Diversity and circulation of Jingmen tick virus in ticks and mammals

Abstract Since its initial identification in ticks in 2010, Jingmen tick virus (JMTV) has been described in cattle, rodents, and primates. To better understand the diversity, evolution, and transmission of JMTV, we sampled 215 ticks, 104 cattle bloods, 216 bats, and 119 rodents in Wenzhou city, Zhejiang Province, China as well as 240 bats from Guizhou and Henan Provinces. JMTV was identified in 107 ticks (from two species), 54 bats (eleven species), 8 rodents (three species), and 10 cattle, with prevalence levels of 49.8, 11.8, 6.7, and 9.6 per cent, respectively, suggesting that bats may be a natural reservoir of JMTV. Phylogenetic analyses revealed that all the newly identified JMTVs were closely related to each other and to previously described viruses. Additionally, all tick and mammalian JMTV sampled in Wenzhou shared a consistent genomic structure, suggesting that the virus can cocirculate between ticks and mammals without observable variation in genome organization. All JMTVs sampled globally could be divided into two phylogenetic groups, Mantel tests suggested that geographic isolation, rather than host species, may be the main driver of JMTV diversity. However, the exact geographical origin of JMTV was difficult to determine, suggesting that this virus has a complex evolutionary history.

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Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa

10.1101/485508 ◽

2018 ◽

Cited By ~ 2

Author(s):

Yuuhiko Tanabe ◽

Haruyo Yamaguchi

Keyword(s):

Evolutionary History ◽

Core Genome ◽

Genomic Organization ◽

Phylogenetic Analyses ◽

Green Light ◽

Water Bloom ◽

Phylogenetic Groups ◽

Genome Phylogeny ◽

History Of ◽

Genomic Basis

AbstractMicrocystis aeruginosais a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, mostM. aeruginosastrains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophylla. Although less common,M. aeruginosastrains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation inM. aeruginosahave only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containingM. aeruginosastrains. Putative PE synthesis and regulation genes (thecpecluster) were identified in all five sequenced genomes as well as in three previously publishedM. aeruginosagenomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence ofccaS/ccaR, a hallmark of type II chromatic adapter, in thecpecluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of thecpecluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced intoM. aeruginosaearly during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE inM. aeruginosa.

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The evolutionary history of Shigella flexneri serotype 6 in Asia

Microbial Genomics ◽

10.1099/mgen.0.000736 ◽

2021 ◽

Vol 7 (12) ◽

Author(s):

Si-Nguyen T. Mai ◽

Ladaporn Bodhidatta ◽

Paul Turner ◽

Sonam Wangchuk ◽

Tuyen Ha Thanh ◽

...

Keyword(s):

Type Species ◽

Evolutionary History ◽

Vaccine Development ◽

Phylogenetic Analyses ◽

Shigella Flexneri ◽

Epidemiological Studies ◽

Genomic Research ◽

Phylogenetic Groups ◽

Content Type ◽

Link Type

Shigella flexneri serotype 6 is an understudied cause of diarrhoeal diseases in developing countries, and has been proposed as one of the major targets for vaccine development against shigellosis. Despite being named as S. flexneri , Shigella flexneri serotype 6 is phylogenetically distinct from other S. flexneri serotypes and more closely related to S. boydii . This unique phylogenetic relationship and its low sampling frequency have hampered genomic research on this pathogen. Herein, by utilizing whole genome sequencing (WGS) and analyses of Shigella flexneri serotype 6 collected from epidemiological studies (1987–2013) in four Asian countries, we revealed its population structure and evolutionary history in the region. Phylogenetic analyses supported the delineation of Asian Shigella flexneri serotype 6 into two phylogenetic groups (PG-1 and −2). Notably, temporal phylogenetic approaches showed that extant Asian S. flexneri serotype 6 could be traced back to an inferred common ancestor arising in the 18th century. The dominant lineage PG-1 likely emerged in the 1970s, which coincided with the times to most recent common ancestors (tMRCAs) inferred from other major Southeast Asian S. flexneri serotypes. Similar to other S. flexneri serotypes in the same period in Asia, genomic analyses showed that resistance to first-generation antimicrobials was widespread, while resistance to more recent first-line antimicrobials was rare. These data also showed a number of gene inactivation and gene loss events, particularly on genes related to metabolism and synthesis of cellular appendages, emphasizing the continuing role of reductive evolution in the adaptation of the pathogen to an intracellular lifestyle. Together, our findings reveal insights into the genomic evolution of the understudied Shigella flexneri serotype 6, providing a new piece in the puzzle of Shigella epidemiology and evolution.

