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Background: The oceanic whitetip shark Carcharhinus longimanus (family Carcharhinidae) is one of the largest sharks inhabiting all tropical and subtropical oceanic regions. Due to their life history traits and mortality attributed to pelagic longline fishing practices, this species is experiencing substantial population decline. Currently, C. longimanus is considered by the IUCN Red List of Threatened Species as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. This study sequences and describes the complete mitochondrial genome of C. longimanus in detail. Methods and results: The mitochondrial genome of C. longimanus was assembled through next-generation sequencing and then analyzed using specialized bioinformatics tools. The circular, double-stranded AT-rich mitogenome of C. longimanus is 16,704 bp long and contains 22 tRNA genes, 2 rRNA genes, 13 protein coding genes and a 1,065 bp long control region (CR). Out of the 22 tRNA genes, only one (tRNA-Ser1) lacked a typical 'cloverleaf' secondary structure. The prevalence of TTA (Leu), ATT (Ile) and CTA (Leu) codons in the PCGs likely contributes to the AT-rich nature of this mitogenome. In the CR, ten microsatellites were detected but no tandem repeats were found. Stem-and-loop secondary structures were common along the entire length of the CR. Ka/Ks values estimated for all PCGs were < 1, indicating that all the PCGs experience purifying selection. A phylomitogenomic analysis based on translated PCGs confirms the sister relationship between C. longimanus and C. obscurus. The analysis did not support the monophyly of the genus Carcharhinus. Conclusions: The assembled mitochondrial genome of this pelagic shark can provide insight into the phylogenetic relationships in the genus Carcharhinus and aid conservation and management efforts in the Central Pacific Ocean. [ABSTRACT FROM AUTHOR]

We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. We use these examples to show how the study of conserved functions can integrate knowledge of a trait’s causal effects on fitness and its history of natural selection without invoking adaptation. We also show how conserved function provides a novel basis for addressing objections against evolutionary functions raised by Robert Cummins. [ABSTRACT FROM AUTHOR]

Type IB topoisomerases relax the torsional stress associated with DNA metabolism in the nucleus and mitochondria and constitute important molecular targets of anticancer drugs. Vertebrates stand out among eukaryotes by having two Type IB topoisomerases acting specifically in the nucleus (TOP1) and mitochondria (TOP1MT). Despite their major importance, the origin and evolution of these paralogues remain unknown. Here, we examine the molecular evolutionary processes acting on both TOP1 and TOP1MT in Chordata, taking advantage of the increasing number of available genome sequences. We found that both TOP1 and TOP1MT evolved under strong purifying selection, as expected considering their essential biological functions. Critical active sites, including those associated with resistance to anticancer agents, were found particularly conserved. However, TOP1MT presented a higher rate of molecular evolution than TOP1, possibly related with its specialized activity on the mitochondrial genome and a less critical role in cells. We could place the duplication event that originated the TOP1 and TOP1MT paralogues early in the radiation of vertebrates, most likely associated with the first round of vertebrate tetraploidization (1R). Moreover, our data suggest that cyclostomes present a specialized mitochondrial Type IB topoisomerase. Interestingly, we identified two missense mutations replacing amino acids in the Linker region of TOP1MT in Neanderthals, which appears as a rare event when comparing the genome of both species. In conclusion, TOP1 and TOP1MT differ in their rates of evolution, and their evolutionary histories allowed us to better understand the evolution of chordates. [ABSTRACT FROM AUTHOR]

Feather colours are used by avian species for defense, adaptation and signaling. Melanocortin-1 receptor (MC1R) gene is one of the genes responsible for feather colour. This study identified selection signatures in MC1R gene of Nigerian indigenous turkeys (NIT) using British United turkeys (BUT) as control breed to investigate the evolutionary processes that have shaped NIT with various feather colours. Complete MC1R gene of 146 NIT (76 males and 70 females) and 32 BUT (18 males and 14 females) were sequenced. Transition/transversion and codon usage biases were predicted using MEGA v6 software. The selective force acting on the gene was predicted using HyPhy software. The FST values were estimated using Arlequin v3.5. The highest transition/transversion bias was predicted for white BUT (1.00) while the lowest was predicted for black NIT (0.50). Negative dN-dS values, indicative of purifying selection, were observed in MC1R gene of all the turkeys. The highest pairwise FST was observed between the MC1R gene of white BUT and black NIT while the least was observed between lavender NIT and white NIT. No recombination event was observed in black NIT and white BUT. The relative synonymous codon usage was the same among different colours for some codons. Presence of purifying selection in MC1R gene of all the turkeys with different feather colours confirms that the gene plays role in many biological processes such as feather colouration, behaviour, pain perception, immunity, growth and adaptation. The results also suggested that the genetic mechanisms generating different feather colours in turkeys are conserved. [ABSTRACT FROM AUTHOR]

