scholarly journals Natural selection and repeated patterns of molecular evolution following allopatric divergence

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Yibo Dong ◽  
Shichao Chen ◽  
Shifeng Cheng ◽  
Wenbin Zhou ◽  
Qing Ma ◽  
...  
Keyword(s):  
Positive Selection ◽  
Divergence Time ◽  
Purifying Selection ◽  
Single Copy ◽  
Orthologous Genes ◽  
Allopatric Species ◽  
Genome Wide ◽  
Allopatric Divergence ◽  
Selective Forces ◽  
Repeated Pattern

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10–15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.

scholarly journals A Genome-Wide Identification of Genes Undergoing Recombination and Positive Selection inNeisseria

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Dong Yu ◽  
Yuan Jin ◽  
Zhiqiu Yin ◽  
Hongguang Ren ◽  
Wei Zhou ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Molecular Mechanisms ◽  
Acid Sites ◽  
Gram Negative Bacteria ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
History Of ◽  
Functional Analyses

Currently, there is particular interest in the molecular mechanisms of adaptive evolution in bacteria.Neisseriais a genus of gram negative bacteria, and there has recently been considerable focus on its two human pathogenic speciesN. meningitidisandN. gonorrhoeae. Until now, no genome-wide studies have attempted to scan for the genes related to adaptive evolution. For this reason, we selected 18Neisseriagenomes (14N. meningitidis, 3N. gonorrhoeaeand 1 commensalN. lactamics) to conduct a comparative genome analysis to obtain a comprehensive understanding of the roles of natural selection and homologous recombination throughout the history of adaptive evolution. Among the 1012 core orthologous genes, we identified 635 genes with recombination signals and 10 genes that showed significant evidence of positive selection. Further functional analyses revealed that no functional bias was found in the recombined genes. Positively selected genes are prone to DNA processing and iron uptake, which are essential for the fundamental life cycle. Overall, the results indicate that both recombination and positive selection play crucial roles in the adaptive evolution ofNeisseriagenomes. The positively selected genes and the corresponding amino acid sites provide us with valuable targets for further research into the detailed mechanisms of adaptive evolution inNeisseria.

scholarly journals In-silico genome wide identification, expressional profiling and regulation of NHX (Sodium/ Hydrogen Antiporter) gene family in Camellia sinensis

2021 ◽  
Author(s):  
Abhirup Paul ◽  
Archita Chatterjee ◽  
shreya Subrahmanya ◽  
Guoxin Shen ◽  
Neelam Mishra
Keyword(s):  
Expression Profiles ◽  
Abiotic Factors ◽  
Purifying Selection ◽  
Tea Plant ◽  
Functional Study ◽  
Functional Interaction ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Search

Abstract Background Salt stress affects the plant growth and productivity worldwide and NHX is one of those genes that are well known to improve salt tolerance in transgenic plants. It is well characterized in several plants such as Arabidopsis and cotton however not much is known about NHXs in tea plant. Result In the present study, NHX genes of tea were obtained through a genome wide search using Arabidopsis thaliana as reference genome. Out of the 9 NHX genes in tea, 7 genes were localized in vacuole while the remaining 2 genes were localized in the endoplasmic reticulum (ER) (TEA014468.1) and plasma membrane (PM) (TEA006997.1) respectively. Furthermore, phylogenetic relationships along with structural analysis which includes gene structure, location as well as protein conserved motifs and domains, were systematically examined and further, predictions were validated by the expression analysis. The dN/dS values show that the majority of tea NHX genes are subjected to strong purifying selection under the course of evolution. Also, functional interaction was carried out in C. sinensis based on the orthologous genes in Arabidopsis. The expression profiles linked to various stress treatments revealed wide involvement of NHX genes from tea in response to various abiotic factors. Conclusion This study provides the targets for further comprehensive identification, functional study, and also contributed for a better understanding of the NHX regulatory network in C. sinensis.

scholarly journals Functional Bias and Demographic History Obscure Patterns of Selection among Single-Copy Genes in a Fungal Species Complex

