裸子植物中光敏色素PHY-PAS1 结构域的适应性进化

光敏色素是一类红光/远红光受体, 在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHYPAS1 结构域存在于光敏色素基因家族的所有成员中, 对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生, 而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的, 并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化, 该研究利用分支模型、位点模型以及分支-位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明, 在由PHY-PAS1结构域序列构建的系统树中, 多数分支处于强烈的负选择压力下 (w<1); 有14个分支处于正选择压力下 (w>1), 其中13个分支发生在属内种间; 与之相比, 在较为古老的谱系中相对缺少这种正选择压力。     

裸子植物中光敏色素PHY-PAS1结构域的适应性进化

光敏色素是一类红光／远红光受体,在植物种子萌发到成熟的整个生长发育过程中均起重要的调节作用。光敏色素PHY-PAS1结构域存在于光敏色素基因家族的所有成员中,对调节发色团的光谱特性和光信号转导非常关键。光敏色素基因家族通过基因重复产生,而基因重复可能与物种形成有关。PHYP基因是裸子植物光敏色素基因家族发生第1次重复后产生的,并且以单拷贝形式存在。为了研究不同裸子植物PHYP基因编码蛋白的PHY-PAS1结构域在进化过程中是否受到相同的选择压力以及是否发生了适应性进化,该研究利用分支模型、位点模型以及分支．位点模型对裸子植物31条PHYP基因序列编码蛋白的PHY-PAS1结构域所受到的选择压力进行了分析。结果表明,在由PHY-PAS1结构域序列构建的系统树中,多数分支处于强烈的负选择压力下（ω〈1）：有14个分支处于正选择压力下（ω〉1）,其中13个分支发生在属内种间;与之相比,在较为古老的谱系中相对缺少这种正选择压力。     

Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages

The nonsynonymous (amino acid-altering) to synonymous (silent) substitution rate ratio (omega = d(N)/d(S)) provides a measure of natural selection at the protein level, with omega = 1, >1, and <1, indicating neutral evolution, purifying selection, and positive selection, respectively. Previous studies that used this measure to detect positive selection have often taken an approach of pairwise comparison, estimating substitution rates by averaging over all sites in the protein. As most amino acids in a functional protein are under structural and functional constraints and adaptive evolution probably affects only a few sites at a few time points, this approach of averaging rates over sites and over time has little power. Previously, we developed codon-based substitution models that allow the omega ratio to vary either among lineages or among sites. In this paper we extend previous models to allow the omega ratio to vary both among sites and among lineages and implement the new models in the likelihood framework. These models may be useful for identifying positive selection along prespecified lineages that affects only a few sites in the protein. We apply those branch-site models as well as previous branch- and site-specific models to three data sets: the lysozyme genes from primates, the tumor suppressor BRCA1 genes from primates, and the phytochrome (PHY) gene family in angiosperms. Positive selection is detected in the lysozyme and BRCA genes by both the new and the old models. However, only the new models detected positive selection acting on lineages after gene duplication in the PHY gene family. Additional tests on several data sets suggest that the new models may be useful in detecting positive selection after gene duplication in gene family evolution.     

Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites

Maximum-likelihood models of codon substitution were used to analyze sperm lysin genes of 25 abalone (HALIOTIS:) species to identify lineages and amino acid sites under diversifying selection. The models used the nonsynonymous/synonymous rate ratio (omega = d(N)/d(S)) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio tests suggested significant variation in selective pressure among lineages. The variable selective pressure provided an explanation for the previous observation that the omega ratio is >1 in comparisons of closely related species and <1 in comparisons of distantly related species. Computer simulations demonstrated that saturation of nonsynonymous substitutions and constraint on lysin structure were unlikely to account for the observed pattern. Lineages linking closely related sympatric species appeared to be under diversifying selection, while lineages separating distantly related species from different geographic locations were associated with low evolutionary rates. The selective pressure indicated by the omega ratio was found to vary greatly among amino acid sites in lysin. Sites under potential diversifying selection were identified. Ancestral lysins were inferred to trace the route of evolution at individual sites and to provide lysin sequences for future laboratory studies.     