Background: The 'Zacatuche', 'Teporingo', or Volcano rabbit (Romerolagus diazi) belongs to the family Leporidae, is an endemic species restricted to the Central part of the Trans-Mexican Volcanic Belt, and is considered 'endangered' by the IUCN Red List of Threatened Species. Methods and Results: This study reports, for the first time, the complete mitochondrial genome of R. diazi and examined the phylogenetic position of R. diazi among other closely related co-familiar species using mitochondrial protein-coding genes (PCGs). The mitogenome of R. diazi was assembled from short Illumina 150 bp pair-end reads with a coverage of 189x. The AT-rich mitochondrial genome of R. diazi is 17,400 bp in length and is comprised of 13 PCGs, two ribosomal RNA genes, and 22 transfer RNA genes. The gene order observed in the mitochondrial genome of R. diazi is identical to that reported for other leporids. Phylogenetic analyses based on PCGs support the basal position of Romerolagus within the Leporidae, at least when compared to the genera Oryctolagus and Lepus. Nonetheless, additional mitochondrial genomes from species belonging to the genera Bunolagus, Sylvilagus, and Pronolagus, among others, are needed before a more robust conclusion about the derived vs basal placement of Romerolagus within the family Leporidae can be reached based on mitochondrial PCGs. Conclusions: This is the first genomic resource developed for R. diazi and it represents a tool to improve our understanding about the ecology and evolutionary biology of this iconic and endangered species. [ABSTRACT FROM AUTHOR]

Evolvulus alsinoides, belonging to the family Convolvulaceae, is an important medicinal plant widely used as a nootropic in the Indian traditional medicine system. In the genus Evolvulus, no research on the chloroplast genome has been published. Hence, the present study focuses on annotation, characterization, identification of mutational hotspots, and phylogenetic analysis in the complete chloroplast genome (cp) of E. alsinoides. Genome comparison and evolutionary dynamics were performed with the species of Solanales. The cp genome has 114 genes (80 protein-coding genes, 30 transfer RNA, and 4 ribosomal RNA genes) that were unique with total genome size of 157,015 bp. The cp genome possesses 69 RNA editing sites and 44 simple sequence repeats (SSRs). Predicted SSRs were randomly selected and validated experimentally. Six divergent hotspots such as trnQ-UUG, trnF-GAA, psaI, clpP, ndhF, and ycf1 were discovered from the cp genome. These microsatellites and divergent hot spot sequences of the Taxa 'Evolvulus' could be employed as molecular markers for species identification and genetic divergence investigations. The LSC area was found to be more conserved than the SSC and IR region in genome comparison. The IR contraction and expansion studies show that nine genes rpl2, rpl23, ycf1, ycf2, ycf1, ndhF, ndhA, matK, and psbK were present in the IR-LSC and IR-SSC boundaries of the cp genome. Fifty-four protein-coding genes in the cp genome were under negative selection pressure, indicating that they were well conserved and were undergoing purifying selection. The phylogenetic analysis reveals that E. alsinoides is closely related to the genus Cressa with some divergence from the genus Ipomoea. This is the first time the chloroplast genome of the genus Evolvulus has been published. The findings of the present study and chloroplast genome data could be a valuable resource for future studies in population genetics, genetic diversity, and evolutionary relationship of the family Convolvulaceae. [ABSTRACT FROM AUTHOR]

The composition of Potato virus Y strains found on the territory of Belarus, as well as the molecular variability of their genomes, was studied. The presence of strains PVYNTN (genotype A) and PVYNW (genotypes A and B) was shown. The degree of the identity between individual genome regions of the studied isolates ranges from 100 to 97.33%. Nucleotides that are under purifying selection were revealed in the sequences. [ABSTRACT FROM AUTHOR]

Background: WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. Objective: In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. Methods: For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. Results: We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2–7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress–response pathways. Conclusion: This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses. [ABSTRACT FROM AUTHOR]

