Phylogeny Analysis and Adaptive Evolution of rbcL Gene in Lilium

2013 ◽  
Vol 781-784 ◽  
pp. 1835-1841
Author(s):  
Yong Xiong ◽  
Chun Yan Zhao ◽  
Qing Song Yang
Keyword(s):  
Phylogenetic Tree ◽  
Positive Selection ◽  
Adaptive Evolution ◽  
3D Model ◽  
Gc Content ◽  
Specific Model ◽  
Rbcl Gene ◽  
Site Specific ◽  
Phylogeny Analysis ◽  
Lilium Species

Rbcl gene of 13 Lilium species were amplified, sequenced and analyzed. By comparing the rbcL sequences with 32 other species retrieved from GenBank, the sequence divergences and the phyletic evolution were analyzed and the phylogenetic tree was constructed. All rbcL sequences across 45 species are 732 bp with an average GC content of 45.1%. Potentially parsimony informative characters (PIC) are 39. From the phylogenetic tree, it can be found that it consists of three branches which are Liliaceae Lilium (I), other Liliaceae genus (II), Trilliaceae and Palmae (III).3D model was structured by homology comparative SWISS-Model online and showed with RasTop sofeware.The evolutionary analyses from the site-specific model, the 142nd and 225th codon sites are found to be under positive selection in rbcL gene.

A Phenotype–Genotype Codon Model for Detecting Adaptive Evolution

2019 ◽  
Vol 69 (4) ◽  
pp. 722-738 ◽  
Author(s):  
Christopher T Jones ◽  
Noor Youssef ◽  
Edward Susko ◽  
Joseph P Bielawski
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary History ◽  
Life History Trait ◽  
Molecular Adaptation ◽  
Simulation Studies ◽  
Site Model ◽  
Branch Site ◽  
A Site ◽  
Post Hoc

Abstract A central objective in biology is to link adaptive evolution in a gene to structural and/or functional phenotypic novelties. Yet most analytic methods make inferences mainly from either phenotypic data or genetic data alone. A small number of models have been developed to infer correlations between the rate of molecular evolution and changes in a discrete or continuous life history trait. But such correlations are not necessarily evidence of adaptation. Here, we present a novel approach called the phenotype–genotype branch-site model (PG-BSM) designed to detect evidence of adaptive codon evolution associated with discrete-state phenotype evolution. An episode of adaptation is inferred under standard codon substitution models when there is evidence of positive selection in the form of an elevation in the nonsynonymous-to-synonymous rate ratio $\omega$ to a value $\omega > 1$. As it is becoming increasingly clear that $\omega > 1$ can occur without adaptation, the PG-BSM was formulated to infer an instance of adaptive evolution without appealing to evidence of positive selection. The null model makes use of a covarion-like component to account for general heterotachy (i.e., random changes in the evolutionary rate at a site over time). The alternative model employs samples of the phenotypic evolutionary history to test for phenomenological patterns of heterotachy consistent with specific mechanisms of molecular adaptation. These include 1) a persistent increase/decrease in $\omega$ at a site following a change in phenotype (the pattern) consistent with an increase/decrease in the functional importance of the site (the mechanism); and 2) a transient increase in $\omega$ at a site along a branch over which the phenotype changed (the pattern) consistent with a change in the site’s optimal amino acid (the mechanism). Rejection of the null is followed by post hoc analyses to identify sites with strongest evidence for adaptation in association with changes in the phenotype as well as the most likely evolutionary history of the phenotype. Simulation studies based on a novel method for generating mechanistically realistic signatures of molecular adaptation show that the PG-BSM has good statistical properties. Analyses of real alignments show that site patterns identified post hoc are consistent with the specific mechanisms of adaptation included in the alternate model. Further simulation studies show that the covarion-like component of the PG-BSM plays a crucial role in mitigating recently discovered statistical pathologies associated with confounding by accounting for heterotachy-by-any-cause. [Adaptive evolution; branch-site model; confounding; mutation-selection; phenotype–genotype.]

scholarly journals The complete mitochondrial genome of the intertidal spider (Desis jiaxiangi) provides novel insights into the adaptive evolution of the mitogenome and the evolution of spiders

