Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis

Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies and the other that diversifies. Here, we propose a biphasic (bow-tie) theory of module emergence. In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels. Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism, elementary functionomes, and protein domain organization.

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Agromyces humi sp. nov., actinobacterium isolated from farm soil

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004376 ◽

2020 ◽

Vol 70 (9) ◽

pp. 5032-5039 ◽

Cited By ~ 3

Author(s):

Jae-Chan Lee ◽

Kyung-Sook Whang

Keyword(s):

Type Species ◽

Phylogenomic Analysis ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Gene Sequence Analysis ◽

Phyletic Line ◽

Phylogenomic Analyses ◽

The 16S Rrna Gene ◽

Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated ANK073T, was isolated from rhizosphere soil sampled at a spinach farming field in Shinan, Republic of Korea. Cells of strain ANK073T were found to be aerobic, non-motile, non-spore-forming rods which could grow at 20–40 °C (optimum, 30 °C), at pH 6.0–10.0 (optimum, pH 6.5–7.5) and at salinities of 0–4 % (w/v) NaCl (optimum, 0 % NaCl). The 16S rRNA gene sequence analysis showed that strain ANK073T belongs to the genus Agromyces with high sequence similarities to Agromyces humatus CD5T (98.8 %), Agromyces tardus SJ-23T (98.5 %) and Agromyces iriomotensis IY07-20T (98.4 %). The phylogenetic analysis indicated that strain ANK073T formed a distinct phyletic line in the genus Agromyces and the results of DNA–DNA relatedness and phylogenomic analysis based on whole genome sequences demonstrated that strain ANK073T could be separated from its closest relatives in the genus Agromyces . The strain contained 2,4-diaminobutylic acid, glycine, d-glutamic acid and d-alanine in the peptidoglycan. The predominant menaquinones were identified as MK-12 and MK-11, and the major fatty acids were anteiso-C17 : 0, anteiso-C15 : 0 and iso-C15:0. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The G+C content of the genome was determined to be 70.2 mol%. On the basis of its phenotypic and chemotaxonomic properties and the results of phylogenetic and phylogenomic analyses, strain ANK073T is considered to represent a novel species in the genus Agromyces , for which the name Agromyces humi sp. nov. is proposed. The type strain is ANK073T (=KACC 18683T=NBRC 111825T).

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Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.003973 ◽

2020 ◽

Vol 70 (3) ◽

pp. 1785-1792 ◽

Cited By ~ 6

Author(s):

Jae-Chan Lee ◽

Kyung-Sook Whang

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenomic Analysis ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

The Family ◽

Diamino Acid ◽

Phylogenomic Analyses ◽

Sequence Similarities

A Gram-stain-positive actinobacterial strain, designated YJ01T, was isolated from a spinach farming field soil at Shinan in Korea. Strain YJ01T was aerobic, non-motile, non-spore-forming cocci with diameters of 1.5–1.9 µm, and was able to grow at 10–37 °C (optimum, 28–30 °C), at pH 4.5–9.0 (optimum, pH 7.0–8.0) and at salinities of 0–7.5 % (w/v) NaCl (optimum, 1.0 % NaCl). Sequence similarities of the 16S rRNA gene of strain YJ01T with closely related relatives were in the range 96.2–92.8 %, and the results of phylogenomic analysis indicated that strain YJ01T was clearly separated from species of genera in the family Intrasporangiaceae showing average nucleotide identity values of 84.2–83.4 %. The predominant isoprenoid quinone was identified as MK-8(H4) and the major fatty acids were iso-C15 : 0, iso-C16:1 h, iso-C16 : 0 and anteiso-C17 : 1ω9c. The diagnostic diamino acid of the peptidoglycan was ornithine, and the interpeptide bridge was l-Orn–Gly2–d-Glu. The major polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylserine, an unidentified phosphatidylglycolipid, two unidentified phosphoaminolipids and an unidentified phosphoglycoaminolipid. The G+C content of the genome was 70.1 mol%. On the basis of phenotypic and chemotaxonomic properties and phylogenetic and phylogenomic analyses using 16S rRNA gene sequences and whole-genome sequences, strain YJ01T is considered to represent a novel species of a new genus in the family Intrasporangiaceae , for which the name Segeticoccus rhizosphaerae gen. nov. sp. nov. is proposed. The type strain of Segeticoccus rhizosphaerae is YJ01T (=KACC 19547T=NBRC 113173T).