Introduction: The high-affinity potassium transporter (HKT) gene family is implicated in the regulation of response to salt stress in different plants. Yet, knowledge remains very limited for them in the Rosaceae species. The whole genome sequences of the five Rosaceae species, including Fragaria vesca (woodland strawberry), Malus domestica (apple), Pyrus communis (pear), Prunus mume (mei) and Prunus persica (peach), give the opportunity to uncover the evolutionary pattern of the HKT genes among Rosaceae genomes. Objectives: The primary objective of this study was to identify the HKT genes in five Rosaceae species and understand the potential biological functions of the HKT genes in response to salt stress in Fragaria vesca. Methods: In this study, the HKT genes in five Rosaceae species were identified by bioinformatics. The phylogenetic tree was constructed and Ka and Ks values were calculated by MEGA 5.0. Genetic mapping of these genes were processed by MapInspect software. In addition, the physico-chemical properties, the cis-acting elements, the intron/exon structures, and the conserved domain motifs of these genes were analyzed and predicted by the websites of ProtParam, Pfam, PlantCARE, GSDS, MEME, and Motif Scan. Results: In the present study, a total of 12 HKT genes were identified from five Rosaceae species. In the phylogenetic tree, orthologous genes were clustering together rather than paralogous genes and PcHKTs underwent two species-specific duplications before the divergence of pear and apple.. Furthermore, various expression levels of FvHKT genes revealed that woodland strawberry HKT genes are associated in responding to the salt stress. The activities of ROS-scavenging enzymes, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) were also measured in different treatments of salt-stressed woodland strawberry leaves, which suggested that the three enzymes may also take part in response to salt stress. Conclusion: The Ka/Ks ratio demonstrated that purifying selection played a major role in the evolutionary processes of HKT genes among the Rosaceae species, and FvHKT genes are involved in response to salt stress. [ABSTRACT FROM AUTHOR]

Crassostrea gigas is a model mollusk, but its genetic features have not been studied comprehensively. In this study, we used whole-genome resequencing data to identify and characterize nucleotide diversity and population recombination rate in a diverse collection of 21 C. gigas samples. Our analyses revealed that C. gigas harbors both extremely high genetic diversity and recombination rates across the whole genome as compared with those of the other taxa. The noncoding regions, introns, intergenic spacers, and untranslated regions (UTRs) showed a lower level diversity than the synonymous sites. The larger introns tended to have lower diversity. Moreover, we found a negative association of the non-synonymous diversity with gene expression, which suggested that purifying selection played an important role in shaping genetic diversity. The nucleotide diversity at the 100- and 50-kb levels was positively correlated with population recombination rates, which was expected if the diversity was shaped by purifying selection or hitchhiking of advantageous mutants. Our work gives a general picture of the oyster’s polymorphism pattern and its association with recombination rates. [ABSTRACT FROM AUTHOR]

Disease-resistant genes (R genes) encode proteins that are involved in protecting plants from their pathogens and pests. Availability of complete genome sequences from soybean and common bean allowed us to perform a genome-wide identification and analysis of the Toll interleukin-1 receptor-like nucleotide-binding site leucine-rich repeat (TNL) proteins. Hidden Markov model (HMM) profiling of all protein sequences resulted in the identification of 117 and 77 regular TNL genes in soybean and common bean, respectively. We also identified TNL gene homologs with unique domains, and signal peptides as well as nuclear localization signals. The TNL genes in soybean formed 28 clusters located on 10 of the 20 chromosomes, with the majority found on chromosome 3, 6 and 16. Similarly, the TNL genes in common bean formed 14 clusters located on five of the 11 chromosomes, with the majority found on chromosome 10. Phylogenetic analyses of the TNL genes from Arabidopsis, soybean and common bean revealed less divergence within legumes relative to the divergence between legumes and Arabidopsis. Syntenic blocks were found between chromosomes Pv10 and Gm03, Pv07 and Gm10, as well as Pv01 and Gm14. The gene expression data revealed basal level expression and tissue specificity, while analysis of available microRNA data showed 37 predicted microRNA families involved in targeting the identified TNL genes in soybean and common bean. [ABSTRACT FROM AUTHOR]

A low ratio of nonsynonymous and synonymous substitution rates (dN/dS) at a codon is an indicator of functional constraint caused by purifying selection. Intuitively, the functional constraint would also be expected to prevent such a codon from being deleted. However, to the best of our knowledge, the correlation between the rates of deletion and substitution has never actually been estimated. Here, we use 8595 protein-coding region sequences from nine mammalian species to examine the relationship between deletion rate and dN/dS. We find significant positive correlations at the levels of both sites and genes. We compared our data against controls consisting of simulated coding sequences evolving along identical phylogenetic trees, where deletions occur independently of substitutions. A much weaker correlation was found in the corresponding simulated sequences, probably caused by alignment errors. In the real data, the correlations cannot be explained by alignment errors. Separate investigations on nonsynonymous (dN) and synonymous (dS) substitution rates indicate that the correlation is most likely due to a similarity in patterns of selection rather than in mutation rates. [ABSTRACT FROM AUTHOR]