2017 ◽  
Author(s):  
Santiago Sánchez-Ramírez ◽  
Jean-Marc Moncalvo
Keyword(s):  
Natural Selection ◽  
Positive Selection ◽  
Dna Sequences ◽  
Demographic History ◽  
Purifying Selection ◽  
Single Copy ◽  
Fungal Species ◽  
Ratio Test ◽  
Ontology Term ◽  
Slightly Deleterious Mutations

AbstractMany different evolutionary processes may be responsible for explaining natural variation within genomes, some of which include natural selection at the molecular level and changes in population size. Fungi are highly adaptable organisms, and their relatively small genomes and short generation times make them pliable for evolutionary genomic studies. However, adaptation in wild populations has been relatively less documented compared to experimental or clinical studies. Here, we analyzed DNA sequences from 502 putative single-copy orthologous genes in 63 samples that represent seven recently diverged North American Amanita (jacksonii-complex) lineages. For each gene and each species, we measured the genealogical sorting index (gsi) and infinite-site-based summary statistics, such as , and DTaj in coding and intron regions. MKT-based approaches and likelihood-ratio-test Kn/Ks models were used to measure natural selection in all coding sequences. Multi-locus (Extended) Bayesian Skyline Plots (eBSP) were used to model intraspecific demographic changes through time based on unlinked, putative neutral regions (introns). Most genes show evidence of long-term purifying selection, likely reflecting a functional bias implicit in single-copy genes. We find that two species have strongly negatively skewed Tajima’s D, while three other have a positive skew, corresponding well with patterns of demographic expansion and contraction. Standard MKT analyses resulted in a high incidence of near-zero α with a tendency towards negative values. In contrast, α estimates based on the distribution of fitness effects (DFE), which accounts for demographic effects and slightly deleterious mutations, suggest a higher proportion of sites fixed by positive selection. The difference was more notorious in species with expansion signatures or with historically low population sizes, evidencing the concealing effects of specific demographic histories. Finally, we attempt to mitigate Gene Ontology term overrepresentation, highlighting the potential adaptive or ecological roles of some genes under positive selection.

scholarly journals Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

2021 ◽  
Vol 288 (1942) ◽  
pp. 20201804
Author(s):  
Brendan Epstein ◽  
Peter Tiffin
Keyword(s):  
Positive Selection ◽  
Horizontal Transfer ◽  
Purifying Selection ◽  
Comparative Genomic ◽  
N Fixation ◽  
Functional Roles ◽  
Genome Wide ◽  
Rhizobial Symbiosis ◽  
Legume Symbiosis ◽  
Insight Into

Horizontal transfer (HT) alters the repertoire of symbiosis genes in rhizobial genomes and may play an important role in the on-going evolution of the rhizobia–legume symbiosis. To gain insight into the extent of HT of symbiosis genes with different functional roles (nodulation, N-fixation, host benefit and rhizobial fitness), we conducted comparative genomic and selection analyses of the full-genome sequences from 27 rhizobial genomes. We find that symbiosis genes experience high rates of HT among rhizobial lineages but also bear signatures of purifying selection (low Ka : Ks). HT and purifying selection appear to be particularly strong in genes involved in initiating the symbiosis (e.g. nodulation) and in genome-wide association candidates for mediating benefits provided to the host. These patterns are consistent with rhizobia adapting to the host environment through the loss and gain of symbiosis genes, but not with host-imposed positive selection driving divergence of symbiosis genes through recurring bouts of positive selection.

scholarly journals Protein Coding Gene Nucleotide Substitution Pattern in the Apicomplexan ProtozoaCryptosporidium parvumandCryptosporidium hominis

2008 ◽  
Vol 2008 ◽  
pp. 1-6 ◽  
Author(s):  
Guangtao Ge ◽  
Lenore Cowen ◽  
Xiaochuan Feng ◽  
Giovanni Widmer
Keyword(s):  
Positive Selection ◽  
Purifying Selection ◽  
High Ratio ◽  
Genome Comparison ◽  
Nucleotide Substitutions ◽  
Substitution Pattern ◽  
Protein Coding ◽  
Genome Wide ◽  
The Impact ◽  
Selection Of