Gene duplication and adaptive evolution of the CHS-like genes within the genus Rheum (Polygonaceae)

It is suggested that gene duplication plays an important role in adaptation and evolution of plants. In this study, we examined whether the genus Rheum, with extensive diversification in the Qinghai-Tibeten Plateau (QTP) and adjacent regions, possessed the duplication of the chalcone synthase (CHS) genes and whether it underwent positive evolution. Here we cloned CHS-like genes from 16 Rheum species. Phylogenetic analyses suggested that CHS-like genes from Rheum comprised two monophyletic lineages (subfamilies), both of which were sisters to another related genus. The results showed that a genus-specific duplication occurred after this genus originated. The comparison of non-synonymous/synonymous substitution ratios between the two lineages in Rheum further indicated that a few sites along the duplicate branch underwent positive selection. The findings indicate that the duplication of Rheum species could contribute to their adaptive ability to rapidly changing environments which was resulted from the large-scale uplifts stages of QTP.     

Evolutionary history and complementary selective relaxation of the duplicated PI genes in grasses

Gene duplication plays an important role in the evolution of organisms by allowing functional innovation and the divergence of duplicate genes. Previous studies found two PI-like genes in grass species, suggesting functional divergence between the paralogous copies. Here, we reconstructed the evolutionary history of two PI genes from major lineages of grasses and other monocot species, and demonstrated that two PI genes (PI1 and PI2) arose from a whole genome duplication that occurred in a common ancestor of extant grasses. Molecular evolutionary analyses at the family and tribal levels found strong purifying selection acting on two genes in grasses, consistent with the conserved class B function of the PI genes. Importantly, we detected different patterns of selective relaxation between the duplicated PI genes although no signature of positive selection was found. Likelihood ratio tests revealed that the ω ratio for M domain is significantly higher in PI1 than in PI2 but that for K domain is significantly higher in PI2 than in PI1. These findings imply that complementary selective relaxation occurs in two PI genes after duplication, and provide additional molecular evidence for the subfunctionalization of the duplicated PI genes in grasses.     

Physicochemical evolution and positive selection of the gymnosperm matK proteins

It is not clear whether matK evolves under Darwinian selection. In this study, the gymnosperm Taxaceae, Cephalotaxaceae and Pinaceae were used to illustrate the physicochemical evolution, molecular adaptation and evolutionary dynamics of gene divergence in matKs. matK sequences were amplified from 27 Taxaceae and 12 Cephalotaxaceae species. matK sequences of 19 Pinaceae species were retrieved from GenBank. The phylogenetic tree was generated using conceptual-translated amino acid sequences. Selective influences were investigated using standard d _N/d _S ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a phylogenetic context. Analyses revealed the presence of positive selection in matKs (N-terminal region, RT domain and domain X) of Taxaceae and Pinaceae, and found positive destabilizing selection in N-terminal region and RT domain of Cephalotaxaceae matK. Moreover, various amino acid properties were found to be influenced by destabilizing positive selection. Amino acid sites relating to these properties and to different secondary structures were found and have the potential to affect group II intron maturase function. Despite the evolutionary constraint on the rapidly evolving matK, this protein evolves under positive selection in gymnosperm. Several regions of matK have experienced molecular adaptation which fine-tunes maturase performance.     

Likelihood Analysis of the Chalcone Synthase Genes Suggests the Role of Positive Selection in Morning Glories (<Emphasis Type="Italic">Ipomoea</Emphasis>)

Chalcone synthase (CHS) is a key enzyme in the biosynthesis of flavonoides, which are important for the pigmentation of flowers and act as attractants to pollinators. Genes encoding CHS constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. In morning glories (Ipomoea), five functional CHS genes (A–E) have been described. Phylogenetic analysis of the Ipomoea CHS gene family revealed that CHS A, B, and C experienced accelerated rates of amino acid substitution relative to CHS D and E. To examine whether the CHS genes of the morning glories underwent adaptive evolution, maximum-likelihood models of codon substitution were used to analyze the functional sequences in the Ipomoea CHS gene family. These models used the nonsynonymous/synonymous rate ratio ( = d_N/d_S) as an indicator of selective pressure and allowed the ratio to vary among lineages or sites. Likelihood ratio test suggested significant variation in selection pressure among amino acid sites, with a small proportion of them detected to be under positive selection along the branches ancestral to CHS A, B, and C. Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication.     

Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton

Background

Heterophyllous aquatic plants show marked phenotypic plasticity. They adapt to environmental changes by producing different leaf types: submerged, floating and terrestrial leaves. By contrast, homophyllous plants produce only submerged leaves and grow entirely underwater. Heterophylly and submerged homophylly evolved under selective pressure modifying the species-specific optima for photosynthesis, but little is known about the evolutionary outcome of habit. Recent evolutionary analyses suggested that rbcL, a chloroplast gene that encodes a catalytic subunit of RuBisCO, evolves under positive selection in most land plant lineages. To examine the adaptive evolutionary process linked to heterophylly or homophylly, we analyzed positive selection in the rbcL sequences of ecologically diverse aquatic plants, Japanese Potamogeton.

Principal Findings

Phylogenetic and maximum likelihood analyses of codon substitution models indicated that Potamogeton rbcL has evolved under positive Darwinian selection. The positive selection has operated specifically in heterophyllous lineages but not in homophyllous ones in the branch-site models. This suggests that the selective pressure on this chloroplast gene was higher for heterophyllous lineages than for homophyllous lineages. The replacement of 12 amino acids occurred at structurally important sites in the quaternary structure of RbcL, two of which (residue 225 and 281) were identified as potentially under positive selection.

Conclusions/Significance

Our analysis did not show an exact relationship between the amino acid replacements and heterophylly or homophylly but revealed that lineage-specific positive selection acted on the Potamogeton rbcL. The contrasting ecological conditions between heterophyllous and homophyllous plants have imposed different selective pressures on the photosynthetic system. The increased amino acid replacement in RbcL may reflect the continuous fine-tuning of RuBisCO under varying ecological conditions.     

Duplication and diversification of trehalase confers evolutionary advantages on lepidopteran insects

Gene duplication provides a major source of new genes for evolutionary novelty and ecological adaptation. However, the maintenance of duplicated genes and their relevance to adaptive evolution has long been debated. Insect trehalase (Treh) plays key roles in energy metabolism, growth, and stress recovery. Here, we show that the duplication of Treh in Lepidoptera (butterflies and moths) is linked with their adaptation to various environmental stresses. Generally, two Treh genes are present in insects: Treh1 and Treh2. We report three distinct forms of Treh in lepidopteran insects, where Treh1 was duplicated into two gene clusters (Treh1a and Treh1b). These gene clusters differ in gene expression patterns, enzymatic properties, and subcellular localizations, suggesting that the enzymes probably underwent sub‐ and/or neofunctionalization in the lepidopteran insects. Interestingly, selective pressure analysis provided significant evidence of positive selection on duplicate Treh1b gene in lepidopteran insect lineages. Most positively selected sites were located in the alpha‐helical region, and several sites were close to the trehalose binding and catalytic sites. Subcellular adaptation of duplicate Treh1b driven by positive selection appears to have occurred as a result of selected changes in specific sequences, allowing for rapid reprogramming of duplicated Treh during evolution. Our results suggest that gene duplication of Treh and subsequent functional diversification could increase the survival rate of lepidopteran insects through various regulations of intracellular trehalose levels, facilitating their adaptation to diverse habitats. This study provides evidence regarding the mechanism by which gene family expansion can contribute to species adaptation through gene duplication and subsequent functional diversification.     

Evidence for positive selection on the floral scent gene isoeugenol-O-methyltransferase

Isoeugenol-O-methyltransferase (IEMT) is an enzyme involved in the production of the floral volatile compounds methyl eugenol and methyl isoeugenol in Clarkia breweri (Onagraceae). IEMT likely evolved by gene duplication from caffeic acid-O-methyltransferase followed by amino acid divergence, leading to the acquisition of its novel function. To investigate the selective context under which IEMT evolved, maximum likelihood methods that estimate variable d(N)/d(S) ratios among lineages, among sites, and among a combination of both lineages and sites were utilized. Statistically significant support was obtained for a hypothesis of positive selection driving the evolution of IEMT since its origin. Subsequent Bayesian analyses identified several sites in IEMT that have experienced positive selection. Most of these positions are in the active site of IEMT and have been shown by site-directed mutagenesis to have large effects on substrate specificity. Although the selective agent is unknown, the adaptive evolution of this gene may have resulted in increased effectiveness of pollinator attraction or herbivore repellence.     