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Phylogenomic analyses confirm a novel invasive North American Corbicula (Bivalvia: Cyrenidae) lineage

PeerJ ◽

10.7717/peerj.7484 ◽

2019 ◽

Vol 7 ◽

pp. e7484 ◽

Cited By ~ 2

Author(s):

Amanda E. Haponski ◽

Diarmaid Ó Foighil

Keyword(s):

New World ◽

Genomic Structure ◽

Initial Study ◽

Illinois River ◽

Phylogenomic Analysis ◽

Tropical Regions ◽

Population Genomic ◽

Sequencing Method ◽

Freshwater Clams ◽

Phylogenomic Analyses

The genus Corbicula consists of estuarine or freshwater clams native to temperate/tropical regions of Asia, Africa, and Australia that collectively encompass both sexual species and clonal (androgenetic) lineages. The latter have become globally invasive in freshwater systems and they represent some of the most successful aquatic invasive lineages. Previous studies have documented four invasive clonal lineages, Forms A, B, C, and Rlc, with varying known distributions. Form A (R in Europe) occurs globally, Form B is found solely in North America, mainly the western United States, Form C (S in Europe) occurs both in European watersheds and in South America, and Rlc is known from Europe. A putative fifth invasive morph, Form D, was recently described in the New World from the Illinois River (Great Lakes watershed), where it occurs in sympatry with Forms A and B. An initial study showed Form D to be conchologically distinct: possessing rust-colored rays and white nacre with purple teeth. However, its genetic distinctiveness using standard molecular markers (mitochondrial cytochrome c oxidase subunit I and nuclear ribosomal 28S RNA) was ambiguous. To resolve this issue, we performed a phylogenomic analysis using 1,699–30,027 nuclear genomic loci collected via the next generation double digested restriction-site associated DNA sequencing method. Our results confirmed Form D to be a distinct invasive New World lineage with a population genomic profile consistent with clonality. A majority (7/9) of the phylogenomic analyses recovered the four New World invasive Corbicula lineages (Forms A, B, C, and D) as members of a clonal clade, sister to the non-clonal Lake Biwa (Japan) endemic, Corbicula sandai. The age of the clonal clade was estimated at 1.49 million years (my; ± 0.401–2.955 my) whereas the estimated ages of the four invasive lineage crown clades ranged from 0.27 to 0.44 my. We recovered very little evidence of nuclear genomic admixture among the four invasive lineages in our study populations. In contrast, 2/6 C. sandai individuals displayed partial nuclear genomic Structure assignments with multiple invasive clonal lineages. These results provide new insights into the origin and maintenance of clonality in this complex system.

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Phylogenomics of parasitic and non-parasitic lice (Insecta: Psocodea): Combining sequence data and Exploring compositional bias solutions in Next Generation Datasets

Systematic Biology ◽

10.1093/sysbio/syaa075 ◽

2020 ◽

Cited By ~ 1

Author(s):

Robert S de Moya ◽

Kazunori Yoshizawa ◽

Kimberly K O Walden ◽

Andrew D Sweet ◽

Christopher H Dietrich ◽

...

Keyword(s):

Sequence Data ◽

Compositional Bias ◽

Phylogenomic Analysis ◽

Data Set ◽

Genomic Changes ◽

Insect Order ◽

Codon Positions ◽

Phylogenomic Analyses ◽

Ordinal Level ◽

Likelihood Mapping

Abstract The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.

