Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

Abstract Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-19 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, with limited progress. Here we applied phylogenetic supertree analysis to study the origin and evolution of SARS-CoV-2. Phylogenetic supertree analysis firmly disputes the accuracy of bat coronavirus RaTG13 be the last common ancestor of SARS- CoV-2s reported in other phylogenetic tree analysis based on viral genome sequences, although RaTG13 shows 96.5% similarity with SARS-CoV-2 in the genome. Therefore, viewing RaTG13 as the last common ancestor of SARS-CoV-2 would seriously mislead phylogenetic inference of SARS-CoV-2. Importantly, the discovery of evolution and mutation in SARS-CoV-2s was achieved by phylogenetic supertree analysis. Taken together, the phylogenetic supertree showed extraordinary priority on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

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Phylogenetic supertree reveals detailed evolution of SARS-CoV-2

Scientific Reports ◽

10.1038/s41598-020-79484-8 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Tingting Li ◽

Dongxia Liu ◽

Yadi Yang ◽

Jiali Guo ◽

Yujie Feng ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Tree ◽

Virus Disease ◽

Evolutionary Relationship ◽

Critical Issue ◽

Last Common Ancestor ◽

Phylogenetic Tree Analysis ◽

Origin And Evolution ◽

Supertree Method ◽

The Matrix

AbstractCorona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.

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Recombinant transfer in the basic genome ofEscherichia coli

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1510839112 ◽

2015 ◽

Vol 112 (29) ◽

pp. 9070-9075 ◽

Cited By ~ 59

Author(s):

Purushottam D. Dixit ◽

Tin Yau Pang ◽

F. William Studier ◽

Sergei Maslov

Keyword(s):

Common Ancestor ◽

Recipient Cell ◽

Gene Clusters ◽

Selective Advantage ◽

Last Common Ancestor ◽

Genome Sequences ◽

Bacterial Genomes ◽

Basic Genome ◽

Single Base Pair ◽

Generalized Transduction

An approximation to the ∼4-Mbp basic genome shared by 32 strains ofEscherichia colirepresenting six evolutionary groups has been derived and analyzed computationally. A multiple alignment of the 32 complete genome sequences was filtered to remove mobile elements and identify the most reliable ∼90% of the aligned length of each of the resulting 496 basic-genome pairs. Patterns of single base-pair mutations (SNPs) in aligned pairs distinguish clonally inherited regions from regions where either genome has acquired DNA fragments from diverged genomes by homologous recombination since their last common ancestor. Such recombinant transfer is pervasive across the basic genome, mostly between genomes in the same evolutionary group, and generates many unique mosaic patterns. The six least-diverged genome pairs have one or two recombinant transfers of length ∼40–115 kbp (and few if any other transfers), each containing one or more gene clusters known to confer strong selective advantage in some environments. Moderately diverged genome pairs (0.4–1% SNPs) show mosaic patterns of interspersed clonal and recombinant regions of varying lengths throughout the basic genome, whereas more highly diverged pairs within an evolutionary group or pairs between evolutionary groups having >1.3% SNPs have few clonal matches longer than a few kilobase pairs. Many recombinant transfers appear to incorporate fragments of the entering DNA produced by restriction systems of the recipient cell. A simple computational model can closely fit the data. Most recombinant transfers seem likely to be due to generalized transduction by coevolving populations of phages, which could efficiently distribute variability throughout bacterial genomes.

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Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera

Genome Biology and Evolution ◽

10.1093/gbe/evaa106 ◽

2020 ◽

Vol 12 (7) ◽

pp. 1099-1188

Author(s):

Jan Philip Oeyen ◽

Patrice Baa-Puyoulet ◽

Joshua B Benoit ◽

Leo W Beukeboom ◽

Erich Bornberg-Bauer ◽

...

Keyword(s):

Species Richness ◽

Transposable Element ◽

Common Ancestor ◽

Odorant Receptors ◽

Last Common Ancestor ◽

Gene Repertoire ◽

Genome Sequences ◽

Reliable Identification ◽

Efficient Detection ◽

Co2 Detection

Abstract The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

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Phylogenetic Analysis of Spike and Envelope Proteins for a Number of Bat Coronaviruses for Understanding the Hypothesis of Possible Origin for the Novel 2019-nCoV

Kurdistan Journal of Applied Research ◽

10.24017/science.2020.ichms2020.15 ◽

2020 ◽

pp. 137-144

Author(s):

Salar Ibrahim Ali

Keyword(s):

