The Evolutionary History of Archaeal MCM Helicases: A Case Study of Vertical Evolution Combined with Hitchhiking of Mobile Genetic Elements

ABSTRACT Escherichia coli sequence type 131 (ST131) has emerged globally as the most predominant extraintestinal pathogenic lineage within this clinically important species, and its association with fluoroquinolone and extended-spectrum cephalosporin resistance impacts significantly on treatment. The evolutionary histories of this lineage, and of important antimicrobial resistance elements within it, remain unclearly defined. This study of the largest worldwide collection ( n = 215) of sequenced ST131 E. coli isolates to date demonstrates that the clonal expansion of two previously recognized antimicrobial-resistant clades, C1/ H 30R and C2/ H 30Rx, started around 25 years ago, consistent with the widespread introduction of fluoroquinolones and extended-spectrum cephalosporins in clinical medicine. These two clades appear to have emerged in the United States, with the expansion of the C2/ H 30Rx clade driven by the acquisition of a bla CTX-M-15 -containing IncFII-like plasmid that has subsequently undergone extensive rearrangement. Several other evolutionary processes influencing the trajectory of this drug-resistant lineage are described, including sporadic acquisitions of CTX-M resistance plasmids and chromosomal integration of bla CTX-M within subclusters followed by vertical evolution. These processes are also occurring for another family of CTX-M gene variants more recently observed among ST131, the bla CTX-M-14/14-like group. The complexity of the evolutionary history of ST131 has important implications for antimicrobial resistance surveillance, epidemiological analysis, and control of emerging clinical lineages of E. coli . These data also highlight the global imperative to reduce specific antibiotic selection pressures and demonstrate the important and varied roles played by plasmids and other mobile genetic elements in the perpetuation of antimicrobial resistance within lineages. IMPORTANCE Escherichia coli , perennially a major bacterial pathogen, is becoming increasingly difficult to manage due to emerging resistance to all preferred antimicrobials. Resistance is concentrated within specific E. coli lineages, such as sequence type 131 (ST131). Clarification of the genetic basis for clonally associated resistance is key to devising intervention strategies. We used high-resolution genomic analysis of a large global collection of ST131 isolates to define the evolutionary history of extended-spectrum beta-lactamase production in ST131. We documented diverse contributory genetic processes, including stable chromosomal integrations of resistance genes, persistence and evolution of mobile resistance elements within sublineages, and sporadic acquisition of different resistance elements. Both global distribution and regional segregation were evident. The diversity of resistance element acquisition and propagation within ST131 indicates a need for control and surveillance strategies that target both bacterial strains and mobile genetic elements.

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Where Fossils Dare and Males Matter: combined morphological and molecular analysis untangles the evolutionary history of the spider ant genus Leptomyrmex Mayr (Hymenoptera : Dolichoderinae)

Invertebrate Systematics ◽

10.1071/is16067 ◽

2017 ◽

Vol 31 (6) ◽

pp. 765 ◽

Cited By ~ 3

Author(s):

Phillip Barden ◽

Brendon Boudinot ◽

Andrea Lucky

Keyword(s):

Evolutionary History ◽

Morphological Evolution ◽

Sister Group ◽

Morphological Characters ◽

Fossil Material ◽

First Case ◽

History Of ◽

The Impact ◽

Surprising Discovery

The distinctive ant genus Leptomyrmex Mayr, 1862 had been thought to be endemic to Australasia for over 150 years, but enigmatic Neotropical fossils have challenged this view for decades. The present study responds to a recent and surprising discovery of extant Leptomyrmex species in Brazil with a thorough evaluation of the Dominican Republic fossil material, which dates to the Miocene. In the first case study of direct fossil inclusion within Formicidae Latreille, 1809, we incorporated both living and the extinct Leptomyrmex species. Through simultaneous analysis of molecular and morphological characters in both Bayesian and parsimony frameworks, we recovered the fossil taxon as sister-group to extant Leptomyrmex in Brazil while considering the influence of taxonomic and character sampling on inferred hypotheses relating to tree topology, biogeography and morphological evolution. We also identified potential loss of signal in the binning of morphological characters and tested the impact of parameterisation on divergence date estimation. Our results highlight the importance of securing sufficient taxon sampling for extant lineages when incorporating fossils and underscore the utility of diverse character sources in accurate placement of fossil terminals. Specifically, we find that fossil placement in this group is influenced by the inclusion of male-based characters and the newly discovered Neotropical ‘Lazarus taxon’.

