scholarly journals Wheat Domestication Accelerated Evolution and Triggered Positive Selection in the β-Xylosidase Enzyme of Mycosphaerella graminicola

PLoS ONE ◽  
2009 ◽  
Vol 4 (11) ◽  
pp. e7884 ◽  
Author(s):  
Patrick C. Brunner ◽  
Nicolas Keller ◽  
Bruce A. McDonald
Keyword(s):  
Positive Selection ◽  
Mycosphaerella Graminicola ◽  
Accelerated Evolution

scholarly journals New exon ignites accelerated evolution of placental gene Nrk in the ancestral lineage of eutherians

2021 ◽  
Author(s):  
Guopeng Liu ◽  
Chunxiao Zhang ◽  
Yuting Wang ◽  
Guangyi Dai ◽  
Shu-Qun Liu ◽  
...  
Keyword(s):  
Positive Selection ◽  
Fitness Landscape ◽  
Induction Of Labor ◽  
Placental Development ◽  
Terrestrial Vertebrates ◽  
Regulatory Domains ◽  
Ancestral Lineage ◽  
Accelerated Evolution ◽  
Rate Test ◽  
Chorioallantoic Placenta

AbstractAccelerated evolution is often driven by the interaction between environmental factors and genes. However, it remains unclear whether accelerated evolution can be ignited. Here, we focused on adaptive events during the emergence of chorioallantoic placenta. We scanned the chromosome X and identified eight accelerated regions in the ancestral lineage of eutherian mammals. Five of these regions (P = 5.61 × 10−11 ~ 9.03 × 10−8) are located in the five exons of Nik-related kinase (Nrk), which is essential in placenta development and fetoplacental induction of labor. Moreover, a eutherian-specific exogenous exon lack of splice variant was found to be conserved. Structure modelling of NRK suggests that the accelerated exons and the eutherian-specific exon could change the enzymatic activity of eutherian NRK. Since the eutherian-specific exon was surrounded by accelerated exons, it indicates that the accelerated evolution of Nrk may be ignited by the emergence of the new exon in the ancestral lineage of eutherian mammals. The new exon might shift the function of Nrk and provide a new fitness landscape for eutherian species to explore. Although multiple exons were accelerated in both of the Nrk catalytic and regulatory domains, positive selection can only be revealed on the regulatory domain if the branch specific nonsynonymous and synonymous rate test was performed by PAML. Thus, it may be important to detect accelerated evolution when studying positive selection on coding regions. Overall, this work suggests that the fundamental process of placental development and fetoplacental induction of labor has been targeted by positive Darwinian selection. Identifying positively selected placental genes provides insights into how eutherian mammals gain benefits from the invasive chorioallantoic placenta to form one of the most successful groups among terrestrial vertebrates.

scholarly journals Positive selection drives accelerated evolution of mosquito salivary genes associated with blood-feeding

2013 ◽  
Vol 23 (1) ◽  
pp. 122-131 ◽  
Author(s):  
B. Arcà ◽  
C. J. Struchiner ◽  
V. M. Pham ◽  
G. Sferra ◽  
F. Lombardo ◽  
...  
Keyword(s):  
Positive Selection ◽  
Blood Feeding ◽  
Accelerated Evolution

scholarly journals Molecular evolution of PCSK family: Analysis of natural selection rate and gene loss

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0259085
Author(s):  
Najmeh Parvaz ◽  
Zahra Jalali
Keyword(s):  
Molecular Evolution ◽  
Positive Selection ◽  
Gene Loss ◽  
Experimental Studies ◽  
Bile Acid Metabolism ◽  
Future Studies ◽  
Accelerated Evolution ◽  
Family Analysis ◽  
Bioinformatics Study ◽  
Functional Relevance

Proprotein convertases subtilisin kexins are serine endoproteases, playing critical roles in the biological functions, including lipid, glucose, and bile acid metabolism, as well as cell proliferation, migration, and metastasis. Experimental studies have demonstrated the physiological functions of PCSKs and their association with diseases; however, studies on the evolutionary history and diversification of these proteins are missing. In the present research, a bioinformatics study was conducted on the molecular evolution of several PCSKs family members and gene loss events across placental mammalian. In order to detect evolutionary constraints and positive selection, the CodeML program of the PAML package was used. The results showed the positive selection to occur in PCSK1, PCSK3, PCSK5, and PCSK7. A decelerated rate of evolution was observed in PCSK7, PCSK3, and MBTPS1 in Carnivores compared to the rest of phylogeny, and an accelerated evolution of PCSK1, PCSK7, and MBTPS1 in Muridae family of rodents was found. Additionally, our results indicated pcsk9 gene loss in 12 species comprising Carnivores and bats (Chiroptera). Future studies are required to evaluate the functional relevance and selective evolutionary advantages associated with these modifications in PCSK proteins during evolution.

scholarly journals The evolution of brain size among the Homininae and selection at ASPM and MCPH1 genes

