Domain-Specific Positive Selection Contributes to the Evolution of Arabidopsis Leucine-Rich Repeat Receptor-Like Kinase (LRR RLK) Genes

Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and development, the evolutionary mechanism for this functional diversification is currently unclear. In this study, we focused on the LRRII RLK subfamily to investigate the molecular mechanisms that might have led to the functional differentiation of Arabidopsis LRR RLK genes. Phylogenetic analysis of 14 genes in this subfamily revealed three well-supported groups (I, II, and III). RT-PCR analysis did not find many qualitative differences in expression among these 14 genes in various Arabidopsis tissues, suggesting that evolution of regulatory sequences did not play a major role in their functional divergence. We analyzed substitution patterns in the predicted ligand-binding regions of these genes to examine if positive selection has acted to produce novel ligand-binding specificities, using the nonsynonymous/synonymous rate ratio (d _N/d _S) as an indicator of selective pressure. Estimates of d _N/d _S ratios from multiple methods indicate that nonsynonymous substitutions accumulated during divergence of the three lineages. Positive selection is likely to have occurred along the lineages ancestral to groups II and III. We suggest that positive selection on the ligand-binding sites of LRRII RLKs promoted diversification of ligand-binding specificities and thus contributed to the functional differentiation of Arabidopsis LRRII RLK genes during evolution. [Reviewing Editor: Dr. Martin Kreitman]     

The effect of positive selection on a sexual reproduction gene in Thalassiosira weissflogii (Bacillariophyta): results obtained from maximum-likelihood and parsimony-based methods

Maximum-Likelihood-based and parsimony-based methods were used to test for potential effects of positive selection on the sexually induced gene 1 (Sig1) in Thalassiosira weissflogii. The Sig proteins are thought to play a role in mediating sperm-egg recognition during the sexual reproduction phase. The results obtained from parsimony-based analyses showed that none of the amino acid sites were influenced by positive selection. Maximum-likelihood analyses indicated that positive selection was affecting a maximum of seven and a minimum of four amino acid sites in the polypeptide derived from Sig1. It was concluded that the results obtained from the maximum-likelihood-based method are more reliable than those obtained from the parsimony-based approach. This is apparently the first study that has shown that reproductive proteins in unicellular eukaryotes are influenced by positive selection.     

Evidence of Positive Darwinian Selection in Putative Meningococcal Vaccine Antigens

Meningococcal meningitidis is a life-threatening disease. In Europe and the United States the majority of cases are caused by virulent meningococcal strains belonging to serogroup B. Presently there is no effective vaccine against serogroup B strains, as traditional vaccine antigens such as polysaccharide capsules are unusable as they lead to autoimmunity. The year 2000 saw the publication of the complete genome of Neisseria meningitidis MC58, a virulent serogroup B bacterium. Working in conjunction with the sequencing project, researchers endeavored to locate highly conserved membrane-associated proteins that elicit an immune response. It is hoped that these proteins will provide a basis for novel vaccines against serogroup B strains. A number of potential vaccine antigens have been located and are presently in phase I clinical trials. Recently many reports pertaining to the evidence of positive Darwinian selection in membrane proteins of pathogens have been reported. This study utilized in silico methods to test for evidence of historical positive Darwinian selection in seven such vaccine candidates. We found that two of these proteins show signatures of adaptive evolution, while the remaining proteins show evidence of strong purifying selection. This has significant implications for the design of a vaccine against serogroup B strains, as it has been shown that vaccines that target epitopes that are under strong purifying selection are better than those that target variable epitopes.[Reviewing Editor: Rasmus Nielsen]     

Molecular Evolution and Positive Selection of the Symbiotic Gene NORK in Medicago truncatula

Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be explored through the study of nucleotide polymorphism at loci controlling specificity. The membrane-anchored receptor NORK (nodulation receptor kinase) of the legume Medicago truncatula controls early steps of root infection by two symbiotic microorganisms: nitrogen-fixing bacteria (rhizobia) and endomycorrhizal fungi (Glomales). We analyzed the diversity of the gene NORK by sequencing 4 kilobases in 28 inbred lines sampled from natural populations. We detected 33 polymorphic sites with only one nonsynonymous change. Analysis based on Tajima’s D and Fay and Wu’s H summary statistics revealed no departure from the neutral model. We analyzed divergence using sequences from the closely related species M. coerulea. The McDonald-Kreitman test indicated a significant excess of nonsynonymous changes contributing to this divergence. Furthermore, maximum-likelihood analysis of a molecular phylogeny of a few legume species indicated that a number of amino acid sites, likely located in the receptor domain of the protein, evolved under the regime of positive selection. Further research should focus on the rate and direction of molecular coevolution between microorganisms’ signaling molecules and legumes’ receptors. [Reviewing Editor: Dr. Deborah Charlesworth] Sequence data were deposited in the GenBank database under accession nos. AY676428 to AY676457 and AJ884582.     