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Decoding evolutionary history of provenance from beach placer monazites: A case study from Kanyakumari coast, southwest India

Chemical Geology ◽

10.1016/j.chemgeo.2016.02.018 ◽

2016 ◽

Vol 427 ◽

pp. 83-97 ◽

Cited By ~ 6

Author(s):

C. Perumalsamy ◽

Subhadip Bhadra ◽

S. Balakrishnan

Keyword(s):

Evolutionary History ◽

Southwest India ◽

History Of

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Ecological associations between organisms of different evolutionary history: mangrove pneumatophore arthropods as a case study

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315404009257h ◽

2004 ◽

Vol 84 (2) ◽

pp. 341-344 ◽

Cited By ~ 4

Author(s):

Şerban Procheş

Keyword(s):

Environmental Stress ◽

Evolutionary History ◽

Marine Species ◽

Insect Larvae ◽

Direct Sunlight ◽

Terrestrial Species ◽

As Species ◽

Species Pairs ◽

History Of

Typical marine arthropods (crustaceans and halacarid mites), as well as species of recent terrestrial ancestry (insect larvae and mesostigmatid mites) coexist on mangrove pneumatophores. Both groups are affected by desiccation and are less abundant towards the tips of the pneumatophores. The degree of species associations within and between the two groups was investigated. The number of negative associations is higher for marine–marine, as compared to terrestrial–terrestrial and terrestrial–marine species pairs. When environmental stress (as represented by direct sunlight, and elevation on pneumatophores, both resulting in increased desiccation) is considered, associations tend to shift from negative to positive, and this is more obvious in terrestrial–terrestrial species pairs. These results are attributed to the longer co-evolutionary history of the marine species, resulting in a more precise partitioning of the microhabitats, while the relationships between terrestrial species are less stable, and more susceptible to environmental stress.

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Integrated pipeline for inferring the evolutionary history of a gene family embedded in the species tree: a case study on the STIMATE gene family

BMC Bioinformatics ◽

10.1186/s12859-017-1850-2 ◽

2017 ◽

Vol 18 (1) ◽

Cited By ~ 1

Author(s):

Jia Song ◽

Sisi Zheng ◽

Nhung Nguyen ◽

Youjun Wang ◽

Yubin Zhou ◽

...

Keyword(s):

Gene Family ◽

Evolutionary History ◽

Species Tree ◽

History Of

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Accessing and applying molecular history

10.7287/peerj.preprints.1293 ◽

2015 ◽

Author(s):

Joshua G Stern ◽

Eric A Gaucher

Keyword(s):

Machine Learning ◽

Molecular Evolution ◽

Real World ◽

Evolutionary History ◽

Learning Algorithm ◽

Machine Learning Algorithm ◽

History Of ◽

Evolution And Medicine ◽

Real World Problems

Studying the evolutionary history of life’s molecules - DNA, RNA, and protein - reveals nature-based solutions to real-world problems. We discuss an approach to applied molecular evolution that is well-known within the field but may be unfamiliar to a wider audience. Using a case study at the intersection of molecular evolution and medicine, we introduce the fundamental concepts of orthology and paralogy. We also explain a practical entry point to molecular evolution named STORI: Selectable Taxon Ortholog Retrieval Iteratively. STORI is a machine learning algorithm designed to clear a bottleneck that researchers encounter when studying evolution.

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Entanglements of Time, Temperature, Technology, and Place in Ancient DNA Research: The Case of the Denisovan Hominin

Science Technology & Human Values ◽

10.1177/0162243919879991 ◽

2019 ◽

Vol 45 (6) ◽

pp. 1119-1141

Author(s):

Venla Oikkonen

Keyword(s):