Hong Kong ◽

Amino Acid ◽

Amino Acid Sequence ◽

Phylogenetic Tree ◽

Envelope Protein ◽

Spike Protein ◽

Phylogenetic Tree Analysis ◽

Tree Analysis ◽

Close Relationship ◽

Bat Coronavirus

Coronavirus Disease 19 (COVID-19) emergence reveals globally a great health issue and due to the limited information and knowledge on the origin of this novel coronavirus 2019 (2019-nCoV). Therefore, this study aims to investigate the evolution and analysis of molecular epidemiology for both Spike and Envelope proteins of 20 available complete genome sequences of different bat coronaviruses including 2019-nCoV in order to find out which type of bat coronaviruses is more likely to be the origin of this new 2019-nCoV and also multiple amino acid sequences of Envelope protein for all bat coronaviruses were aligned for the purpose of finding the greater probability of novel 2019-nCoV original host among bat coronaviruses. Phylogenetic tree analysis for Spike protein revealed that all 2019-nCoV related coronaviruses isolated from these species of species are discovered in China and Hong Kong and the Middle East bat are less likely to contribute in spreading or to become the origin of 2019-nCoV and all coronaviruses that from Hong Kong and China are located into one clade next to the clade that contains 2019-nCoV coronaviruses which indicates that this group of coronaviruses are genetically different for 2019-nCoV; moreover, Hong Kong and USA bat coronaviruses does not contain the bat coronavirus from China and are located into one clade far from the clade that contains 2019-nCoV indicates that all coronaviruses are genetically very different from 2019-nCoV, and USA bat coronavirus may has no role in generating of 2019-nCoV. The phylogenetic trees analysis of Envelope protein showed that Envelope protein of different coronaviruses are more similar in comparison to Spike protein, USA bat coronavirus has a relatively closeness relationship to 2019-nCoV. Furthermore, Envelope protein alignment showed the closely related amino acid sequence which confirms that the outcomes of phylogenetic tree analysis in which that these bat coronaviruses have genetically close relationship together and more interestingly amino acid sequence (MG772934.1) shows 100% identity with the amino acid sequence of 2019-nCoV (NC 045512.2) and the same virus has a close relationship in both Spike and Envelope due to that in both phylogenetic tree analysis are neighbored with 2019-nCoV in the same clade.

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Bacterial proteins pinpoint a single eukaryotic root

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1420657112 ◽

2015 ◽

Vol 112 (7) ◽

pp. E693-E699 ◽

Cited By ~ 100

Author(s):

Romain Derelle ◽

Guifré Torruella ◽

Vladimír Klimeš ◽

Henner Brinkmann ◽

Eunsoo Kim ◽

...

Keyword(s):

Common Ancestor ◽

Innovative Approach ◽

Phylogenetic Position ◽

Last Common Ancestor ◽

Phylogenetic Distance ◽

Genome Sequences ◽

Bacterial Proteins ◽

Eukaryotic Genes

The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between “Unikonta” and “Bikonta,” with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.

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Origin and Evolution of Water Oxidation before the Last Common Ancestor of the Cyanobacteria

Molecular Biology and Evolution ◽

10.1093/molbev/msv024 ◽

2015 ◽

Vol 32 (5) ◽

pp. 1310-1328 ◽

Cited By ~ 63

Author(s):

Tanai Cardona ◽

James W. Murray ◽

A. William Rutherford

Keyword(s):

Water Oxidation ◽

Common Ancestor ◽

Last Common Ancestor ◽

Origin And Evolution

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Phylogenetic analyses and genomic variation of the 2019-nCoV

Journal of Pharmaceutical and Biopharmaceutical Research ◽

10.25082/jpbr.2020.01.004 ◽

2020 ◽

Vol 2 (1) ◽

pp. 126-130

Author(s):

Faiz Ul Haq ◽

◽

Sidrah Saleem ◽

Muhammad Imran ◽

Ayesha Ghazal ◽

...

Keyword(s):

Phylogenetic Tree ◽

Sequence Similarity ◽

Phylogenetic Analyses ◽

Genomic Analysis ◽

Genomic Variation ◽

Molecular Characteristics ◽

Phylogenetic Tree Analysis ◽

High Sequence Similarity ◽

Human Environment ◽

Bat Coronavirus

There is a rising global concern about the SARS CoV-2 as a public health threat. Complete genome sequence have been released by the worldwide scientific community for understanding the molecular characteristics and evolutionary origin of this virus. Aim of the current context is to present phylogenetic relationship and genomic variation of 2019-nCoV. Based on availability of genomic information, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Middle East respiratory syndrome, severe acute respiratory syndrome and Bat coronavirus. The phylogenetic tree analysis suggested that SARS CoV-2 significantly clustered with bat SARS like coronavirus genome, however structural analysis revealed mutation in Spike Glycoprotein and nucleocapsid protein. However our phylogenetic and genomic analysis suggests that bats can be the reservoir for this virus. Lack of forest might be the fact in association of bats with human environment. It is also difficult to study on bats due to absence of proper reagent and availability of few species for research. We confirm high sequence similarity (>99%) among sequenced SARS CoV-2 genomes, and 96% genome identity with the bat coronavirus, confirming the notion of a zoonotic origin of SARS CoV-2.

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What have the revelations about Neanderthal DNA revealed about Homo sapiens?

