scholarly journals Ghost lineages invalidate or reverse several results on gene flow

2022 ◽  
Author(s):  
Theo Tricou ◽  
Eric Tannier ◽  
Damien M de Vienne
Keyword(s):  
Gene Flow ◽  
Gene Transfer ◽  
Statistical Tests ◽  
Detection Methods ◽  
Malaria Vectors ◽  
Realistic Condition ◽  
Branch Lengths ◽  
Evolutionary Studies ◽  
Domains Of Life

Introgression, endosymbiosis and gene transfer, i.e. Horizontal Gene Flow (HGF), are primordial sources of innovation in all domains of life. Our knowledge on HGF relies on detection methods that exploit some of its signatures left on extant genomes. One of them is the effect of HGF on branch lengths of constructed phylogenies. This signature has been formalized in statistical tests for HGF detection, and used for example to detect massive adaptive gene flows in malaria vectors or to order evolutionary events involved in eukaryogenesis. However these studies rely on the assumption that ghost lineages (all unsampled extant and extinct taxa) have little influence. We demonstrate here with simulations and data re-analysis, that when considering the more realistic condition that unsampled taxa are legion compared to sampled ones, the conclusion of these studies become unfounded or even reversed. This illustrates the necessity to recognize the existence of ghosts in evolutionary studies.

scholarly journals Minimal and RNA-free RNase P in Aquifex aeolicus

2017 ◽  
Vol 114 (42) ◽  
pp. 11121-11126 ◽  
Author(s):  
Astrid I. Nickel ◽  
Nadine B. Wäber ◽  
Markus Gößringer ◽  
Marcus Lechner ◽  
Uwe Linne ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Saccharomyces Cerevisiae ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Rnase P ◽  
Aquifex Aeolicus ◽  
Trna Processing ◽  
Hyperthermophilic Bacterium ◽  
Domains Of Life

RNase P is an essential tRNA-processing enzyme in all domains of life. We identified an unknown type of protein-only RNase P in the hyperthermophilic bacterium Aquifex aeolicus: Without an RNA subunit and the smallest of its kind, the 23-kDa polypeptide comprises a metallonuclease domain only. The protein has RNase P activity in vitro and rescued the growth of Escherichia coli and Saccharomyces cerevisiae strains with inactivations of their more complex and larger endogenous ribonucleoprotein RNase P. Homologs of Aquifex RNase P (HARP) were identified in many Archaea and some Bacteria, of which all Archaea and most Bacteria also encode an RNA-based RNase P; activity of both RNase P forms from the same bacterium or archaeon could be verified in two selected cases. Bioinformatic analyses suggest that A. aeolicus and related Aquificaceae likely acquired HARP by horizontal gene transfer from an archaeon.

scholarly journals 3D magneto-hydrodynamical simulations of stellar convective noise for improved exoplanet detection

2020 ◽  
Vol 635 ◽  
pp. A146 ◽  
Author(s):  
S. Sulis ◽  
D. Mary ◽  
L. Bigot
Keyword(s):  
Time Series ◽  
Statistical Tests ◽  
Amplitude Distribution ◽  
False Alarm Probability ◽  
Detection Methods ◽  
Reliable Estimate ◽  
Critical Element ◽  
Adaptive Tests ◽  
Mhd Simulations ◽  
Hydrodynamical Simulations

Context. Convective motions at the stellar surface generate a stochastic colored noise source in the radial velocity (RV) data. This noise impedes the detection of small exoplanets. Moreover, the unknown statistics (amplitude, distribution) related to this noise make it difficult to estimate the false alarm probability (FAP) for exoplanet detection tests. Aims. In this paper, we investigate the possibility of using 3D magneto-hydrodynamical (MHD) simulations of stellar convection to design detection methods that can provide both a reliable estimate of the FAP and a high detection power. Methods. We tested the realism of 3D simulations in producing solar RV by comparing them with the observed disk integrated velocities taken by the GOLF instrument on board the SOHO spacecraft. We presented a new detection method based on periodograms standardized by these simulated time series, applying several detection tests to these standarized periodograms. Results. The power spectral density of the 3D synthetic convective noise is consistent with solar RV observations for short periods. For regularly sampled observations, the analytic expressions of FAP derived for several statistical tests applied to the periodogram standardized by 3D simulation noise are accurate. The adaptive tests considered in this work (Higher-Criticism, Berk-Jones), which are new in the exoplanet field, may offer better detection performance than classical tests (based on the highest periodogram value) in the case of multi-planetary systems and planets with eccentric orbits. Conclusions. 3D MHD simulations are now mature enough to produce reliable synthetic time series of the convective noise affecting RV data. These series can be used to access to the statistics of this noise and derive accurate FAP of tests that are a critical element in the detection of exoplanets down to the cm s−1 level.

scholarly journals Horizontal gene transfer from extinct and extant lineages: biological innovation and the coral of life