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New Phylogenomic Analysis of the Enigmatic Phylum Telonemia Further Resolves the Eukaryote Tree of Life

Molecular Biology and Evolution ◽

10.1093/molbev/msz012 ◽

2019 ◽

Vol 36 (4) ◽

pp. 757-765 ◽

Cited By ~ 32

Author(s):

Jürgen F H Strassert ◽

Mahwash Jamy ◽

Alexander P Mylnikov ◽

Denis V Tikhonenkov ◽

Fabien Burki

Keyword(s):

Phylogenetic Signal ◽

Evolutionary Origin ◽

Phylogenetic Position ◽

Aquatic Environments ◽

Phylogenomic Analysis ◽

Data Sets ◽

Transcriptome Data ◽

Phylogenetic Reconstructions ◽

Phylogenomic Analyses ◽

Alignment Length

AbstractThe resolution of the broad-scale tree of eukaryotes is constantly improving, but the evolutionary origin of several major groups remains unknown. Resolving the phylogenetic position of these “orphan” groups is important, especially those that originated early in evolution, because they represent missing evolutionary links between established groups. Telonemia is one such orphan taxon for which little is known. The group is composed of molecularly diverse biflagellated protists, often prevalent although not abundant in aquatic environments. Telonemia has been hypothesized to represent a deeply diverging eukaryotic phylum but no consensus exists as to where it is placed in the tree. Here, we established cultures and report the phylogenomic analyses of three new transcriptome data sets for divergent telonemid lineages. All our phylogenetic reconstructions, based on 248 genes and using site-heterogeneous mixture models, robustly resolve the evolutionary origin of Telonemia as sister to the Sar supergroup. This grouping remains well supported when as few as 60% of the genes are randomly subsampled, thus is not sensitive to the sets of genes used but requires a minimal alignment length to recover enough phylogenetic signal. Telonemia occupies a crucial position in the tree to examine the origin of Sar, one of the most lineage-rich eukaryote supergroups. We propose the moniker “TSAR” to accommodate this new mega-assemblage in the phylogeny of eukaryotes.

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Flux-based classification of reactions reveals a functional bow-tie organization of complex metabolic networks

Physical Review E ◽

10.1103/physreve.87.052708 ◽

2013 ◽

Vol 87 (5) ◽

Cited By ~ 5

Author(s):

Shalini Singh ◽

Areejit Samal ◽

Varun Giri ◽

Sandeep Krishna ◽

Nandula Raghuram ◽

...

Keyword(s):

Metabolic Networks ◽

Bow Tie

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Evolution of Networks of Protein Domain Organization

10.21203/rs.3.rs-119891/v1 ◽

2020 ◽

Author(s):

M. Fayez Aziz ◽

Gustavo Caetano-Anollés

Keyword(s):

Dna Binding ◽

Protein Function ◽

Preferential Attachment ◽

Big Bang ◽

Binding Activity ◽

Protein Domain ◽

Domain Organization ◽

Evolving Networks ◽

Dna Binding Activity

Abstract Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. These networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity of networks showed yin-and-yang complementary transition patterns along the evolutionary timeline. Remarkably, evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis (NRPS) pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.

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Comparative genomics and characterization of SARS-CoV-2 P.1 (Gamma) Variant of Concern (VOC) from Amazonas, Brazil

10.1101/2021.10.30.21265694 ◽

2021 ◽

Author(s):

Ricardo Ariel Zimerman ◽

Patricia Aline Grohs Ferrareze ◽

Flavio Adsuara Cadegiani ◽

Carlos Gustavo Wambier ◽

Daniel do Nascimento Fonseca ◽

...

Keyword(s):