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Global Epidemiology and Evolutionary History of Staphylococcus aureus ST45

Journal of Clinical Microbiology ◽

10.1128/jcm.02198-20 ◽

2020 ◽

Vol 59 (1) ◽

pp. e02198-20

Author(s):

N. Effelsberg ◽

M. Stegger ◽

L. Peitzmann ◽

O. Altinok ◽

G. W. Coombs ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Evolutionary History ◽

De Novo ◽

Clinical Symptoms ◽

Phylogenetic Analyses ◽

Invasive Disease ◽

Phylogenetic Groups ◽

Content Type ◽

Global Epidemiology ◽

History Of

ABSTRACTStaphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage.

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Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

Genome Biology and Evolution ◽

10.1093/gbe/evz155 ◽

2019 ◽

Cited By ~ 4

Author(s):

Sergio A Muñoz-Gómez ◽

Keira Durnin ◽

Laura Eme ◽

Christopher Paight ◽

Christopher E Lane ◽

...

Keyword(s):

Life Style ◽

Metabolic Pathways ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Phylogenetic Position ◽

Biosynthetic Pathways ◽

History Of ◽

Sea Squirts ◽

Shed Light ◽

Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

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Systematic Analysis and Biochemical Characterization of the Caffeoyl Shikimate Esterase Gene Family in Poplar

International Journal of Molecular Sciences ◽

10.3390/ijms222413366 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13366

Author(s):

Xuechun Wang ◽

Nan Chao ◽

Aijing Zhang ◽

Jiaqi Kang ◽

Xiangning Jiang ◽

...

Keyword(s):

Gene Family ◽

Biochemical Characterization ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Lignin Biosynthesis ◽

Phenylpropanoid Pathway ◽

Biochemical Properties ◽

Phylogenetic Groups ◽

Systematic Analysis ◽

A Genome

Caffeoyl shikimate esterase (CSE) hydrolyzes caffeoyl shikimate into caffeate and shikimate in the phenylpropanoid pathway. In this study, we performed a systematic analysis of the CSE gene family and investigated the possible roles of CSE and CSE-like genes in Populus. We conducted a genome-wide analysis of the CSE gene family, including functional and phylogenetic analyses of CSE and CSE-like genes, using the poplar (Populus trichocarpa) genome. Eighteen CSE and CSE-like genes were identified in the Populus genome, and five phylogenetic groups were identified from phylogenetic analysis. CSEs in Group Ia, which were proposed as bona fide CSEs, have probably been lost in most monocots except Oryza sativa. Primary functional classification showed that PoptrCSE1 and PoptrCSE2 had putative function in lignin biosynthesis. In addition, PoptrCSE2, along with PoptrCSE12, might also respond to stress with a function in cell wall biosynthesis. Enzymatic assay of PoptoCSE1 (Populus tomentosa), -2 and -12 showed that PoptoCSE1 and -2 maintained CSE activity. PoptoCSE1 and 2 had similar biochemical properties, tissue expression patterns and subcellular localization. Most of the PoptrCSE-like genes are homologs of AtMAGL (monoacylglycerol lipase) genes in Arabidopsis and may function as MAG lipase in poplar. Our study provides a systematic understanding of this novel gene family and suggests the function of CSE in monolignol biosynthesis in Populus.