Molecular evolution of the ent-kaurenoic acid oxidase gene in Oryzeae

We surveyed the substitution patterns in the ent-kaurenoic acid oxidase (KAO) gene in 11 species of Oryzeae with an outgroup in the Ehrhartoidaea. The synonymous and non-synonymous substitution rates showed a high positive correlation with each other, but were negatively correlated with codon usage bias and GC content at third codon positions. The substitution rate was heterogenous among lineages. Likelihood-ratio tests showed that the non-synonymous/synonymous rate ratio changed significantly among lineages. Site-specific models provided no evidence for positive selection of particular amino acid sites in any codon of the KAO gene. This finding suggested that the significant rate heterogeneity among some lineages may have been caused by variability in the relaxation of the selective constraint among lineages or by neutral processes.     

Molecular evolution of psbA gene in ferns: unraveling selective pressure and co-evolutionary pattern

ABSTRACT: BACKGROUND: The photosynthetic oxygen-evolving photo system II (PS II) produces almost the entire oxygen in the atmosphere. This unique biochemical system comprises a functional core complex that is encoded by psbA and other genes. Unraveling the evolutionary dynamics of this gene is of particular interest owing to its direct role in oxygen production. psbA underwent gene duplication in leptosporangiates, in which both copies have been preserved since. Because gene duplication is often followed by the non-fictionalization of one of the copies and its subsequent erosion, preservation of both psbA copies pinpoint functional or regulatory specialization events. The aim of this study was to investigate the molecular evolution of psbA among fern lineages. RESULTS: We sequenced psbA, which encodes D1 protein in the core complex of PSII, in 20 species representing 8 orders of extant ferns; then we searched for selection and convolution signatures in psbA across the 11 fern orders. Collectively, our results indicate that: (1) selective constraints among D1 protein relaxed after the duplication in 4 leptosporangiate orders; (2) a handful positively selected codons were detected within species of single copy psbA, but none in duplicated ones; (3) a few sites among D1 protein were involved in co-evolution process which may intimate significant functional/structural communications between them. CONCLUSIONS: The strong competition between ferns and angiosperms for light may have been the main cause for a continuous fixation of adaptive amino acid changes in psbA, in particular after its duplication. Alternatively, a single psbA copy may have undergone bursts of adaptive changes at the molecular level to overcome angiosperms competition. The strong signature of positive Darwinian selection in a major part of D1 protein is testament to this. At the same time, species own two psbA copies hardly have positive selection signals among the D1 protein coding sequences. In this study, eleven co-evolving sites have been detected via different molecules, which may be more important than others.     

Evolutionary Genomics and Adaptive Evolution of the Hedgehog Gene Family (Shh,Ihh and Dhh) in Vertebrates

The Hedgehog (Hh) gene family codes for a class of secreted proteins composed of two active domains that act as signalling molecules during embryo development, namely for the development of the nervous and skeletal systems and the formation of the testis cord. While only one Hh gene is found typically in invertebrate genomes, most vertebrates species have three (Sonic hedgehog – Shh; Indian hedgehog – Ihh; and Desert hedgehog – Dhh), each with different expression patterns and functions, which likely helped promote the increasing complexity of vertebrates and their successful diversification. In this study, we used comparative genomic and adaptive evolutionary analyses to characterize the evolution of the Hh genes in vertebrates following the two major whole genome duplication (WGD) events. To overcome the lack of Hh-coding sequences on avian publicly available databases, we used an extensive dataset of 45 avian and three non-avian reptilian genomes to show that birds have all three Hh paralogs. We find suggestions that following the WGD events, vertebrate Hh paralogous genes evolved independently within similar linkage groups and under different evolutionary rates, especially within the catalytic domain. The structural regions around the ion-binding site were identified to be under positive selection in the signaling domain. These findings contrast with those observed in invertebrates, where different lineages that experienced gene duplication retained similar selective constraints in the Hh orthologs. Our results provide new insights on the evolutionary history of the Hh gene family, the functional roles of these paralogs in vertebrate species, and on the location of mutational hotspots.     