Complete genome sequences of five fig badnavirus-1 (FBV-1) isolates from different geographic origins in Iran were obtained from infected fig plants using conventional sequencing of overlapping PCR fragment with appropriate primers. Phylogenetic analysis of these five Iranian isolates as well as the one previously sequenced USA isolate indicated that the Iranian isolates could be divided into two distinct subgroups, reflecting either divergences or two different origins. Iranian isolates were genetically distinct from the USA isolate. The phylogenetic analysis of the so-called diversity genomic region (992 nt) from 27 FBV-1 Iranian and 44 USA isolates gave two main groups. Sequences from Iran were distributed between two groups and the four subgroups of the first group besides other US isolates, and segregated according to their geographical origin. In contrast to the Iranian isolates, phylogenetic analysis grouped the USA isolates into three subgroups in the first group. To gain insight into the evolutionary forces driving the emergence of these FBV-1 populations, we analyzed the nucleotide sequences of the diversity genomic region from 71 FBV-1 isolates. Neutrality tests suggested the occurrence of purifying selection acting upon the population. For all genomic regions analyzed, diversity values were high for the nucleotide-coding sequences of the open reading frame 3, which suggests different selective constraints from the variation observed in the proteins encoded by this open reading frame. Low natural selection following founder events and rapid expansion of FBV-1 isolates into new ecological niches could result in the observed homogeneity of subpopulations. [ABSTRACT FROM AUTHOR]

The complete genome sequence of leek yellow stripe virus (LYSV) isolate AC-50 from garlic in India was determined and the predicted amino acid (aa) sequence was analyzed. The LYSV RNA genome is 10,131 nucleotides (nt) long excluding the poly(A) tail (KP168261) and has a large open reading frame (ORF) encoding a putative polyprotein of 3152 aa with conserved motifs typical of members of the genus Potyvirus in the family Potyviridae. The pretty interesting Potyviridae ORF (PIPO) coding region was identified in the P3 coding region. LYSV isolate AC-50 shares maximum nt and aa sequence identity of 79.9% and 87.2% with a LYSV isolate from Australia (HQ258895) at the full genome and polyprotein level, respectively, and clusters with clade II isolates from China, Mexico, Australia, Brazil and Spain. The P1 coding region of isolate AC-50 was highly variable with an identity range of 48.9-70.9% with other LYSV isolates and a deletion of 204 nt compared to Japanese and Australian isolates. The ratio of nonsynonymous (dN) and synonymous (dS) polymorphic sites suggested that purifying selection dominates in the evolution of LYSV and the mean dN/dS ratio was highest for P1, confirming that this coding region is under less evolutionary constraints. [ABSTRACT FROM AUTHOR]

Populus euphratica Oliv. is a poplar species that is distributed mainly in deserts, making it an interesting model in which to investigate molecular mechanisms underlying different stress responses. Here, we used molecular population genetic methods to detect potential selection in candidate genes belonging to the P. euphratica glutathione (GSH) peroxidase ( Gpx) family, which are associated with an enzymatic mechanism that combats oxidative damage caused by reactive oxygen species (ROS) in plant cells; earlier studies have shown that Gpx proteins play important roles in coping with increased ROS levels during biotic and abiotic stresses in plants. We analyzed the nucleotide diversity and divergence patterns of five loci encoding Gpx genes, and 16 reference loci used as controls, in order to detect departures from the neutral expectation. Gpx1 has an excess of mid-frequency alleles; high intraspecific nucleotide diversity, distributed in the upper tail of the simulated neutral model; and extensive LD, showing strong evidence of balancing selection/local adaptation. The Gpx3.2 gene exhibits very low nucleotide diversity and divergence, suggesting that it has evolved under strong purifying selection. We failed to detect any evidence for natural selection at the other loci ( Gpx2, Gpx4, and Gpx5) compared with the reference loci. The results show that nucleotide diversity and/or divergence differ greatly between members of the Gpx gene family, resulting from differential selective pressure acting on genes, and that adaptive evolution influenced the distribution of P. euphratica in desert regions. [ABSTRACT FROM AUTHOR]

Zingiberaceae or 'ginger family' is the largest family in the order 'Zingiberales' with more than 1300 species in 52 genera, which are mostly distributed throughout Asia, tropical Africa and the native regions of America with their maximum diversity in Southeast Asia. Many of the members are important spice, medicinal or ornamental plants including ginger, turmeric, cardamom and kaempferia. These plants are distinguished for the highly valuable metabolic products, which are synthesised through phenylpropanoid pathway, where type III polyketide synthase is the key enzyme. In our present study, we used sequence, structural and evolutionary approaches to scrutinise the type III polyketide synthase (PKS) repertoire encoded in the Zingiberaceae family. Highly conserved amino acid residues in the sequence alignment and phylogram suggested strong relationships between the type III PKS members of Zingiberaceae. Sequence and structural level investigation of type III PKSs showed a small number of variations in the substrate binding pocket, leading to functional divergence among these PKS members. Molecular evolutionary studies indicate that type III PKSs within Zingiberaceae evolved under strong purifying selection pressure, and positive selections were rarely detected in the family. Structural modelling and protein-small molecule interaction studies on Zingiber officinale PKS 'a representative from Zingiberaceae' suggested that the protein is comparatively stable without much disorder and exhibited wide substrate acceptance. [ABSTRACT FROM AUTHOR]