2021 ◽  
Vol 2 (2) ◽  
pp. 293-310
Author(s):  
Sandra Leyva-Hernández ◽  
Ricardo Fong-Zazueta ◽  
Luis Medrano-González ◽  
Ana Julia Aguirre-Samudio
Keyword(s):  
Positive Selection ◽  
Nucleotide Substitution ◽  
Brain Size ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Brain Evolution ◽  
Haplotype Blocks ◽  
Accelerated Evolution ◽  
Relationship Of ◽  
The Brain

We examined the evolutionary relationship of the ASPM (abnormal spindle-like microcephaly associated) and MCPH1 (microcephalin-1) genes with brain volume among humans and other primates. We obtained sequences of these genes from 14 simiiform species including hominins. Two phylogenetic analyses of ASPM exon 3 and MCPH1 exons 8 and 11 were performed to maximize taxon sampling or sequence extension to compare the nucleotide substitution and encephalization rates, and examine signals of selection. Further assessment of selection among humans was done through the analysis of non-synonymous and synonymous substitutions (dN/dS), and linkage disequilibrium (LD) patterns. We found that the accelerated evolution of brain size in hominids, is related to synchronic acceleration in the substitution rates of ASPM and MCPH1, and to signals of positive selection, especially in hominins. The dN/dS and LD analyses in Homo detected sites under positive selection and some regions with haplotype blocks at several candidate sites surrounded by blocks in LD-equilibrium. Accelerations and signals of positive selection in ASPM and MCPH1 occurred in different lineages and periods being ASPM more closely related with the brain evolution of hominins. MCPH1 evolved under positive selection in different lineages of the Catarrhini, suggesting independent evolutionary roles of this gene among primates.

scholarly journals Detecting positive selection within genomes: the problem of biased gene conversion

2010 ◽  
Vol 365 (1552) ◽  
pp. 2571-2580 ◽  
Author(s):  
Abhirami Ratnakumar ◽  
Sylvain Mousset ◽  
Sylvain Glémin ◽  
Jonas Berglund ◽  
Nicolas Galtier ◽  
...  
Keyword(s):  
Positive Selection ◽  
Gene Conversion ◽  
Evolutionary Genetics ◽  
Synonymous Substitution ◽  
Nucleotide Substitutions ◽  
Accelerated Evolution ◽  
A Genome ◽  
Biased Gene Conversion ◽  
Synonymous Substitution Rates ◽  
Wide Scale

The identification of loci influenced by positive selection is a major goal of evolutionary genetics. A popular approach is to perform scans of alignments on a genome-wide scale in order to find regions evolving at accelerated rates on a particular branch of a phylogenetic tree. However, positive selection is not the only process that can lead to accelerated evolution. Notably, GC-biased gene conversion (gBGC) is a recombination-associated process that results in the biased fixation of G and C nucleotides. This process can potentially generate bursts of nucleotide substitutions within hotspots of meiotic recombination. Here, we analyse the results of a scan for positive selection on genes on branches across the primate phylogeny. We show that genes identified as targets of positive selection have a significant tendency to exhibit the genomic signature of gBGC. Using a maximum-likelihood framework, we estimate that more than 20 per cent of cases of significantly elevated non-synonymous to synonymous substitution rates ratio ( d N / d S ), particularly in shorter branches, could be due to gBGC. We demonstrate that in some cases, gBGC can lead to very high d N / d S (more than 2). Our results indicate that gBGC significantly affects the evolution of coding sequences in primates, often leading to patterns of evolution that can be mistaken for positive selection.

scholarly journals Molecular Evolution of Tooth-Related Genes Provides New Insights into Dietary Adaptations of Mammals

2021 ◽  
Author(s):  
Yuan Mu ◽  
Ran Tian ◽  
Linlin Xiao ◽  
Di Sun ◽  
Zepeng Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Tooth Enamel ◽  
Feeding Habits ◽  
Positive Association ◽  
Acid Sites ◽  
Tooth Structure ◽  
Dietary Adaptation ◽  
Accelerated Evolution ◽  
Selection For ◽  
Selection Of

AbstractMammals have evolved different tooth phenotypes that are hypothesized to be associated with feeding habits. However, the genetic basis for the linkage has not been well explored. In this study, we investigated 13 tooth-related genes, including seven enamel-related genes (AMELX, AMBN, ENAM, AMTN, ODAM, KLK4 and MMP20) and six dentin-related genes (DSPP, COL1A1, DMP1, IBSP, MEPE and SPP1), from 63 mammals to determine their evolutionary history. Our results showed that different evolutionary histories have evolved among divergent feeding habits in mammals. There was stronger positive selection for eight genes (ENAM, AMTN, ODAM, KLK4, DSPP, DMP1, COL1A1, MEPE) in herbivore lineages. In addition, AMELX, AMBN, ENAM, AMTN, MMP20 and COL1A1 underwent accelerated evolution in herbivores. While relatively strong positive selection was detected in IBSP, SPP1, and DSPP, accelerated evolution was only detected for MEPE and SPP1 genes among the carnivorous lineages. We found positive selection on AMBN and ENAM genes for omnivorous primates in the catarrhini clade. Interestingly, a significantly positive association between the evolutionary rate of ENAM, ODAM, KLK4, MMP20 and the average enamel thickness was found in primates. Additionally, we found molecular convergence in some amino acid sites of tooth-related genes among the lineages whose feeding habit are similar. The positive selection of related genes might promote the formation and bio-mineralization of tooth enamel and dentin, which would make the tooth structure stronger. Our results revealed that mammalian tooth-related genes have experienced variable evolutionary histories, which provide some new insights into the molecular basis of dietary adaptation in mammals.