Population Genetics ◽

Ancient Dna ◽

Science And Technology Studies ◽

Evolutionary History ◽

Science And Society ◽

Hominin Evolution ◽

The Status ◽

History Of ◽

Specific Configuration

The study of ancient DNA (aDNA) has gained increasing attention in science and society as a tool for tracing hominin evolution. While aDNA research overlaps with the history of population genetics, it embodies a specific configuration of technology, temporality, temperature, and place that, this article suggests, cannot be fully unpacked with existing science and technology studies approaches to population genetics. This article explores this configuration through the 2010 discovery of the Denisovan hominin based on aDNA retrieved from a finger bone and tooth in Siberia. The analysis explores how the Denisovan was enacted as a technoscientific object through the cool and even temperatures of Denisova Cave, assumptions about the connection between individual and population, the status of populations as evolutionary entities, and underlying colonialist and imperialist imaginaries of Siberia and Melanesia. The analysis sheds light on how aDNA research is changing the parameters within which evolutionary history is imagined and conceptualized. Through the case study, it also outlines some ways in which the specific technoscientific and cultural entanglements of aDNA can be critically explored.

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Accessing and applying molecular history

10.7287/peerj.preprints.1293v1 ◽

2015 ◽

Author(s):

Joshua G Stern ◽

Eric A Gaucher

Keyword(s):

Machine Learning ◽

Molecular Evolution ◽

Real World ◽

Evolutionary History ◽

Learning Algorithm ◽

Machine Learning Algorithm ◽

History Of ◽

Evolution And Medicine ◽

Real World Problems

Studying the evolutionary history of life’s molecules - DNA, RNA, and protein - reveals nature-based solutions to real-world problems. We discuss an approach to applied molecular evolution that is well-known within the field but may be unfamiliar to a wider audience. Using a case study at the intersection of molecular evolution and medicine, we introduce the fundamental concepts of orthology and paralogy. We also explain a practical entry point to molecular evolution named STORI: Selectable Taxon Ortholog Retrieval Iteratively. STORI is a machine learning algorithm designed to clear a bottleneck that researchers encounter when studying evolution.

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Identification of RAG-like transposons in protostomes suggests an ancient bilaterian origin of the RAG-like transposon family

10.21203/rs.2.19531/v2 ◽

2020 ◽

Author(s):

Eliza C. Martin ◽

Celia Vicari ◽

Louis Tsakou-Ngouafo ◽

Pierre Pontarotti ◽

Andrei J. Petrescu ◽

...

Keyword(s):

Amino Acids ◽

Adaptive Immunity ◽

Active Site ◽

Evolutionary History ◽

Phylogenetic Analyses ◽

Inverted Repeats ◽

Adjacent Gene ◽

Terminal Inverted Repeats ◽

History Of ◽

Vertical Evolution

Abstract Background V(D)J recombination is essential for adaptive immunity in jawed vertebrates and is initiated by the RAG1-RAG2 endonuclease. The RAG1 and RAG2 genes are thought to have evolved from a RAGL (RAG-like) transposon containing convergently-oriented RAG1-like (RAG1L) and RAG2-like (RAG2L) genes. Elements resembling this presumptive evolutionary precursor have thus far only been detected convincingly in deuterostomes, leading to the model that the RAGL transposon first appeared in an early deuterostome. Results We have identified numerous RAGL transposons in the genomes of protostomes, including oysters and mussels (phylum Mollusca) and a ribbon worm (phylum Nemertea), and in the genomes of several cnidarians. Phylogenetic analyses are consistent with vertical evolution of the RAGL transposon family within the Bilateria clade and with its presence in the bilaterian ancestor. Many of the RAGL transposons identified in protostomes are intact elements containing convergently oriented RAG1L and RAG2L genes flanked by terminal inverted repeats (TIRs) and target site duplications with striking similarities with the corresponding elements in deuterostomes. In addition, protostome genomes contain numerous intact RAG1L-RAG2L adjacent gene pairs that lack detectable flanking TIRs. Domains and critical active site and structural amino acids needed for endonuclease and transposase activity are present and conserved in many of the predicted RAG1L and RAG2L proteins encoded in protostome genomes. Conclusions Active RAGL transposons were present in multiple protostome lineages and were likely transmitted vertically during protostome evolution. It appears that the RAGL transposon family was broadly active during bilaterian evolution, undergoing multiple duplication and loss/fossilization events, with the RAGL genes that persist in present day protostomes perhaps constituting both active RAGL transposons and domesticated RAGL genes. Our findings raise the possibility that the RAGL transposon arose earlier in evolution than previously thought, either in an early bilaterian or prior to the divergence of bilaterians and non-bilaterians, and alter our understanding of the evolutionary history of this important transposon family.

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