Mosquitoes are vectors of devastating pathogens and parasites, causing millions of deaths every year. Dengue is a mosquito-borne viral infection found in tropical and subtropical regions around the world. Recently, dengue transmission has strongly increased in urban and semiurban areas, becoming a major international public health concern. Aedes aegypti (Diptera: Culicidae) is a primary vector of dengue. Shedding light on genetic deviation in A. aegypti populations is of crucial importance to fully understand their molecular ecology and evolution. In this research, haplotype and genetic analyses were conducted using individuals of A. aegypti from 31 localities in the north, southeast, northeast and central regions of Tamil Nadu (South India). The mitochondrial DNA region of cytochrome c oxidase 1 ( CO1) gene was used as marker for the analyses. Thirty-one haplotypes sequences were submitted to GenBank and authenticated. The complete haplotype set included 64 haplotypes from various geographical regions clustered into three groups (lineages) separated by three fixed mutational steps, suggesting that the South Indian Ae. aegypti populations were pooled and are linked with West Africa, Columbian and Southeast Asian lineages. The genetic and haplotype diversity was low, indicating reduced gene flow among close populations of the vector, due to geographical barriers such as water bodies. Lastly, the negative values for neutrality tests indicated a bottle-neck effect and supported for low frequency of polymorphism among the haplotypes. Overall, our results add basic knowledge to molecular ecology of the dengue vector A. aegypti, providing the first evidence for multiple introductions of Ae. aegypti populations from Columbia and West Africa in South India. [ABSTRACT FROM AUTHOR]

Darwin's concept of sexual selection has been an area of intense research interest for the past half-century. Research has mainly focused on intersexual selection (selection arising from mate choice), and has particularly focused on the hypothesis that mates are chosen on the basis of 'genetic quality' which is 'honestly' signaled by sexually dimorphic traits. I discuss these models in the light of evidence that most genetic variation in real populations is either selectively neutral or slightly deleterious. Since several well-known models have focused on the immune system as a source of heritable variation in fitness, I examine evidence from studies of the vertebrate major histocompatibility complex and its interaction with pathogens. Finally, I discuss alternative hypotheses for the evolution of secondary sexual characteristics that are consistent with the prevalence of purifying selection rather than positive selection in most populations. One such model, the random walk model, relies only on the well-attested processes of mutation, purifying selection, and genetic drift, thereby providing an attractive alternative to models that assume ubiquitous positive selection. [ABSTRACT FROM AUTHOR]

The genetic variability of blueberry scorch virus (BlScV) isolates from New York was determined within a portion of the RNA-dependent RNA polymerase gene and the triple gene block and coat protein (CP) genes. Phylogenetic analysis of 19 New York isolates and other isolates for which sequence information is available in GenBank revealed two distinct clades, regardless of the coding region analyzed, and limited variability within (0.029 ± 0.007) and between (0.183 ± 0.032) phylogroups. Recombination events were identified in the CP gene of three New York isolates, and codons of the five BlScV genes characterized were found to be under neutral or negative selective pressure. [ABSTRACT FROM AUTHOR]

The teleost fishes depend on their innate immune system for first line of defense. Mannose binding lectin (MBL) is a member of the collectin family of proteins that plays an important role in the innate immune response in many vertebrates including fish. The present study was thus carried out to identify and characterize MBL homologue from snow trout. The cDNA of snow trout MBL homologue (galactose binding; Sch-GBL) was cloned and characterized. The obtained cDNA (778-bp) contains 762 bp long ORF (open reading frame) and a 16 bp partial 3′UTR (untranslated region); transcripts are ubiquitously expressed in all the tissues under study. Sch-GBL encodes a 253-aa protein that clusters with that of common carp, goldfish and contain several common structural motifs. In addition, the K/K ratios of the C-type lectin domain sequences depicts that they are under negative selection. Sch-GBL transcript level increases in response to challenge to Aeromonas hydrophila infection and decreases in response to downshift in temperature. Altogether, these findings suggest that Sch-GBL play an important role in the first line of fish defense mechanisms. [ABSTRACT FROM AUTHOR]