同源盒基因(Hox)与哺乳动物生殖

哺乳动物的同源盒基因（Hox）与果蝇的同源异形基因是同源基因,该基因编码的DNA片段含183碱基对,转录由61个氨基酸残基组成的蛋白质保守结构域,称同源异型域.Hox基因碱基顺序及在染色体中的位置都是高度保守的.Hox基因在体节结构分化等空间信息调控中起着重要作用,按特异的空间模式赋予每一体节其自身的特点.近年来的研究表明,Hox基因不但影响胚胎发育,而且与成体生殖系统分化有关,在着床期子宫接受态的建立及子宫蜕膜反应的发生等生殖过程中起着重要的调节作用.     

Molecular Evolution of Cytochrome c Oxidase Subunit IV: Evidence for Positive Selection in Simian Primates

Cytochrome c oxidase (COX) is a multi-subunit enzyme complex that catalyzes the final step of electron transfer through the respiratory chain on the mitochondrial inner membrane. Up to 13 subunits encoded by both the mitochondrial (subunits I, II, and III) and nuclear genomes occur in eukaryotic organisms ranging from yeast to human. Previously, we observed a high number of amino acid replacements in the human COX IV subunit compared to mouse, rat, and cow orthologues. Here we examined COX IV evolution in the two groups of anthropoid primates, the catarrhines (hominoids, cercopithecoids) and platyrrhines (ceboids), as well as one prosimian primate (lorisiform), by sequencing PCR-amplified portions of functional COX4 genes from genomic DNAs. Phylogenetic analysis of the COX4 sequence data revealed that accelerated nonsynonymous substitution rates were evident in the early evolution of both catarrhines and, to a lesser extent, platyrrhines. These accelerated rates were followed later by decelerated rates, suggesting that positive selection for adaptive amino acid replacement became purifying selection, preserving replacements that had occurred. The evidence for positive selection was especially pronounced along the catarrhine lineage to hominoids in which the nonsynonymous rate was first faster than the synonymous rate, then later much slower. The rates of three types of ``neutral DNA' nucleotide substitutions (synonymous substitutions, pseudogene nucleotide substitutions, and intron nucleotide substitutions) are similar and are consistent with previous observations of a slower rate of such substitutions in the nuclear genomes of hominoids than in the nuclear genomes of other primate and mammalian lineages. Received: 22 May 1996 / Accepted: 24 November 1996     

Observation on the Sexual Reproduction of Peridinium bipes Stein (Dinophyceae)

Sexual reproduction of the dinoflagellate Peridinium bipes Stein was observed. At the late growth season (from late March to early April), the small, unarmored motile cells i.e. gametes are produced by division of the cate cell. Isogamy occurs in this species. Two gametes in fusion are morphologically indistinguishable, but their behavior are different. Before fusion, two gametes are connected by a transparent granular structure and move quickly for about ten minutes. When the plasmogamy almost completes, the fusing cells stop moving for a while and the transverse flagellum of one gamete is cast off. By staining with modified carbol fuchsin, it was proved that the karyogamy takes place soon after plasmogamy and the change of chromosomes in this period was also observed. The zygote keeps motile for about 14 days before casts off its two flagella and becomes aplanozygote. During this period i.e. planozygote stage, the zygote enlarges from 55 × 50 μm to 75 ×70 μm, intercolary bands connecting thecai plates widen, lots of oil droplets are produced as storage granules. After sinking to the bottom of flask, aplano- zygote continues changing: exospore wall is cast off, mesospore wall and endospore wall are thickened, oil droplets turn to starch grains, protoplast contracts and becomes spherical, a large red lipid granule, perhaps eye-spot, appears. Afterward, aplanozygote has become hypnozygote i.e. resting cyst. The type of sexual reproduction, the amphiesma of the zygote, the resistance of hypnozygotic wall to acid and alkali, the relationship between fossil dinoflagellate remain and the wall of hypnozygote were discussed. It was also considered that the three formas of P. bipes named by Huber-Pestalozzi were the different stages of zygote development.     

Sexual dimorphism in cuticular hydrocarbons of the Australian field cricket Teleogryllus oceanicus (Orthoptera: Gryllidae)

Sexual dimorphism is presumed to reflect adaptive divergence in response to selection favouring different optimal character states in the two sexes. Here, we analyse patterns of sexual dimorphism in the cuticular hydrocarbons of the Australian field cricket Teleogryllus oceanicus using gas chromatography. Ten of the 25 peaks found in our chromatographs, differed in their relative abundance between the sexes. The presence of sexual dimorphism in T. oceanicus is discussed in reference to a review of sexual dimorphism in cuticular hydrocarbons of other insects. We found that this trait has been examined in 103 species across seven different orders. Seventy-six of these species (73%) displayed sex specificity of cuticular hydrocarbons, the presence/absence of which does not appear to be directly linked to phylogeny. The occurrence of sexual dimorphism in cuticular hydrocarbons of some but not other species, and the extent of variation within genera, suggest that this divergence has been driven primarily by sexual selection.     