2009 ◽  
Vol 364 (1527) ◽  
pp. 2229-2239 ◽  
Author(s):  
Gregory P. Fournier ◽  
Jinling Huang ◽  
J. Peter Gogarten
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Evolutionary History ◽  
Phylogenetic Reconstruction ◽  
Gene Trees ◽  
Individual Gene ◽  
Evolution Of Life ◽  
Domains Of Life ◽  
Life On Earth ◽  
Simple Tree

Horizontal gene transfer (HGT) is often considered to be a source of error in phylogenetic reconstruction, causing individual gene trees within an organismal lineage to be incongruent, obfuscating the ‘true’ evolutionary history. However, when identified as such, HGTs between divergent organismal lineages are useful, phylogenetically informative characters that can provide insight into evolutionary history. Here, we discuss several distinct HGT events involving all three domains of life, illustrating the selective advantages that can be conveyed via HGT, and the utility of HGT in aiding phylogenetic reconstruction and in dating the relative sequence of speciation events. We also discuss the role of HGT from extinct lineages, and its impact on our understanding of the evolution of life on Earth. Organismal phylogeny needs to incorporate reticulations; a simple tree does not provide an accurate depiction of the processes that have shaped life's history.

scholarly journals Lateral gene transfer shapes the distribution of RuBisCO among Candidate Phyla Radiation bacteria and DPANN archaea

2018 ◽  
Author(s):  
Alexander L. Jaffe ◽  
Cindy J. Castelle ◽  
Christopher L. Dupont ◽  
Jillian F. Banfield
Keyword(s):  
Gene Transfer ◽  
Lateral Gene Transfer ◽  
Carbon Metabolism ◽  
Large Set ◽  
Amino Acid Residues ◽  
Bisphosphate Carboxylase ◽  
Full Diversity ◽  
Domains Of Life ◽  
Genome Level ◽  
Candidate Phyla Radiation

SUMMARYRibulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is considered to be the most abundant enzyme on Earth. Despite this, its full diversity and distribution across the domains of life remain to be determined. Here, we leverage a large set of bacterial, archaeal, and viral genomes recovered from the environment to expand our understanding of existing RuBisCO diversity and the evolutionary processes responsible for its distribution. Specifically, we report a new type of RuBisCO present in Candidate Phyla Radiation (CPR) bacteria that is related to the archaeal Form III enzyme and contains the amino acid residues necessary for catalytic activity. Genome-level metabolic analyses supported the inference that these RuBisCO function in a nucleotide-based, CO2-incorporating pathway. Importantly, some Gottesmanbacteria (CPR) also encode a phosphoribulokinase that may augment carbon metabolism through a partial Calvin-Benson-Bassham Cycle. Based on the scattered distribution of RuBisCO and its discordant evolutionary history, we conclude that this enzyme has been extensively laterally transferred across the CPR bacteria and DPANN archaea. We also report RuBisCO-like proteins in phage genomes from diverse environments. These sequences cluster with proteins in the Beckwithbacteria (CPR), implicating phage as a possible mechanism of RuBisCO transfer. Finally, we synthesize our metabolic and evolutionary analyses to suggest that lateral gene transfer of RuBisCO may have facilitated major shifts in carbon metabolism in several important bacterial and archaeal lineages.

scholarly journals Estimates of gene flow in Drosophila pseudoobscura determined from nucleotide sequence analysis of the alcohol dehydrogenase region.

Genetics ◽  
1992 ◽  
Vol 132 (2) ◽  
pp. 471-480 ◽  
Author(s):  
S W Schaeffer ◽  
E L Miller
Keyword(s):  
Gene Flow ◽  
Sequence Analysis ◽  
Nucleotide Sequence ◽  
Alcohol Dehydrogenase ◽  
Nucleotide Diversity ◽  
Statistical Tests ◽  
Population Substructure ◽  
Nucleotide Sequence Analysis ◽  
Drosophila Pseudoobscura ◽  
Neutral Model

Abstract The genetic structure of Drosophila pseudoobscura populations was inferred from a nucleotide sequence analysis of a 3.4-kb segment of the alcohol dehydrogenase (Adh) region. A total of 99 isochromosomal strains collected from 13 populations in North and South America were used to determine if any population departed from a neutral model and to estimate levels of gene flow between populations. This study also included the nucleotide sequences from two sibling species, D. persimilis and D. miranda. We estimated the neutral mutation parameter, 4N mu, in synonymous and noncoding sites for 17 subregions of Adh in each of nine populations with sample sizes greater than three. The nucleotide diversity data in the nine populations was tested for departures from an equilibrium neutral model with two statistical tests. The Tajima and the Hudson, Kreitman, Aguade tests showed that each population fails to reject a neutral model. Tests for genetic differentiation between populations fail to show any population substructure among the North American populations of D. pseudoobscura. The nucleotide diversity data is consistent with direct and indirect measures of gene flow that show extensive dispersal between populations of D. pseudoobscura.

scholarly journals CYP6P9-Driven Signatures of Selective Sweep of Metabolic Resistance to Pyrethroids in the Malaria Vector Anopheles funestus Reveal Contemporary Barriers to Gene Flow