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fan Li ◽  
Yunyun Lv ◽  
Zhengyong Wen ◽  
Chao Bian ◽  
Xinhui Zhang ◽  
...  
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Physiological Activity ◽  
Complete Mitochondrial Genome ◽  
Dynamic Environment ◽  
Data Set ◽  
History Of ◽  
Complete Mitogenome ◽  
Selection Signal ◽  
Positive Selection Signal

Abstract Background Although almost all extant spider species live in terrestrial environments, a few species live fully submerged in freshwater or seawater. The intertidal spiders (genus Desis) built silk nests within coral crevices can survive submerged in high tides. The diving bell spider, Argyroneta aquatica, resides in a similar dynamic environment but exclusively in freshwater. Given the pivotal role played by mitochondria in supplying most energy for physiological activity via oxidative phosphorylation and the environment, herein we sequenced the complete mitogenome of Desis jiaxiangi to investigate the adaptive evolution of the aquatic spider mitogenomes and the evolution of spiders. Results We assembled a complete mitogenome of the intertidal spider Desis jiaxiangi and performed comparative mitochondrial analyses of data set comprising of Desis jiaxiangi and other 45 previously published spider mitogenome sequences, including that of Argyroneta aquatica. We found a unique transposition of trnL2 and trnN genes in Desis jiaxiangi. Our robust phylogenetic topology clearly deciphered the evolutionary relationships between Desis jiaxiangi and Argyroneta aquatica as well as other spiders. We dated the divergence of Desis jiaxiangi and Argyroneta aquatica to the late Cretaceous at ~ 98 Ma. Our selection analyses detected a positive selection signal in the nd4 gene of the aquatic branch comprising both Desis jiaxiangi and Argyroneta aquatica. Surprisingly, Pirata subpiraticus, Hypochilus thorelli, and Argyroneta aquatica each had a higher Ka/Ks value in the 13 PCGs dataset among 46 taxa with complete mitogenomes, and these three species also showed positive selection signal in the nd6 gene. Conclusions Our finding of the unique transposition of trnL2 and trnN genes indicates that these genes may have experienced rearrangements in the history of intertidal spider evolution. The positive selection signals in the nd4 and nd6 genes might enable a better understanding of the spider metabolic adaptations in relation to different environments. Our construction of a novel mitogenome for the intertidal spider thus sheds light on the evolutionary history of spiders and their mitogenomes.

scholarly journals WATER VAPOUR WEIGHTED MEAN TEMPERATURE MODEL FOR GPS-DERIVED INTEGRATED WATER VAPOUR IN PENINSULAR MALAYSIA

2017 ◽  
Vol XLII-4/W5 ◽  
pp. 127-135 ◽  
Author(s):  
T. A. Musa ◽  
M. H. Mazlan ◽  
Y. D. Opaluwa ◽  
I. A. Musliman ◽  
Z. M. Radzi
Keyword(s):  
Water Vapour ◽  
Diurnal Cycle ◽  
Specific Model ◽  
Regional Model ◽  
Peninsular Malaysia ◽  
Site Specific ◽  
Weighted Mean Temperature ◽  
Integrated Water Vapour ◽  
Relationship Of ◽  
The Impact

This paper presents the development of T<sub>M</sub> model by using the radiosonde stations from Peninsular Malaysia. Two types of T<sub>M</sub> model were developed; site-specific and regional models. The result revealed that the estimation from site-specific model has small improvement compared to the regional model, indicating that the regional model is adequately to use in estimation of GPS-derived IWV over Peninsular Malaysia. Meanwhile, this study found that the diurnal cycle of T<sub>S</sub> has influenced the T<sub>M</sub>&amp;ndash;T<sub>S</sub> relationship. The separation between daytime and nighttime observation can improve the relationship of T<sub>M</sub>&amp;ndash;T<sub>S</sub>. However, the impact of diurnal cycle to IWV estimation is less than 1&amp;thinsp;%. The T<sub>M</sub> model from Global and Tropic also been evaluated. The Tropic T<sub>M</sub> model is superior to be utilized as compared to the Global T<sub>M</sub> model.

