × 1015 molec cm−2 (10 %–20 %).

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New Hosts ofSimplicimonas similisandTrichomitus batrachorumIdentified by 18S Ribosomal RNA Gene Sequences

Journal of Parasitology Research ◽

10.1155/2013/831947 ◽

2013 ◽

Vol 2013 ◽

pp. 1-5 ◽

Cited By ~ 2

Author(s):

Kris Genelyn B. Dimasuay ◽

Orlie John Y. Lavilla ◽

Windell L. Rivera

Keyword(s):

Phylogenetic Trees ◽

18S Rrna ◽

18S Rrna Gene ◽

Bootstrap Support ◽

Rrna Gene ◽

Gene Sequences ◽

Pathogenic Potential ◽

Gene Sequence Analysis ◽

High Bootstrap ◽

Recent Classification

Trichomonads are obligate anaerobes generally found in the digestive and genitourinary tract of domestic animals. In this study, four trichomonad isolates were obtained from carabao, dog, and pig hosts using rectal swab. Genomic DNA was extracted using Chelex method and the 18S rRNA gene was successfully amplified through novel sets of primers and undergone DNA sequencing. Aligned isolate sequences together with retrieved 18S rRNA gene sequences of known trichomonads were utilized to generate phylogenetic trees using maximum likelihood and neighbor-joining analyses. Two isolates from carabao were identified asSimplicimonas similiswhile each isolate from dog and pig was identified asPentatrichomonas hominisandTrichomitus batrachorum, respectively. This is the first report ofS. similisin carabao and the identification ofT. batrachorumin pig using 18S rRNA gene sequence analysis. The generated phylogenetic tree yielded three distinct groups mostly with relatively moderate to high bootstrap support and in agreement with the most recent classification. Pathogenic potential of the trichomonads in these hosts still needs further investigation.

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On Multiple Access of a Large Number of Machine-Type Devices in Cellular Networks

Information and Control Systems ◽

10.31799/1684-8853-2018-4-105-114 ◽

2018 ◽

pp. 105-114

Author(s):

O. S. Galinina ◽

S. D. Andreev ◽

A. M. Tyurlikov

Keyword(s):

Success Probability ◽

Random Access ◽

Time Interval ◽

Short Time Interval ◽

Control Mechanisms ◽

Network Access ◽

Smart Meters ◽

Machine To Machine ◽

Machine To Machine Communication ◽

Machine Communication

Introduction: Machine-to-machine communication assumes data transmission from various wireless devices and attracts attention of cellular operators. In this regard, it is crucial to recognize and control overload situations when a large number of such devices access the network over a short time interval.Purpose:Analysis of the radio network overload at the initial network entry stage in a machine-to-machine communication system.Results: A system is considered that features multiple smart meters, which may report alarms and autonomously collect energy consumption information. An analytical approach is proposed to study the operation of a large number of devices in such a system as well as model the settings of the random-access protocol in a cellular network and overload control mechanisms with respect to the access success probability, network access latency, and device power consumption. A comparison between the obtained analytical results and simulation data is also offered.

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