Study on the Association Between Estrogen Receptor Gene (ESR) and Reproduction Traits in Landrace Pigs

To study the potential use of estrogen receptor gene (ESR) as a genetic marker to improve the reproductive traits of pigs, the genotypes of the ESR PCR product digested by Pvu II were determined in 2 239 litters from 612 Landrace sows. The data of the first, second, and later parities were separately evaluated. Although the frequency of the B allele was much lower than that of the A allele, likelihood ratio test showed that the gene frequencies were in Hardy-Weinberg equilibrium. The effects of ESR of different parities were not equal. In summary, the sows with the BB genotype showed better performance for total number of piglets born (TNB) and number of piglets born alive (NBA), but had a lower average piglet weight at birth (AWB). It was concluded that ESR could be used as a marker for the selection of litter size in the Landrace population.     

Sexual and vegetative reproduction in the aboveground part of a dioecious clonal plant, <Emphasis Type="Italic">Dioscorea japonica</Emphasis> (Dioscoreaceae)

In dioecious clonal plants, the reproductive effort required to set seeds will be responsible for the larger investment in sexual reproduction by females. If there will be a trade-off in resource allocation between sexual and clonal reproduction, this differential sexual reproduction will lead to sexual differentiation in the relative amount of clonal reproduction. To test this prediction, we studied differences between the sexes in their phenologies and investments in sexual and vegetative reproduction (clonal reproduction by means of bulbils) with respect to ramet size in a dioecious clonal plant, Dioscorea japonica Thunb. The period of bulbil production overlapped the period during which infructescences developed. Females flowered later, produced heavier inflorescences, and fewer flowers per inflorescence than did males. Regression analysis using the size of the individual plants demonstrated that large females made smaller investments in inflorescences and larger investments in sexual reproduction than did large males. In contrast, females invested fewer resources in vegetative reproduction than did males. However, the total investments in sexual and vegetative reproduction did not differ between the sexes. These results supported our hypothesis on the sexual differentiation in sexual and clonal reproduction.     

On auxospore formation inCaloneis and the nature ofAmphiraphia (Bacillariophyta)

Amphiraphia Chen & Zhu, together with theAmphiraphiaceae andAmphiraphidales, should be abandoned, sinceAmphiraphia cells are the heterovalvar initial cells ofCaloneis. WhenCaloneis reproduces sexually two cells pair and become surrounded by a two-layered capsule of mucilage. Each cell produces two gametes and these become rearranged within the gametangial frustule before plasmogamy. The gametes are amoeboid and fusion is isogamous. Following plasmogamy the zygote contracts, becomes ellipsoidal, and lays down a primary perizonial band. This is a complete, wide hoop, while subsequent perizonial bands are narrow and open.     

Evidence of Positive Darwinian Selection in Omp85, a Highly ConservedBacterial Outer Membrane Protein Essential for Cell Viability

Omp85 is a highly conserved outer membrane protein found in all gram-negative bacteria. It is essential for bacterial cell viability and plays an integral function in the positioning and folding of other outer membrane proteins into the bacterial outer membrane. We have employed a maximum likelihood and a maximum parsimony approach to detect evidence of positive Darwinian selection in Omp85 homologues from 10 -proteobacteria and have identified 14 amino acid sites that show evidence of being under the influence of adaptive evolution. Interestingly all sites bar one are concentrated within surface loops of the protein that most likely interact with host immune response or the surrounding environment. Alternatively amino acids within membrane-spanning regions of the protein are found to be under purifying selection most likely as a result of structural constraints.Reviewing Editor: Dr. Siv Anderson     

Positive and negative regulation of expression of the l-sorbose (sor) operon by SorC in Klebsiella pneumoniae

Summary In Klebsiella pneumoniae the gene products involved in the degradation of the ketose l-sorbose are encoded in the sor operon. It comprises, besides structural genes for uptake and catabolism, a promoter-proximal gene sorC, encoding a protein SorC of M_r 40 kDa, for which no enzymatic function has been detected. All sor genes are coordinately expressed and inducible by l-sorbose. Polar insertions and frameshift mutations in sorC cause a pleiotropic negative effect on the expression of all other sor genes. This defect is complemented in trans by the wild-type sorC ⁺ allele for frameshift mutations, but not for polar insertions. A single promoter for all sor genes, for which SorC is the activator, thus seems to be located in front of sorC. The repressor activity of SorC was demonstrated by complementation of constitutive sorC alleles with a sorC ⁺ allele leading to inducible expression of all sor genes, including sorC, which, as visualized by the use of a series of lacZ fusions, thus autoregulates its expression, both as an activator and a repressor.     