Purifying selection and positive selection on the myxovirus resistance gene in mammals and chickens

The myxovirus resistance gene (Mx) expresses antiviral activity in many species, e.g. mouse, human and chicken. It is not clear if the antiviral activity of Mx has evolved in these species to inhibit a set of species-specific pathogens, nor what factors drive Mx evolution in different animal lineages. Therefore, it is important to determine the evolutionary pattern of Mx and positively selected sites which affect the antiviral activity of the Mx gene in mammals and birds. We used sequence comparisons among species to detect positively selected sites by conducting phylogenetic analysis. The two-ratio model was significantly better than the one-ratio model in four species (mouse, rat, chicken and duck, p<0.05). Although selection pressure varied among different lineages, Mx had strong purifying selection in mammals and positive selection in chicken and duck lineages. Relative rate test revealed that Mx evolved faster in chickens than in ducks (Tajima's relative rate test, chi(2)=7.17, p<0.01). In the further analysis using a branch-site model A test, 8 sites were positively selected in the chicken lineage while no positive selection signals were observed for any site in the other lineages. The branch-site model A test had a omega value of 4.374 for the chicken lineage (2Deltal=14.20, d.f.=1, p<0.001). Comparisons of all currently available Mx mRNA sequences showed that these predicted positively selected sites had been fixed in the chicken lineage, suggesting that the chicken Mx gene evolved within the species to resist newly challenging environments. There is an increased selection constraint leading to mammals, while positive selection has acted on the chicken Mx.     

Evolution of cd59 gene in mammals

The CD59-coding sequences were obtained from 5 mammals by PCR and BLAST, and combined with the available sequences in GenBank, the nucleotide substitution rates of mammalian cd59 were calcu- lated. Results of synonymous and nonsynonymous substitution rates revealed that cd59 experienced negative selection in mammals overall. Four sites experiencing positive selection were found by using "site-specific" model in PAML software. These sites were distributed on the molecular surface, of which 2 sites located in the key functional domain. Furthermore, "branch-site-specific" model detected 1 positive site in cd59a and cd59b lineages which underwent accelerated evolution caused by positive selection after gene duplication in mouse.     

Positive Darwinian selection at the pantophysin (Pan I) locus in marine gadid fishes

Maximum-likelihood models of codon substitution were used to test for positive Darwinian selection at the vesicle protein pantophysin in two allelic lineages segregating in the Atlantic cod Gadus morhua and in 18 related species of marine gadid fishes. Positive selection was detected in the two intravesicular loops of the integral membrane protein but not in four membrane-spanning regions or the 3' cytoplasmic tail. The proportion of positively selected sites (24.9%) and the mean nonsynonymous/synonymous rate ratio (omega = d(N)/d(S) = 5.35) were both greater in the first intravesicular (IV1) domain compared with the second intravesicular (IV2) domain (11.0% positively selected sites with mean omega = 3.76). Likelihood ratio tests comparing models that assume identical omega ratios along all branches of the phylogeny to those that allow omega ratios to vary among lineages were not significant for either the IV1 or IV2 domains, indicating that the selective pressures favoring amino acid replacements have operated consistently in both regions during the diversification of the group. Positive selection was observed in the IV1 domain in both G. morhua allelic lineages, and, although three of the four codons that differ between alleles were targets of positive selection in the broader group, no similar polymorphisms were detected in other taxa. The two G. morhua Pan I alleles appeared to have evolved before the speciation event separating it from its sister taxon, Theragra chalcogramma, and on the basis of a standard mtDNA clock are estimated to be at least 2 Myr old. Although the function of pantophysin remains unknown, the strong signal of positive selection at specific sites in the IV1 and IV2 domains may help clarify its role in cellular trafficking pathways.     

Two mitochondrial genes under episodic positive selection in subterranean octodontoid rodents

Tuco-tucos (Ctenomys) and related coruros (Spalacopus) are South American subterranean rodents. An energetically demanding lifestyle within the hypoxic, underground atmosphere may change the selective regime on oxidative phosphorylation. We examined whether weak and/or episodic positive directional selection affected the evolution of two mitochondrial genes (COX2, CytB), in a background of purifying selection in these lineages. We estimated rates of synonymous (dS) and non-synonymous (dN) substitutions and found: 1) significantly higher dN/dS ratio in subterranean groups relative to non-subterranean related species, and 2) two codons in each gene under episodic selection: 94 and 277 of COX2 and 269 and 307 of CytB.