The prion protein (PrP) when misfolded into the pathogenic conformer PrP is the major causative agent of several lethal transmissible spongiform encephalopathies in mammals. Studies of evolutionary pressure on the corresponding gene using different datasets have yielded conflicting results. In addition, putative PrP or PrP interacting partners with strong similarity to PrP such as the doppel protein have not been examined to determine if the same evolutionary mechanisms apply to prion paralogs or if there are coselected sites that might indicate how and where the proteins interact. We examined several taxonomic groups that contain model organisms of prion diseases focusing on primates, bovids, and an expanded dataset of rodents for selection pressure on the prion gene ( PRNP) and doppel gene ( PRND) individually and for coevolving sites within. Overall, the results clearly indicate that both proteins are under strong selective constraints with relaxed selection on amino acid residues connecting α-helices 1 and 2. [ABSTRACT FROM AUTHOR]

bHLH/PAS genes encode a family of basic helix-loop-helix (bHLH) transcription factors with bHLH, PAS and PAS_3 domain. bHLH/PAS genes are involved in many essential physiological and developmental processes, such as hypoxic response neural development, the circadian clock, and learning ability. Despite their important functions, the origin and evolution of this bHLH/PAS gene family has yet to be elucidated. In this study, we aim to explore the origin, evolution, gene structure conservation of this gene family and provide a model to analyze the evolution of other gene families. Our results show that genes of the bHLH/PAS family only exist in metazoans. They may have originated from the common ancestor of metazoans and expanded into vertebrates. We identified bHLH/PAS genes in more than ten species representing the main lineages and constructed the phylogenetic trees (Beyasian, ML and NJ) to classify them into three groups. The exon-intron structure analysis revealed that a relatively conserved '1001-0210' eight-exon structure exists in most groups and lineages. In addition, we found the exon fusion pattern in several groups in this conserved eight-exon structure. Further analysis indicated that bHLH/PAS protein paralogs evolved from several gene duplication events followed by functional divergence and purifying selection. We presented a phylogenetic model to describe the evolutionary history of the exon structures of bHLH/PAS genes. Taken together, our study revealed the evolutionary model, functional divergence and gene structure conservation of bHLH/PAS genes. These findings provide clues for the functional and evolutionary mechanism of bHLH/PAS genes. [ABSTRACT FROM AUTHOR]

Neurexophilin 1 ( nxph1) has been considered a potential candidate marker for sperm storage in chicken sperm storage tubules. In this work, one mutation of chicken nxph1 was detected. We analyzed 18 nxph1 gene sequences from 18 species. The coding sequence length of the zebra fish nxph1 gene is 819 bp; that of the other species is 816 bp. Amino acid alignment analysis revealed that the gene product is a conserved protein, especially in mammals. The sequences of mammals are highly conserved. We found 202 conserved amino acids (70-271), and there were only eight mutations in the remaining 69 amino acids. That level of conservation could be due to the nxph1 gene having been subjected to substantial constraints or strong purifying selection during millions of years of evolution. [ABSTRACT FROM AUTHOR]

Single locus variants (SLVs) are bacterial sequence types that differ at only one of the seven canonical multilocus sequence typing (MLST) loci. Estimating the relative roles of recombination and point mutation in the generation of new alleles that lead to SLVs is helpful in understanding how organisms evolve. The relative rates of recombination and mutation for Campylobacter jejuni and Campylobacter coli were estimated at seven different housekeeping loci from publically available MLST data. The probability of recombination generating a new allele that leads to an SLV is estimated to be roughly seven times more than that of mutation for C. jejuni, but for C. coli recombination and mutation were estimated to have a similar contribution to the generation of SLVs. The majority of nucleotide differences (98 % for C. jejuni and 85 % for C. coli) between strains that make up an SLV are attributable to recombination. These estimates are much larger than estimates of the relative rate of recombination to mutation calculated from more distantly related isolates using MLST data. One explanation for this is that purifying selection plays an important role in the evolution of Campylobacter. A simulation study was performed to test the performance of our method under a range of biologically realistic parameters. We found that our method performed well when the recombination tract length was longer than 3 kb. For situations in which recombination may occur with shorter tract lengths, our estimates are likely to be an underestimate of the ratio of recombination to mutation, and of the importance of recombination for creating diversity in closely related isolates. A parametric bootstrap method was applied to calculate the uncertainty of these estimates. [ABSTRACT FROM AUTHOR]