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A test statistic to quantify treelikeness in phylogenetics

10.1101/2021.02.16.431544 ◽

2021 ◽

Author(s):

Caitlin Cherryh ◽

Bui Quang Minh ◽

Rob Lanfear

Keyword(s):

Evolutionary History ◽

Incomplete Lineage Sorting ◽

Phylogenetic Analyses ◽

Phylogenetic Network ◽

Parametric Bootstrap ◽

Lineage Sorting ◽

Test Statistic ◽

Sequence Alignments ◽

Wide Range ◽

History Of

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness

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Morphometric and phylogenetic analyses of the Paleozoic Subulitoidea (Gastropoda)

The Paleontological Society Special Publications ◽

10.1017/s2475262200006535 ◽

1992 ◽

Vol 6 ◽

pp. 93-93

Author(s):

Douglas H. Erwin

Keyword(s):

Evolutionary History ◽

Phylogenetic Analyses ◽

Temporal Trends ◽

Thin Sections ◽

Middle Ordovician ◽

Shell Form ◽

External Shell ◽

Morphometric Analyses ◽

Angular Measurements ◽

Permian Mass Extinction

The gastropod superfamily Subulitoidea first appeared during the Early-Middle Ordovician gastropod radiation, seemingly from within the pleurotomarid family Lophospiridea, and persisted with low diversity and generally low abundance through the Paleozoic. One species survived the end-Permian mass extinction, but like many other Paleozoic remnants, the clade became extinct in the mid-Triassic. Many members of the clade are homeomorphic with later ‘neogastropods' and have frequently been fingered as the ancestors of these later, predatory gastropods. There is however, no direct evidence for an ancestor-descendent relationship. Addressing this possibility and understanding of the systematics and evolutionary history of the clade has been complicated by relatively simple shell form and apparent paucity of shell characters. The strength of the morphological and probable ecologic similarities between subulitids and ‘neogastropods' raises the question why this clade was unable to capitalize on their position as perhaps the only predatory gastropods during the Paleozoic. Such questions of evolutionary history are best addressed within the context of a combination of morphometric and phylogenetic analyses which may resolve the systematic questions and reveal something of the evolutionary relationships of the clade.Morphometric analyses were performed on some 40 specimens covering the 13 described genera (and several undescribed forms). Both linear and angular measurements of external shell form and internal structure from axial thin sections were measured and apertures were analyzed using elliptical Fourier analysis (EFA). The number of specimens analyzed was intentionally limited because of difficulties obtaining specimens with sufficient preservation of the aperture. The results demonstrate the necessity, for this clade at least, of including a more complex description of apertural morphology than simple maximum length and width. Principle component analyses of the EFA data distinguishes complexity of the columellar folds along the first axis and basal rounding along the second - both biologically meaningful aspects of apertural form. Moreover, the occupation of a taxon-specific apertural space defined by the PCA increases through the Paleozoic. Further, the analyses suggest that the two traditionally recognized subfamilies of the Subulitidae (Ordovician-Devonian and Devonian-Triassic) each exhibit increased variance in the occupation of morphologic space, but additional data is required to confirm this pattern and determine if any temporal trends exist.Analyzing patterns of occupation of morphologic space requires a rigorously constructed phylogeny. A cladistic (parsimony) analysis of the superfamily was performed using 16 taxa and over 30 discrete morphologic characters. The resulting cladograms were plotted within the taxon-specific morphospaces produced by the morphometric analyses.

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Adaptive convergent evolution of genome proofreading in SARS-CoV2: insights into the Eigen’s paradox

10.1101/2021.09.11.459886 ◽

2021 ◽

Author(s):

Keerthic Aswin ◽

Srinivasan Ramachandran ◽

Vivek T Natarajan

Keyword(s):

Convergent Evolution ◽

Genome Stability ◽

Evolutionary History ◽

Rna Binding ◽

Phylogenetic Analyses ◽

Comparative Genome Analysis ◽

The Family ◽

History Of ◽

Key Residues

AbstractEvolutionary history of coronaviruses holds the key to understand mutational behavior and prepare for possible future outbreaks. By performing comparative genome analysis of nidovirales that contain the family of coronaviruses, we traced the origin of proofreading, surprisingly to the eukaryotic antiviral component ZNFX1. This common recent ancestor contributes two zinc finger (ZnF) motifs that are unique to viral exonuclease, segregating them from DNA proof-readers. Phylogenetic analyses indicate that following acquisition, genomes of coronaviruses retained and further fine-tuned proofreading exonuclease, whereas related families harbor substitution of key residues in ZnF1 motif concomitant to a reduction in their genome sizes. Structural modelling followed by simulation suggests the role of ZnF in RNA binding. Key ZnF residues strongly coevolve with replicase, and the helicase involved in duplex RNA unwinding. Hence, fidelity of replication in coronaviruses is a result of convergent evolution, that enables maintenance of genome stability akin to cellular proofreading systems.

