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Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on complex patterns of the presence or absence of other accessory genes within a genome. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. We find that the presence or absence of a substantial set of genes is highly predictable from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution and is robust to differences in host evolutionary history. We propose that at least part of the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem's set of interacting organisms. Our findings indicate that intragenomic gene fitness effects may be key drivers of prokaryotic evolution, influencing the repeated emergence of complex gene-gene relationships across the pangenome. [ABSTRACT FROM AUTHOR]

Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes., In prokaryotes, inheritance involves recombination superimposed upon clonal growth (1) and the mechanisms of recombination are the mechanisms of lateral gene transfer (LGT): transformation, conjugation, transduction, and gene transfer agents [...]

The mechanisms that underlie the origin of major prokaryotic groups are poorly understood. In principle, the origin of both species and higher taxa among prokaryotes should entail similar mechanisms--ecological interactions with the environment paired with natural genetic variation involving lineage-specific gene innovations and lineage-specific gene acquisitions (1-4). To investigate the origin of higher taxa in archaea, we have determined gene distributions and gene phylogenies for the 267,568 protein-coding genes of 134 sequenced archaeal genomes in the context of their homologues from 1,847 reference bacterial genomes. Archaeal-specific gene families define 13 traditionally recognized archaeal higher taxa in our sample. Here we report that the origins of these 13 groups unexpectedly correspond to 2,264 group-specific gene acquisitions from bacteria. Interdomain gene transfer is highly asymmetric, transfers from bacteria to archaea are more than fivefold more frequent than vice versa. Gene transfers identified at major evolutionary transitions among prokaryotes specifically implicate gene acquisitions for metabolic functions from bacteria as key innovations in the origin of higher archaeal taxa., Genome evolution in prokaryotes entails both tree-like components generated by vertical descent and network-like components generated by lateral gene transfer (LGT) (5,6). Both processes operate in the formation of prokaryotic [...]

Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes. [ABSTRACT FROM AUTHOR]

Pre-surgical MRIs are obtained routinely in all PD patients scheduled for DBS to rule out secondary pathologies and for lead targeting purposes. PD patients can achieve dramatic improvements in motor symptoms from DBS, including control of medication-refractory tremor and reduction in dyskinesia, motor fluctuations, and/or required dosage of anti-parkinsonian medication [[5], [7], [9]]. 35 Abboud H, Genc G, Thompson NR, Oravivattanakul S, Alsallom F, Reyes D, Wilson K, Cerejo R, Yu XX, Floden D, Ahmed A, Gostkowski M, Ezzeldin A, Marouf H, Mansour OY, Machado A, Fernandez HH (2017) Predictors of functional and quality of life outcomes following deep brain stimulation surgery in Parkinson's disease patients: Disease, patient, and surgical factors. Keywords: Parkinson's disease; deep brain stimulation; MRI; R2*; neuropsychiatric outcomes EN Parkinson's disease deep brain stimulation MRI R2* neuropsychiatric outcomes 851 863 13 04/07/22 20220701 NES 220701 INTRODUCTION Clinically, Parkinson's disease (PD) is characterized by motor symptoms (e.g., tremor, rigidity, and bradykinesia). [Extracted from the article]