The existence of four dengue serotypes is associated with a phenomenon called 'Antibody-Dependent Enhancement' that has been suggested to cause a severe form of dengue hemorrhagic fever and shock syndrome. To study the evolutionary event that drove the serotype separation, we employed the maximum likelihood approach by focusing on the Premembrane ( prM) and Envelop ( E) genes. We showed that the separation of dengue serotypes had been dominantly under purifying selection. In spite of the strong selective constraint, one codon of prM gene and twelve codons of E gene were detected to be under positive selection. This indicates that the E protein might have been under a stronger positive pressure than the PrM protein. The codons under positive selection were identified along the interserotypic branches, suggesting that changes at these sites were probably associated with the emergence of the four serotypes and/or adaptation to the new transmission environments. [ABSTRACT FROM AUTHOR]

Six full-length cDNA encoding boron transporters ( BOR) were isolated from Brassica napus (AACC) by rapid amplification of cDNA ends (RACE). The phylogenic analysis revealed that the six BORs were the orthologues of AtBOR1, which formed companying with the triplication and allotetra-ploidization process of B. napus, and were divided into three groups in B. napus. Each group was comprised of two members, one of which was originated from Brassica rapa (AA) and the other from Brassica oleracea (CC). Based on the phylogenetic relationships, the six genes were named as BnBOR1;1a, BnBOR1;1c, BnBOR1;2a, BnBOR1;2c, BnBOR1;3a and BnBOR1;3c, respectively. The deduced BnBOR1 s had extensive similarity with other plant BORs, with the identity of 74-96.8% in amino acid sequence. The BnBOR1;3a and BnBOR1;3c resembled AtBOR1 in number and positions of the 11 introns, but the others only have 9 introns. After the gene duplication, there was evidence of purifying selection under a divergent selective pressure. The expression patterns of the six BnBOR1 s were detected by semi-quantitative RT-PCR. The BnBOR1;3a and BnBOR1;3c showed a ubiquitous expression in all of the investigated tissues, whereas the other four genes showed similar tissue-specific expression profile. Unlike the non-transcriptional regulation of AtBOR1, the expression of BnBOR1;1c and BnBOR1;2a were obviously induced by boron deficiency. This study suggested that the BOR1 s had undergone a divergent expression pattern in the genome of B. napus after that the B. napus diverged from Arabidopsis thaliana. [ABSTRACT FROM AUTHOR]

Chemotaxis is a process in which bacteria sense their chemical environment and move towards more favorable conditions. Since plant colonization by bacteria is a multifaceted process which requires a response to the complex chemical environment, a finely tuned and sensitive chemotaxis system is needed. Members of the Bacillus subtilis group including Bacillus amyloliquefaciens are industrially important, for example, as bio-pesticides. The group exhibits plant growth-promoting characteristics, with different specificity towards certain host plants. Therefore, we hypothesize that while the principal molecular mechanisms of bacterial chemotaxis may be conserved, the bacterial chemotaxis system may need an evolutionary tweaking to adapt it to specific requirements, particularly in the process of evolution of free-living soil organisms, towards plant colonization behaviour. To date, almost nothing is known about what parts of the chemotaxis proteins are subjected to positive amino acid substitutions, involved in adjusting the chemotaxis system of bacteria during speciation. In this novel study, positively selected and purified sites of chemotaxis proteins were calculated, and these residues were mapped onto homology models that were built for the chemotaxis proteins, in an attempt to understand the spatial evolution of the chemotaxis proteins. Various positively selected amino acids were identified in semi-conserved regions of the proteins away from the known active sites. [ABSTRACT FROM AUTHOR]

While pectate lyases are major parasitism factors in plant-parasitic nematodes, there is little information on the variability of these genes within species and their utility as pathotype or host range molecular markers. We have analysed polymorphisms of pectate lyase 2 ( pel- 2) gene, which degrades the unesterified polygalacturonate (pectate) of the host cell-wall, in the genus Globodera. Molecular variability of the pel- 2 gene and the predicted protein was evaluated in populations of G. rostochiensis, G. pallida, G. ' mexicana' and G. tabacum. Seventy eight pel- 2 sequences were obtained and aligned. Point mutations were observed at 373 positions, 57% of these affect the coding part of the gene and produce 129 aa replacements. The observed polymorphism does not correlate either to the pathotypes proposed in potato cyst nematodes (PCN) or the subspecies described in tobacco cyst nematodes. The trees reveal a topology different from the admitted species topology as G. rostochiensis and G. pallida sequences are more similar to each other than to G. tabacum. Species-specific sites, potentially applicable for identification, and sites distinguishing PCN from tobacco cyst nematodes, were identified. As both G. rostochiensis and G. pallida display the same host range, but distinct from G. tabacum, which cannot parasitize potato plants, it is tempting to speculate that pel- 2 genes polymorphism may be implicated in this adaptation, a view supported by the fact that no active pectate lyase 2 was found in G. ' mexicana', a close relative of G. pallida that is unable to develop on cultivated potato varieties. [ABSTRACT FROM AUTHOR]