scholarly journals Berlian, SOJ A3 and Jawa Local Rice Varieties Phylogenetically Distinct From Oryza sativa Indica and Oryza sativa Japonica

el–Hayah ◽  
2019 ◽  
Vol 6 (4) ◽  
pp. 112-125
Author(s):  
Yudrik Lathif ◽  
Riri Wiyanti Retnaningtyas ◽  
Dwi Listyorini ◽  
Suharti Suharti
Keyword(s):  
Oryza Sativa ◽  
Phylogenetic Tree ◽  
Dna Barcode ◽  
Rbcl Gene ◽  
Tree Reconstruction ◽  
Rice Varieties ◽  
Local Varieties ◽  
Precise Position ◽  
Total Dna ◽  
Taxonomical Position

The genetic resources identification of Indonesian local rice varieties is a crucial work should be done to conserve our native germplasm. This research aimed to know the taxonomical position of East Java local rice varieties including Jawa (JW), Berlian (BR), and SOJ A3 (SJ) using DNA barcode based on rbcL gene. Total DNA of each sample was isolated from leaves. A pair of forward 5'-ATG TCA CCA CAA ACA SJA AC-3' and reverse 5'-TCG GTA CCT GCA GTA GC-3' primers were used to amplify fragments of rbcL gene resulting in 751bp, 755bp, and 754bp fragments from BR, SJ, and JW varieties, respectively. Phylogenetic tree reconstruction revealed that our three local varieties were forming a cluster separated from the widely cultivated subspecies Oryza sativa Indica and Oryza sativa Japonica. However, further studies are necessary to reveal a more precise position of the local varieties in a phylogenetic tree on the species level.

scholarly journals A Bayesian Mutation–Selection Framework for Detecting Site-Specific Adaptive Evolution in Protein-Coding Genes

2020 ◽  
Author(s):  
Nicolas Rodrigue ◽  
Thibault Latrille ◽  
Nicolas Lartillot
Keyword(s):  
Adaptive Evolution ◽  
Real Data ◽  
Data Sets ◽  
Protein Coding ◽  
Site Specific ◽  
Protein Coding Genes ◽  
Codon Substitution ◽  
Selection Framework ◽  
Dna Alignment ◽  
The Impact

Abstract In recent years, codon substitution models based on the mutation–selection principle have been extended for the purpose of detecting signatures of adaptive evolution in protein-coding genes. However, the approaches used to date have either focused on detecting global signals of adaptive regimes—across the entire gene—or on contexts where experimentally derived, site-specific amino acid fitness profiles are available. Here, we present a Bayesian site-heterogeneous mutation–selection framework for site-specific detection of adaptive substitution regimes given a protein-coding DNA alignment. We offer implementations, briefly present simulation results, and apply the approach on a few real data sets. Our analyses suggest that the new approach shows greater sensitivity than traditional methods. However, more study is required to assess the impact of potential model violations on the method, and gain a greater empirical sense its behavior on a broader range of real data sets. We propose an outline of such a research program.

scholarly journals Integrated structural and evolutionary analysis reveals common mechanisms underlying adaptive evolution in mammals

2020 ◽  
Vol 117 (11) ◽  
pp. 5977-5986 ◽  
Author(s):  
Greg Slodkowicz ◽  
Nick Goldman
Keyword(s):  
Positive Selection ◽  
Adaptive Evolution ◽  
Evolutionary Biology ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Protein Structures ◽  
Unexpected Finding ◽  
Evolutionary Analysis ◽  
Genomic Scale ◽  
Evolution Of Mammals

Understanding the molecular basis of adaptation to the environment is a central question in evolutionary biology, yet linking detected signatures of positive selection to molecular mechanisms remains challenging. Here we demonstrate that combining sequence-based phylogenetic methods with structural information assists in making such mechanistic interpretations on a genomic scale. Our integrative analysis shows that positively selected sites tend to colocalize on protein structures and that positively selected clusters are found in functionally important regions of proteins, indicating that positive selection can contravene the well-known principle of evolutionary conservation of functionally important regions. This unexpected finding, along with our discovery that positive selection acts on structural clusters, opens previously unexplored strategies for the development of better models of protein evolution. Remarkably, proteins where we detect the strongest evidence of clustering belong to just two functional groups: Components of immune response and metabolic enzymes. This gives a coherent picture of pathogens and xenobiotics as important drivers of adaptive evolution of mammals.

Sign in / Sign up

Export Citation Format

Share Document