scholarly journals Horizontal Gene Transfers from Bacteria toEntamoebaComplex: A Strategy for Dating Events along Species Divergence

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Miguel Romero ◽  
R. Cerritos ◽  
Cecilia Ximenez
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Entamoeba Histolytica ◽  
Lateral Gene Transfer ◽  
Adaptive Radiation ◽  
Fossil Record ◽  
Evolutionary History ◽  
Divergence Time ◽  
Eukaryotic Evolution ◽  
History Of

Horizontal gene transfer has proved to be relevant in eukaryotic evolution, as it has been found more often than expected and related to adaptation to certain niches. A relatively large list of laterally transferred genes has been proposed and evaluated for the parasiteEntamoeba histolytica. The goals of this work were to elucidate the importance of lateral gene transfer along the evolutionary history of some members of the genusEntamoeba, through identifying donor groups and estimating the divergence time of some of these events. In order to estimate the divergence time of some of the horizontal gene transfer events, the dating of someEntamoebaspecies was necessary, following an indirect dating strategy based on the fossil record of plausible hosts. The divergence betweenE. histolyticaandE. nuttalliiprobably occurred 5.93 million years ago (Mya); this lineage diverged fromE. dispar9.97 Mya, while the ancestor of the latter separated fromE. invadens68.18 Mya. We estimated times for 22 transferences; the most recent occurred 31.45 Mya and the oldest 253.59 Mya. Indeed, the acquisition of genes through lateral transfer may have triggered a period of adaptive radiation, thus playing a major role in the evolution of theEntamoebagenus.

scholarly journals The Linguistics of Bacterial Conflict Systems Reveal Ancient Origins of Eukaryotic Innate Immunity

2020 ◽  
Vol 202 (24) ◽  
Author(s):  
Emily M. Kibby ◽  
Aaron T. Whiteley
Keyword(s):  
Innate Immunity ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Protein Domains ◽  
Arms Race ◽  
Bacterial Populations ◽  
Defense Systems ◽  
History Of ◽  
Novel Protein

ABSTRACT The arms race between bacteria and their competitors has produced an astounding variety of conflict systems that are shared via horizontal gene transfer across bacterial populations. In this issue of the Journal of Bacteriology, Burroughs and Aravind investigate how these biological conflict systems have been mixed and matched into new configurations, often with novel protein domains (A. M. Burroughs and L. Aravind, J Bacteriol 202:e00365-20, 2020, https://doi.org/10.1128/JB.00365-20). The authors additionally characterize the evolutionary history of genes in eukaryotes that appear to have been acquired from these prokaryotic defense systems.

scholarly journals Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0239248 ◽  
Author(s):  
Lewis M. Ward ◽  
Patrick M. Shih
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Apparatus ◽  
Metagenomic Sequencing ◽  
Crown Group ◽  
Environmental Diversity ◽  
Chlorophyll Pigments ◽  
History Of

Photosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

scholarly journals Granick Revisited: Synthesizing Evolutionary and Ecological Evidence for the Late Origin of Bacteriochlorophyll via Ghost Lineages and Horizontal Gene Transfer

2020 ◽  
Author(s):  
Lewis M. Ward ◽  
Patrick M. Shih
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Photosynthetic Bacteria ◽  
Photosynthetic Apparatus ◽  
Metagenomic Sequencing ◽  
Crown Group ◽  
Environmental Diversity ◽  
Chlorophyll Pigments ◽  
History Of

AbstractPhotosynthesis—both oxygenic and more ancient anoxygenic forms—has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic “Granick hypothesis” for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

scholarly journals Horizontal gene transfer of a chloroplast DnaJ-Fer protein to Thaumarchaeota and the evolutionary history of the DnaK chaperone system in Archaea

2012 ◽  
Vol 12 (1) ◽  
pp. 226 ◽  
Author(s):  
Céline Petitjean ◽  
David Moreira ◽  
Purificación López-García ◽  
Céline Brochier-Armanet
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
History Of

The late Berriasian early evolutionary burst of the Orbitolinidae: New insights into taxonomy, origin, diversification and phylogeny of the family based on data from eastern Serbia

2021 ◽  
Vol 21 (15) ◽  
pp. 343-382
Author(s):  
Felix Schlagintweit
Keyword(s):  
Adaptive Radiation ◽  
Fossil Record ◽  
Evolutionary History ◽  
Large Benthic Foraminifera ◽  
Time Period ◽  
The Family ◽  
History Of ◽  
Phylogenetic Evolution ◽  
Family Based ◽  
A New Species