scholarly journals Robust inference of positive selection on regulatory sequences in the human brain

2020 ◽  
Vol 6 (48) ◽  
pp. eabc9863
Author(s):  
Jialin Liu ◽  
Marc Robinson-Rechavi
Keyword(s):  
Human Brain ◽  
Positive Selection ◽  
Binding Sites ◽  
A Priori ◽  
Cell Types ◽  
Ctcf Binding ◽  
Regulatory Sequences ◽  
Accelerated Evolution ◽  
Mouse Tissues ◽  
Affinity Change

A longstanding hypothesis is that divergence between humans and chimpanzees might have been driven more by regulatory level adaptations than by protein sequence adaptations. This has especially been suggested for regulatory adaptations in the evolution of the human brain. We present a new method to detect positive selection on transcription factor binding sites on the basis of measuring predicted affinity change with a machine learning model of binding. Unlike other methods, this approach requires neither defining a priori neutral sites nor detecting accelerated evolution, thus removing major sources of bias. We scanned the signals of positive selection for CTCF binding sites in 29 human and 11 mouse tissues or cell types. We found that human brain–related cell types have the highest proportion of positive selection. This result is consistent with the view that adaptive evolution to gene regulation has played an important role in evolution of the human brain.

scholarly journals Robust inference of positive selection on regulatory sequences in human brain

2020 ◽  
Author(s):  
Jialin Liu ◽  
Marc Robinson-Rechavi
Keyword(s):  
Human Brain ◽  
Positive Selection ◽  
Binding Sites ◽  
A Priori ◽  
Cell Types ◽  
Ctcf Binding ◽  
Sign Test ◽  
Regulatory Sequences ◽  
Accelerated Evolution ◽  
Mouse Tissues

AbstractA long standing hypothesis is that divergence between humans and chimpanzees might have been driven more by regulatory level adaptions than by protein sequence adaptations. This has especially been suggested for regulatory adaptions in the evolution of the human brain. There is some support for this hypothesis, but it has been limited by the lack of a reliable and powerful way to detect positive selection on regulatory sequences. We present a new method to detect positive selection on transcription factor binding sites, based on Orr’s sign test applied to a machine learning model of binding. Unlike other methods, this requires neither defining a priori neutral sites, nor detecting accelerated evolution, thus removing major sources of bias. The method is validated in flies, mice, and primates, by a McDonald-Kreitman-like measure of polymorphism vs. divergence, by experimental binding site gains and losses, and by changes in expression levels. We scanned the signals of positive selection for CTCF binding sites in 29 human and 11 mouse tissues or cell types. We found that human brain related cell types have the highest proportion of positive selection. This is consistent with the importance of adaptive evolution on gene regulation in the evolution of the human brain.

scholarly journals Genomic Evidence for Sensorial Adaptations to a Nocturnal Predatory Lifestyle in Owls

2020 ◽  
Vol 12 (10) ◽  
pp. 1895-1908 ◽  
Author(s):  
Pamela Espíndola-Hernández ◽  
Jakob C Mueller ◽  
Martina Carrete ◽  
Stefan Boerno ◽  
Bart Kempenaers
Keyword(s):  
Positive Selection ◽  
Genetic Basis ◽  
Sexual Size Dimorphism ◽  
Coding Regions ◽  
Accelerated Evolution ◽  
Genome Wide ◽  
Ancestral Branch ◽  
A Genome ◽  
History Of ◽  
Reversed Sexual Size Dimorphism

Abstract Owls (Strigiformes) evolved specific adaptations to their nocturnal predatory lifestyle, such as asymmetrical ears, a facial disk, and a feather structure allowing silent flight. Owls also share some traits with diurnal raptors and other nocturnal birds, such as cryptic plumage patterns, reversed sexual size dimorphism, and acute vision and hearing. The genetic basis of some of these adaptations to a nocturnal predatory lifestyle has been studied by candidate gene approaches but rarely with genome-wide scans. Here, we used a genome-wide comparative analysis to test for selection in the early history of the owls. We estimated the substitution rates in the coding regions of 20 bird genomes, including 11 owls of which five were newly sequenced. Then, we tested for functional overrepresentation across the genes that showed signals of selection. In the ancestral branch of the owls, we found traces of positive selection in the evolution of genes functionally related to visual perception, especially to phototransduction, and to chromosome packaging. Several genes that have been previously linked to acoustic perception, circadian rhythm, and feather structure also showed signals of an accelerated evolution in the origin of the owls. We discuss the functions of the genes under positive selection and their putative association with the adaptation to the nocturnal predatory lifestyle of the owls.

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