Genes ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1314
Author(s):  
Delia Doreen Djuicy ◽  
Jack Hearn ◽  
Magellan Tchouakui ◽  
Murielle J. Wondji ◽  
Helen Irving ◽  
...  
Keyword(s):  
Gene Flow ◽  
Selective Sweep ◽  
Pyrethroid Resistance ◽  
Resistance Mechanism ◽  
Anopheles Funestus ◽  
Central Africa ◽  
Eastern Africa ◽  
Malaria Vectors ◽  
Metabolic Resistance ◽  
Diversity Pattern

Pyrethroid resistance in major malaria vectors such as Anopheles funestus threatens malaria control efforts in Africa. Cytochrome P450-mediated metabolic resistance is best understood for CYP6P9 genes in southern Africa in An. funestus. However, we do not know if this resistance mechanism is spreading across Africa and how it relates to broader patterns of gene flow across the continent. Nucleotide diversity of the CYP6P9a gene and the diversity pattern of five gene fragments spanning a region of 120 kb around the CYP6P9a gene were surveyed in mosquitoes from southern, eastern and central Africa. These analyses revealed that a Cyp6P9a resistance-associated allele has swept through southern and eastern Africa and is now fixed in these regions. A similar diversity profile was observed when analysing genomic regions located 34 kb upstream to 86 kb downstream of the CYP6P9a locus, concordant with a selective sweep throughout the rp1 locus. We identify reduced gene flow between southern/eastern Africa and central Africa, which we hypothesise is due to the Great Rift Valley. These potential barriers to gene flow are likely to prevent or slow the spread of CYP6P9-based resistance mechanism to other parts of Africa and would to be considered in future vector control interventions such as gene drive.

scholarly journals Antibacterial gene transfer across the tree of life

eLife ◽  
2014 ◽  
Vol 3 ◽  
Author(s):  
Jason A Metcalf ◽  
Lisa J Funkhouser-Jones ◽  
Kristen Brileya ◽  
Anna-Louise Reysenbach ◽  
Seth R Bordenstein
Keyword(s):  
Gene Transfer ◽  
Glycosyl Hydrolase ◽  
Antibiotic Resistance Genes ◽  
Dependent Manner ◽  
Domains Of Life ◽  
Functional Explanations ◽  
Lysozyme Family ◽  
Family Integrated ◽  
Dose Dependent

Though horizontal gene transfer (HGT) is widespread, genes and taxa experience biased rates of transferability. Curiously, independent transmission of homologous DNA to archaea, bacteria, eukaryotes, and viruses is extremely rare and often defies ecological and functional explanations. Here, we demonstrate that a bacterial lysozyme family integrated independently in all domains of life across diverse environments, generating the only glycosyl hydrolase 25 muramidases in plants and archaea. During coculture of a hydrothermal vent archaeon with a bacterial competitor, muramidase transcription is upregulated. Moreover, recombinant lysozyme exhibits broad-spectrum antibacterial action in a dose-dependent manner. Similar to bacterial transfer of antibiotic resistance genes, transfer of a potent antibacterial gene across the universal tree seemingly bestows a niche-transcending adaptation that trumps the barriers against parallel HGT to all domains. The discoveries also comprise the first characterization of an antibacterial gene in archaea and support the pursuit of antibiotics in this underexplored group.

scholarly journals Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph

2019 ◽  
Author(s):  
Melissa J. Hubisz ◽  
Amy L. Williams ◽  
Adam Siepel
Keyword(s):  
Gene Flow ◽  
Genetic Relationships ◽  
Convincing Evidence ◽  
Demographic Model ◽  
Modern Humans ◽  
Bayesian Algorithm ◽  
Branch Lengths ◽  
Mapping Gene ◽  
Ancestral Recombination Graphs ◽  
And Migration

AbstractThe sequencing of Neanderthal and Denisovan genomes has yielded many new insights about interbreeding events between extinct hominins and the ancestors of modern humans. While much attention has been paid to the relatively recent gene flow from Neanderthals and Denisovans into modern humans, other instances of introgression leave more subtle genomic evidence and have received less attention. Here, we present an extended version of the ARGweaver algorithm, ARGweaver-D, which can infer local genetic relationships under a user-defined demographic model that includes population splits and migration events. This Bayesian algorithm probabilistically samples ancestral recombination graphs (ARGs) that specify not only tree topology and branch lengths along the genome, but also indicate migrant lineages. The sampled ARGs can therefore be parsed to produce probabilities of introgression along the genome. We show that this method is well powered to detect the archaic migration into modern humans, even with only a few samples. We then show that the method can also detect introgressed regions stemming from older migration events, or from unsampled populations. We apply it to human, Neanderthal, and Denisovan genomes, looking for signatures of older proposed migration events, including ancient humans into Neanderthal, and unknown archaic hominins into Denisovans. We identify 3% of the Neanderthal genome that is putatively introgressed from ancient humans, and estimate that the gene flow occurred between 200-300kya. We find no convincing evidence that negative selection acted against these regions. We also identify 1% of the Denisovan genome which was likely introgressed from an unsequenced hominin ancestor, and note that 15% of these regions have been passed on to modern humans through subsequent gene flow.

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