Cryptosporidium parvumandC. hominisare related protozoan pathogens which infect the intestinal epithelium of humans and other vertebrates. To explore the evolution of these parasites, and identify genes under positive selection, we performed a pairwise whole-genome comparison between all orthologous protein coding genes inC. parvumandC. hominis. Genome-wide calculation of the ratio of nonsynonymous versus synonymous nucleotide substitutions (dN/dS) was performed to detect the impact of positive and purifying selection. Of 2465 pairs of orthologous genes, a total of 27 (1.1%) showed a high ratio of nonsynonymous substitutions, consistent with positive selection. A majority of these genes were annotated as hypothetical proteins. In addition, proteins with transmembrane and signal peptide domains are significantly more frequent in the highdN/dSgroup.

scholarly journals Genome-wide identification and characterization of TIFY family genes in Moso Bamboo (Phyllostachys edulis) and expression profiling analysis under dehydration and cold stresses

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e2620 ◽  
Author(s):  
Zhuo Huang ◽  
Si-Han Jin ◽  
Han-Du Guo ◽  
Xiao-Juan Zhong ◽  
Jiao He ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Abiotic Stress Tolerance ◽  
Divergence Time ◽  
Purifying Selection ◽  
Moso Bamboo ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
Phyllostachys Edulis ◽  
Genome Wide

The proteins containing the TIFY domain belong to a plant-specific family of putative transcription factors and could be divided into four subfamilies: ZML, TIFY, PPD and JAZ. They not only function as key regulators of jasmonate hormonal response, but are also involved in responding to abiotic stress. In this study, we identified 24 TIFY genes (PeTIFYs) in Moso bamboo (Phyllostachys edulis) of Poaceae by analyzing the whole genome sequence. OnePeTIFYbelongs to TIFY subfamily, 18 and five belong to JAZ and ZML subfamilies, respectively. Two equivocal gene models were re-predicted and a putative retrotransposition event was found in a ZML protein. The distribution and conservation of domain or motif, and gene structure were also analyzed. Phylogenetic analysis with TIFY proteins ofArabidopsisandOryza sativaindicated that JAZ subfamily could be further divided to four groups. Evolutionary analysis revealed intragenomic duplication and orthologous relationship betweenP. edulis,O. sativa, andB. distachyon. Calculation of the non-synonymous (Ka) and synonymous (Ks) substitution rates and their ratios indicated that the duplication ofPeTIFYmay have occurred around 16.7 million years ago (MYA), the divergence time of TIFY family among theP. edulis-O. sativa,P. edulis-B. distachyon,andO. sativa-B. distachyonwas approximately 39 MYA, 39 MYA, and 45 MYA, respectively. They appear to have undergone extensive purifying selection during evolution. Transcriptome sequencing revealed that more than 50% ofPeTIFYgenes could be up-regulated by cold and dehydration stresses, and somePeTIFYsalso share homology to know TIFYs involved in abiotic stress tolerance. Our results made insights into TIFY family of Moso bamboo, an economically important non-timber forest resource, and provided candidates for further identification of genes involved in regulating responses to abiotic stress.

scholarly journals PSGfinder: fast identification of genes under divergent positive selection using the dynamic windows method

2017 ◽  
Author(s):  
Joël Tuberosa ◽  
Juan I. Montoya-Burgos
Keyword(s):  
Positive Selection ◽  
Research Laboratory ◽  
Orthologous Genes ◽  
Simple Method ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Link Type ◽  
Genome Wide ◽  
User Friendly ◽  
Multiple Comparison Correction