Anthropological Review ◽

10.2478/anre-2020-0008 ◽

2020 ◽

Vol 83 (1) ◽

pp. 93-107

Author(s):

Santiago Wolnei Ferreira Guimarães ◽

Hilton P. Silva

Keyword(s):

Gene Flow ◽

Morphological Traits ◽

Common Ancestor ◽

Homo Sapiens ◽

Explanatory Models ◽

The Other ◽

Last Common Ancestor ◽

Genetic Studies ◽

Origin And Evolution ◽

Out Of Africa

AbstractGenetic studies have presented increasing indications about the complexity of the interactions between Homo sapiens, Neanderthals and Denisovans, during Pleistocene. The results indicate potential replacement or admixture of the groups of hominins that lived in the same region at different times. Recently, the time of separation among these hominins in relation to the Last Common Ancestor – LCA has been reasonably well established. Events of mixing with emphasis on the Neanderthal gene flow into H. sapiens outside Africa, Denisovans into H. sapiens ancestors in Oceania and continental Asia, Neanderthals into Denisovans, as well as the origin of some phenotypic features in specific populations such as the color of the skin, eyes, hair and predisposition to develop certain kinds of diseases have also been found. The current information supports the existence of both replacement and interbreeding events, and indicates the need to revise the two main explanatory models, the Multiregional and the Out-of-Africa hypotheses, about the origin and evolution of H. sapiens and its co-relatives. There is definitely no longer the possibility of justifying only one model over the other. This paper aims to provide a brief review and update on the debate around this issue, considering the advances brought about by the recent genetic as well as morphological traits analyses.

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Genome sequences reveal divergence times of malaria parasite lineages

Parasitology ◽

10.1017/s0031182010001575 ◽

2010 ◽

Vol 138 (13) ◽

pp. 1737-1749 ◽

Cited By ~ 34

Author(s):

JOANA C. SILVA ◽

AMY EGAN ◽

ROBERT FRIEDMAN ◽

JAMES B. MUNRO ◽

JANE M. CARLTON ◽

...

Keyword(s):

Evolutionary History ◽

Common Ancestor ◽

Orthologous Gene ◽

The Other ◽

Divergence Times ◽

Last Common Ancestor ◽

Genome Sequences ◽

Malaria Parasites ◽

Human Malaria ◽

History Of

SUMMARYObjectiveThe evolutionary history of human malaria parasites (genus Plasmodium) has long been a subject of speculation and controversy. The complete genome sequences of the two most widespread human malaria parasites, P. falciparum and P. vivax, and of the monkey parasite P. knowlesi are now available, together with the draft genomes of the chimpanzee parasite P. reichenowi, three rodent parasites, P. yoelii yoelli, P. berghei and P. chabaudi chabaudi, and one avian parasite, P. gallinaceum.MethodsWe present here an analysis of 45 orthologous gene sequences across the eight species that resolves the relationships of major Plasmodium lineages, and provides the first comprehensive dating of the age of those groups.ResultsOur analyses support the hypothesis that the last common ancestor of P. falciparum and the chimpanzee parasite P. reichenowi occurred around the time of the human-chimpanzee divergence. P. falciparum infections of African apes are most likely derived from humans and not the other way around. On the other hand, P. vivax, split from the monkey parasite P. knowlesi in the much more distant past, during the time that encompasses the separation of the Great Apes and Old World Monkeys.ConclusionThe results support an ancient association between malaria parasites and their primate hosts, including humans.

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Cytoskeletal architecture and its evolutionary significance in amoeboid eukaryotes and their mode of locomotion

Royal Society Open Science ◽

10.1098/rsos.160283 ◽

2016 ◽

Vol 3 (9) ◽

pp. 160283 ◽

Cited By ~ 7

Author(s):

Yonas I. Tekle ◽

Jessica R. Williams

Keyword(s):

Common Ancestor ◽

Granular Cell ◽

Evolutionary Significance ◽

Last Common Ancestor ◽

Eukaryotic Evolution ◽

Potential Significance ◽

Origin And Evolution ◽

Cellular Processes ◽

Diverse Groups ◽

First Time

The cytoskeleton is the hallmark of eukaryotic evolution. The molecular and architectural aspects of the cytoskeleton have been playing a prominent role in our understanding of the origin and evolution of eukaryotes. In this study, we seek to investigate the cytoskeleton architecture and its evolutionary significance in understudied amoeboid lineages belonging to Amoebozoa. These amoebae primarily use cytoplasmic extensions supported by the cytoskeleton to perform important cellular processes such as movement and feeding. Amoeboid structure has important taxonomic significance, but, owing to techniques used, its potential significance in understanding diversity of the group has been seriously compromised, leading to an under-appreciation of its value. Here, we used immunocytochemistry and confocal microscopy to study the architecture of microtubules (MTs) and F-actin in diverse groups of amoebae. Our results demonstrate that all Amoebozoa examined are characterized by a complex cytoskeletal array, unlike what has been previously thought to exist. Our results not only conclusively demonstrate that all amoebozoans possess complex cytoplasmic MTs, but also provide, for the first time, a potential synapomorphy for the molecularly defined Amoebozoa clade. Based on this evidence, the last common ancestor of amoebozoans is hypothesized to have had a complex interwoven MT architecture limited within the granular cell body. We also generate several cytoskeleton characters related to MT and F-actin, which are found to be robust for defining groups in deep and shallow nodes of Amoebozoa.

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