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Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2018.2929 ◽

2019 ◽

Vol 286 (1897) ◽

pp. 20182929 ◽

Cited By ~ 2

Author(s):

Elena A. Ritschard ◽

Robert R. Fitak ◽

Oleg Simakov ◽

Sönke Johnsen

Keyword(s):

Signal Transduction ◽

Positive Selection ◽

G Protein ◽

Evolutionary History ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Expression Patterns ◽

Genomic Signatures ◽

History Of ◽

G Protein Coupled

Coleoid cephalopods show unique morphological and neural novelties, such as arms with tactile and chemosensory suckers and a large complex nervous system. The evolution of such cephalopod novelties has been attributed at a genomic level to independent gene family expansions, yet the exact association and the evolutionary timing remain unclear. In the octopus genome, one such expansion occurred in the G-protein-coupled receptors (GPCRs) repertoire, a superfamily of proteins that mediate signal transduction. Here, we assessed the evolutionary history of this expansion and its relationship with cephalopod novelties. Using phylogenetic analyses, at least two cephalopod- and two octopus-specific GPCR expansions were identified. Signatures of positive selection were analysed within the four groups, and the locations of these sequences in the Octopus bimaculoides genome were inspected. Additionally, the expression profiles of cephalopod GPCRs across various tissues were extracted from available transcriptomic data. Our results reveal the evolutionary history of cephalopod GPCRs. Unexpanded cephalopod GPCRs shared with other bilaterians were found to be mainly nervous tissue specific. By contrast, duplications that are shared between octopus and the bobtail squid or specific to the octopus' lineage generated copies with divergent expression patterns devoted to tissues outside of the brain. The acquisition of novel expression domains was accompanied by gene order rearrangement through either translocation or duplication and gene loss. Lastly, expansions showed signs of positive selection and some were found to form tandem clusters with shared conserved expression profiles in cephalopod innovations such as the axial nerve cord. Altogether, our results contribute to the understanding of the molecular and evolutionary history of signal transduction and provide insights into the role of this expansion during the emergence of cephalopod novelties and/or adaptations.

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Systematics of the Etheostoma cinereum (Teleostei: Percidae) species complex (subgenus Allohistium)

Zootaxa ◽

10.11646/zootaxa.3277.1.3 ◽

2012 ◽

Vol 3277 (1) ◽

pp. 43 ◽

Cited By ~ 6

Author(s):

STEVEN L. POWERS ◽

BERNARD R. KUHAJDA ◽

SARAH E. AHLBRAND

Keyword(s):

Geographic Variation ◽

Species Complex ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Taxonomic Status ◽

Species Concepts ◽

Cyt B ◽

Cumberland River

We examined geographic variation within the Ashy Darter, Etheostoma cinereum, of the mitochondrially enconded cyto-chrome b gene (cyt b) and nuclear recombination activation gene 1 (RAG1) as well as pigmentation, 6 meristic variables,and 20 morphometric variables for patterns indicative of speciation within the complex. Four geographically disjunct en-tities were identified by at least one of the datasets corresponding to the Cumberland, Duck, Elk, and upper Tennesseeriver systems. Monophyly of cyt b and RAG1 sequences, modal meristic differences, moderate morphometric divergence,and unique pigmentation in specimens from the Cumberland River suggest this entity represents an evolutionary speciesunder many different species concepts and is described herein as Etheostoma maydeni. Other populations exhibit varyingdegrees of divergence in the different datasets and have conflicting relationships in phylogenetic analyses using cyt b andRAG1 sequences, leaving the evolutionary history and taxonomic status of the Duck, Elk and upper Tennessee populations unclear.

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