Proximate Mechanisms of Sexual Selection in the Firefly Photinus pyralis (Coleoptera: Lampyridae)

Male competition in courtships of the firefly Photinus pyralis is intense. Morphometric analysis revealed that male size is variable, possibly exhibiting alternative body plans. We examined the outcomes of courtships to determine the proximate mechanisms of selection that may have led to male allometry. Two distinct selective events exist within mate competition: (1) searching and (2) scramble competition. Although many courtships failed, those without rivals were shorter and successful males spent less time in the mate-guarding position than when several males were in competition. Winners outflashed rivals, but flash dialogs occurred at similar frequencies across rival densities, indicating that females require some quantum of information before mating. Female flash preference was examined in choice tests to evaluate female discrimination ability. Females preferred flashes of greater intensity and precedence. This suggests that flash synchronization is a competitive display rather than a cooperative behavior to maintain female responsiveness. Selection for male size was density dependent: females preferred large males in searching, while small males were favored in scrambles. Simulated scrambles showed that small males have superior locomotor abilities, allowing them to reach the female rapidly. Comparison with a species lacking scrambles, P. macdermotti, revealed that selection in P. pyralis is disruptive, targeting traits alternately, and may have led to the evolution of higher allometric ratios in a species with direct male competition. Both male competition and female choice are important determinants of the outcome of P. pyralis courtships.     

Sexual reproduction inEudorina elegans (chlorophyta,volvocales)

Sexual reproduction inEudorina elegans Ehr. was studied in detail in laboratory cultures, with particular regard to conjugation between gametes and gone colony formation. Male and female gametes fused after being induced by changing the medium. The anterior end, including the flagellar base, of the male gamete entered the anterior region of the female gamete. Fusion of the two protoplasts proceeded laterally and posteriorly. The male gamete bore a slender cytoplasmic protrusion at the base of the flagella. This structure has not been previously described in the male gamete ofEudorina, and may participate in plasmogamy. A biflagellate gone cell swam from the germinating zygote and secreted a gelatinous envelope. It then divided to form a gone colony within the gelatious envelope, which moved during colony formation by means of the two flagella which were retained intact from the original gone cell.     

Positive Selection on Nucleotide Substitutions and Indels in Accessory Gland Proteins of the Drosophila pseudoobscura Subgroup

Genes encoding reproductive proteins often diverge rapidly due to positive selection on nucleotide substitutions. While this general pattern is well established, the extent to which specific reproductive genes experience similar selection in different clades has been little explored, nor have possible targets of positive selection other than nucleotide substitutions, such as indels, received much attention. Here, we inspect for the signature of positive selection in the genes encoding five accessory gland proteins (Acps) (Acp26Aa, Acp32CD, Acp53Ea, Acp62F, and Acp70A) originally described from Drosophila melanogaster but with recognizable orthologues in the D. pseudoobscura subgroup. We compare patterns of selection within the D. psuedoobscura subgroup to those in the D. melanogaster subgroup. Similar patterns of positive selection were found in Acp26Aa and Acp62F in the two subgroups, while Acp53Ea and Acp70A experienced purifying selection in both subgroups. These proteins have thus remained targets for similar types of selection over long (>21-MY) periods of time. We also found several indel substitutions and polymorphisms in Acp26Aa and Acp32CD. These indels occur in the same regions as positively selected nucleotide substitutions for Acp26Aa in the D. pseudoobscura subgroup but not in the D. melanogaster subgroup. Rates of indel substitution within Acp26Aa in the D. pseudoobscura subgroup were up to several times those in noncoding regions of the Drosophila genome. This suggests that indel substitutions may be under positive selection and may play a key role in the divergence of some Acps. Electronic Supplementary Material Electronic Supplementary material is available for this article at and accessible for authorised users. [Reviewing Editor: Dr. Willis Swanson]     

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.     

Sexual competition in a group of captive bonobos (Pan paniscus)

We describe the occurrence of sexual competition, expressed as harassment of sexual interactions in a captive group of bonobos. We monitored all aggressive and pestering interventions during sexual interactions of three captive adult females, one adolescent, and three adult males. The study period covered two complete menstrual cycles for each female, with continuous daily observations. There was relatively little overt sexual competition by the males, in analogy with other studies. Most male interventions occurred towards interactions with the alfa female. The alfa female performed the most intense and the highest number of interventions towards the sexual interactions of the other females. The data provide evidence for female intra-sexual competition in this female dominant species.