AbstractSummaryOrthologous genes evolving under divergent positive selection are those involved in divergent adaptive trajectories between related species. Current methods to identify such genes are complex and conservative or present some imperfections, limiting genome-wide searches. We present a simple method, Dynamic Windows, to detect regions of protein-coding genes evolving under divergent positive selection. This method is implemented in PSGfinder, a user-friendly and flexible software, allowing rapid genome-wide screenings of regions with a dN/dS >1. PSGfinder additionally includes an alignment cleaning procedure and an adapted multiple comparison correction to identify significant signals of positive selection.Availability and ImplementationPSGfinder is a software that implements the DWin method, is written in Python and is freely available with its documentation at: https://genev.unige.ch/research/laboratory/Juan-Montoya or at: https://github.com/joel-tuberosa/[email protected]; [email protected]

scholarly journals GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level

2020 ◽  
Vol 10 (12) ◽  
pp. 4369-4372
Author(s):  
Laura G. Macías ◽  
Eladio Barrio ◽  
Christina Toft
Keyword(s):  
Phylogenetic Analysis ◽  
Maximum Likelihood ◽  
Positive Selection ◽  
Molecular Level ◽  
Variable Number ◽  
Orthologous Genes ◽  
Genome Wide ◽  
A Genome ◽  
One To One ◽  
Python Package

One of the most widely used programs for detecting positive selection, at the molecular level, is the program codeml, which is implemented in the Phylogenetic Analysis by Maximum Likelihood (PAML) package. However, it has a limitation when it comes to genome-wide studies, as it runs on a gene-by-gene basis. Furthermore, the size of such studies will depend on the number of orthologous genes the genomes have income and these are often restricted to only account for instances where a one-to-one relationship is observed between the genomes. In this work, we present GWideCodeML, a Python package, which runs a genome-wide codeml with the option of parallelization. To maximize the number of analyzed genes, the package allows for a variable number of taxa in the alignments and will automatically prune the topology to fit each of them, before running codeml.

scholarly journals Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

2015 ◽  
Vol 112 (9) ◽  
pp. 2806-2811 ◽  
Author(s):  
Gavin M. Douglas ◽  
Gesseca Gos ◽  
Kim A. Steige ◽  
Adriana Salcedo ◽  
Karl Holm ◽  
...  
Keyword(s):  
Positive Selection ◽  
Large Scale ◽  
Gene Loss ◽  
Strong Support ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Flowering Plant ◽  
Whole Genome ◽  
Widespread Species ◽  
Genome Wide

Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000–300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a “head start” through a legacy of deleterious variants and differential expression originating in parental diploid populations.

scholarly journals Genome-Wide Comprehensive Analysis of the SABATH Gene Family in Arabidopsis and Rice

2019 ◽  
Vol 15 ◽  
pp. 117693431986086 ◽  
Author(s):  
Bin Wang ◽  
Min Li ◽  
Yijun Yuan ◽  
Shaofang Liu
Keyword(s):  
Positive Selection ◽  
Gene Family ◽  
Functional Divergence ◽  
Purifying Selection ◽  
Motif Analysis ◽  
Functional Conservation ◽  
Branch Site ◽  
Functional Differences ◽  
Genome Wide ◽  
Expansion Mechanism

Low molecular weight metabolites are important plant hormones and signaling molecules, and play an important part among the processes of plant development. Their activities may also be affected by the chemical modifications of methylation performed by SABATH. In this study, a total of 24 and 21 SABATH genes in Arabidopsis and rice, respectively, were identified and taken a comprehensive study. Phylogenetic analysis showed that AtSABATH and OsSABATH genes could be classified into 4 major groups and 6 subgroups. Gene expansion analysis showed that the main expansion mechanism of SABATH gene family in Arabidopsis and rice was tandem duplication and segmental duplication. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of 12 pairs paralogous of AtSABATH and OsSABATH genes indicated that the SABATH gene family in Arabidopsis and rice had gone through purifying selection. Positive selection analysis with site models and branch-site models revealed that AtSABATH and OsSABATH genes had undergone selective pressure for adaptive evolution. Motif analysis showed that certain motifs only existed in specific subgroups or species, which indicated that the SABATH proteins of Arabidopsis and rice appear divergence in different species and subgroups. Functional divergence analysis also suggested that the AtSABATH and OsSABATH subgroup genes had functional differences, and the positive selection sites which contributed to functional divergence among subgroups were detected. These results provide insights into functional conservation and diversification of SABATH gene family, and are useful information for further elucidating SABATH gene family functions.

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