Neutralizing Antibodies ◽

Phylogenetic Analyses ◽

Illumina Miseq ◽

The State ◽

Likelihood Method ◽

Phylogenomic Analysis ◽

Structural Protein ◽

Evolutionary Forces ◽

Multiple Alignments ◽

Phylogenomic Analyses

Background: P.1 lineage (Gamma) was first described in the State of Amazonas, northern Brazil, in the end of 2020, and has emerged as a very important variant of concern (VOC) of SARS-CoV-2 worldwide. P.1 has been linked to increased infectivity, higher mortality and immune evasion, leading to reinfections and potentially reduced efficacy of vaccines and neutralizing antibodies. Methods: The samples of 276 patients from the State of Amazonas were sent to a central referral laboratory for sequencing by gold standard techniques, through Illumina MiSeq platform. Both global and regional phylogenetic analyses of the successfully sequenced genomes were conducted through maximum likelihood method. Multiple alignments were obtained including previously obtained unique human SARS-CoV-2 sequences. The evolutionary histories of spike and non-structural proteins from ORF1a of northern genomes were described and their molecular evolution was analyzed for detection of positive (FUBAR, FEL, and MEME) and negative (FEL and SLAC) selective pressures. To further evaluate the possible pathways of evolution leading to the emergence of P.1, we performed specific analysis for copy-choice recombination events. A global phylogenomic analysis with subsampled P.1 and B.1.1.28 genomes was applied to evaluate the relationship among samples. Results: Forty-four samples from the State of Amazonas were successfully sequenced and confirmed as P.1 (Gamma) lineage. In addition to previously described P.1 characteristic mutations, we find evidence of continuous diversification of SARS-CoV-2, as rare and previously unseen P.1 mutations were detected in spike and non-structural protein from ORF1a. No evidence of recombination was found. Several sites were demonstrated to be under positive and negative selection, with various mutations identified mostly in P.1 lineage. According to the Pango assignment, phylogenomic analyses indicate all samples as belonging to the P.1 lineage. Conclusion: P.1 has shown continuous evolution after its emergence. The lack of clear evidence for recombination and the positive selection demonstrated for several sites suggest that this lineage emergence resulted mainly from strong evolutionary forces and progressive accumulation of a favorable signature set of mutations.

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Phylogenomic analysis of the Chilean clade ofLiolaemuslizards (Squamata: Liolaemidae) based on sequence capture data

PeerJ ◽

10.7717/peerj.3941 ◽

2017 ◽

Vol 5 ◽

pp. e3941 ◽

Cited By ~ 7

Author(s):

Alejandra Panzera ◽

Adam D. Leaché ◽

Guillermo D’Elía ◽

Pedro F. Victoriano

Keyword(s):

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Strong Support ◽

Taxon Sampling ◽

Phylogenomic Analysis ◽

Molecular Systematic ◽

Data Set ◽

Protein Coding ◽

Protein Coding Genes ◽

Phylogenomic Analyses

The genusLiolaemusis one of the most ecologically diverse and species-rich genera of lizards worldwide. It currently includes more than 250 recognized species, which have been subject to many ecological and evolutionary studies. Nevertheless,Liolaemuslizards have a complex taxonomic history, mainly due to the incongruence between morphological and genetic data, incomplete taxon sampling, incomplete lineage sorting and hybridization. In addition, as many species have restricted and remote distributions, this has hampered their examination and inclusion in molecular systematic studies. The aims of this study are to infer a robust phylogeny for a subsample of lizards representing the Chilean clade (subgenusLiolaemus sensu stricto), and to test the monophyly of several of the major species groups. We use a phylogenomic approach, targeting 541 ultra-conserved elements (UCEs) and 44 protein-coding genes for 16 taxa. We conduct a comparison of phylogenetic analyses using maximum-likelihood and several species tree inference methods. The UCEs provide stronger support for phylogenetic relationships compared to the protein-coding genes; however, the UCEs outnumber the protein-coding genes by 10-fold. On average, the protein-coding genes contain over twice the number of informative sites. Based on our phylogenomic analyses, all the groups sampled are polyphyletic.Liolaemus tenuis tenuisis difficult to place in the phylogeny, because only a few loci (nine) were recovered for this species. Topologies or support values did not change dramatically upon exclusion ofL. t. tenuisfrom analyses, suggesting that missing data did not had a significant impact on phylogenetic inference in this data set. The phylogenomic analyses provide strong support for sister group relationships betweenL. fuscus,L. monticola,L. nigroviridisandL. nitidus, andL. plateiandL. velosoi. Despite our limited taxon sampling, we have provided a reliable starting hypothesis for the relationships among many major groups of the Chilean clade ofLiolaemusthat will help future work aimed at resolving theLiolaemusphylogeny.

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