New data from the Carpatho-Balkanides of eastern Serbia evidence the more or less near-simultaneous "explosive" first appearances of several genera of the Orbitolinidae in the late Berriasian. Most of the observed taxa were previously recorded from strata not older than the Late Hauterivian (= classical Urgonian of southeastern France), evidence that these ages refer to local first appearance data. The diversified assemblage from Serbia includes representatives of the subfamilies Dictyoconinae: genera Cribellopsis ARNAUD-VANNEAU, Montseciella CHERCHI & SCHROEDER, Orbitolinopsis HENSON, Urgonina FOURY & MOULLADE, Valserina SCHROEDER & CONRAD, Vanneauina SCHLAGINTWEIT, and Dictyorbitolininae: genus Paracoskinolina MOULLADE. Representatives of the Orbitolininae (with complex embryo) have not been observed. They appeared later in the fossil record seemingly during the Late Hauterivian-early Barremian. All together 17 taxa are reported, of which three in open nomenclature. A new species is described as Cribellopsis sudari n. sp. The majority of the observed species display medium- to high-conical tests and a rather simple exoskeleton lacking horizontal partitions (rafters). The new data contradict a phylogenetic evolution of distinct genera displaying different internal test structures one after the other in time (= ancestor-descendant relationships) as postulated by some authors. The explosive radiation ("early burst") of the Orbitolinidae in the late Berriasian is accompanied by the first appearance date of several other large benthic foraminifera including mostly agglutinating (e.g., Ammocycloloculina, Choffatella, Drevennia, Eclusia, Moulladella, Pfenderina, Pseudotextulariella) but also complex porcelaneous taxa (Pavlovcevina) providing evidence for a bioevent in this time period that exceeds the number of taxa originating in the previous (Tithonian) and the following stage (Valanginian). The early evolutionary history of the Orbitolinidae can be considered a classical example of adaptive radiation within the clade's history.

Reconstruction of the evolutionary history of the LexA-binding sequence

Microbiology ◽  
2004 ◽  
Vol 150 (11) ◽  
pp. 3783-3795 ◽  
Author(s):  
Gerard Mazón ◽  
Ivan Erill ◽  
Susana Campoy ◽  
Pilar Cortés ◽  
Evelyne Forano ◽  
...  
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Evolutionary History ◽  
Bacterial Species ◽  
Evolutionary Relationship ◽  
Gram Positive ◽  
Recognition Motif ◽  
Lexa Binding ◽  
History Of ◽  
Binding Sequence

In recent years, the recognition sequence of the SOS repressor LexA protein has been identified for several bacterial clades, such as the Gram-positive, green non-sulfur bacteria and Cyanobacteria phyla, or the ‘Alphaproteobacteria’, ‘Deltaproteobacteria’ and ‘Gammaproteobacteria’ classes. Nevertheless, the evolutionary relationship among these sequences and the proteins that recognize them has not been analysed. Fibrobacter succinogenes is an anaerobic Gram-negative bacterium that branched from a common bacterial ancestor immediately before the Proteobacteria phylum. Taking advantage of its intermediate position in the phylogenetic tree, and in an effort to reconstruct the evolutionary history of LexA-binding sequences, the F. succinogenes lexA gene has been isolated and its product purified to identify its DNA recognition motif through electrophoretic mobility assays and footprinting experiments. After comparing the available LexA DNA-binding sequences with the F. succinogenes one, reported here, directed mutagenesis of the F. succinogenes LexA-binding sequence and phylogenetic analyses of LexA proteins have revealed the existence of two independent evolutionary lanes for the LexA recognition motif that emerged from the Gram-positive box: one generating the Cyanobacteria and ‘Alphaproteobacteria’ LexA-binding sequences, and the other giving rise to the F. succinogenes and Myxococcus xanthus ones, in a transitional step towards the current ‘Gammaproteobacteria’ LexA box. The contrast between the results reported here and the phylogenetic data available in the literature suggests that, some time after its emergence as a distinct bacterial class, the ‘Alphaproteobacteria’ lost its vertically received lexA gene, but received later through lateral gene transfer a new lexA gene belonging to either a cyanobacterium or a bacterial species closely related to this phylum. This constitutes the first report based on experimental evidence of lateral gene transfer in the evolution of a gene governing such a complex regulatory network as the bacterial SOS system.

scholarly journals Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

2014 ◽  
Vol 281 (1789) ◽  
pp. 20140848 ◽  
Author(s):  
Maxime Bruto ◽  
Claire Prigent-Combaret ◽  
Patricia Luis ◽  
Yvan Moënne-Loccoz ◽  
Daniel Muller
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Eukaryotic Cells ◽  
Phylogenomic Analysis ◽  
Catabolic Gene ◽  
Bacterial Phyla ◽  
Bacterial Origin ◽  
History Of ◽  
Complex Evolutionary History

Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.

scholarly journals Indirect identification of horizontal gene transfer

2021 ◽  
Vol 83 (1) ◽  
Author(s):  
David Schaller ◽  
Manuel Lafond ◽  
Peter F. Stadler ◽  
Nicolas Wieseke ◽  
Marc Hellmuth
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Polynomial Time ◽  
Divergence Time ◽  
Recognition Algorithm ◽  
Vertex Coloring ◽  
Implicit Methods ◽  
Colored Graphs ◽  
Wide Range ◽  
Complete Multipartite

AbstractSeveral implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

scholarly journals Out of the Qinghai-Tibetan Plateau (QTP) and rapid radiation across Eurasia for Allium section Daghestanica (Amaryllidaceae)

AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He
Keyword(s):  
Evolutionary History ◽  
Divergence Time ◽  
Time Estimation ◽  
Adjacent Region ◽  
Rapid Radiation ◽  
Divergence Time Estimation ◽  
Species Diversification ◽  
The Third ◽  
Evolutionary Line ◽  
History Of

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.

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