far as protein-coding genes are concerned, there is a non-zero probability that at least one of the five possible overlapping sequences of any gene will contain an open-reading frame (ORF) of a length that may be suitable for coding a functional protein. It is, however, very difficult to determine whether or not such an ORF is functional. Recently, we proposed a method that predicts functionality of an overlapping ORF if it can be shown that it has been subject to purifying selection during its evolution. Here, we use simulation to test this method under several conditions and compare it with the method of Firth and Brown. We found that under most conditions, our method detects functional overlapping genes with higher sensitivity than Firth and Brown’s method, while maintaining high specificity. Further, we tested the hypothesis that the two aminoacyl tRNA synthetase classes have originated from a pair of overlapping genes. A central piece of evidence ostensibly supporting this hypothesis is the assertion that an overlapping ORF of a heat-shock protein-70 gene, which exhibits some similarity to class 2 aminoacyl tRNA synthetases, is functional. We found signature of purifying selection only in highly divergent sequences, suggesting that the method yields false-positives in high sequence divergence and that the overlapping ORF is not a functional gene. Finally, we examined three cases of overlap in the human genome. We find varying signatures of purifying selection acting on these overlaps, raising the possibility that two of the overlapping genes may not be functional. [ABSTRACT FROM AUTHOR]

Silk production has independently evolved in numerous arthropod lineages, such as Lepidoptera, the moths and butterflies. Lepidopteran larvae (caterpillars) synthesize silk proteins in modified salivary glands and spin silk fibers into protective tunnels, escape lines, and pupation cocoons. Molecular sequence data for these proteins are necessary to determine critical features of their function and evolution. To this end, we constructed an expression library from the silk glands of the ghost moth, Hepialus californicus, and characterized light chain fibroin and heavy chain fibroin gene transcripts. The predicted H. californicus silk fibroins share many elements with other lepidopteran and trichopteran fibroins, such as conserved placements of cysteine, aromatic, and polar amino acid residues. Further comparative analyses were performed to determine site-specific signatures of selection and to assess whether fibroin genes are informative as phylogenetic markers. We found that purifying selection has constrained mutation within the fibroins and that light chain fibroin is a promising molecular marker. Thus, by characterizing the H. californicus fibroins, we identified key functional amino acids and gained insight into the evolutionary processes that have shaped these adaptive molecules. [ABSTRACT FROM AUTHOR]

The principal energy generating system in animals is the oxidative phosphorylation (OXPHOS) pathway, which depends on the tight interaction of nuclear- and mitochondrial-encoded genes to function properly. Mitochondrial genes accumulate substitutions more quickly than nuclear genes, yet the impact of selection on mitochondrial genes is significantly reduced relative to nuclear genes because of the non-recombining nature of the mitochondrial genome and its predicted smaller effective population size. It has therefore been hypothesized that the nuclear-encoded genes of the OXPHOS pathway are under strong selective pressure to compensate for the accumulation of deleterious nucleotide substitutions in mitochondrial-encoded OXPHOS genes, a process known as compensatory co-adaptation. We evaluated this hypothesis by analyzing nuclear-encoded OXPHOS genes for signatures of positive selection as well as evolutionary constraints at amino acid sites. We considered OXPHOS genes of six holometabolous insects and their orthologs from three Nasonia parasitoid wasps, the hybrids of which suffer from an increased mortality rate caused by cytonuclear genic incompatibilities. Although nuclear OXPHOS genes are typically highly conserved, we found significant evidence for elevated amino acid divergence in 4 of the 59 studied nuclear-encoded OXPHOS genes. We also found that three of these four genes, as well as six other OXPHOS genes, contain amino acid substitutions between Nasonia species at evolutionarily constrained sites. It is possible that these genes account for the reported incompatibility in Nasonia hybrids and their characterization may lead to a better understanding of the role of positive selection in the genetics of speciation. [ABSTRACT FROM AUTHOR]

In mammals, the matrix extracellular phosphoglycoprotein (MEPE) is known to activate osteogenesis and mineralization via a particular region called dentonin, and to inhibit mineralization via its ASARM (acidic serine-aspartate rich MEPE-associated motif) peptide that also plays a role in phosphatemia regulation. In order to understand MEPE evolution in mammals, and particularly that of its functional regions, we conducted an evolutionary analysis based on the study of selective pressures. Using 37 mammalian sequences we: (1) confirmed the presence of an additional coding exon in most placentals; (2) highlighted several conserved residues and regions that could have important functions; (3) found that dentonin function was recruited in a placental ancestor; and (4) revealed that ASARM function was present earlier, pushing the recruitment of MEPE deep into amniote origins. Our data indicate that MEPE was involved in various functions (bone and eggshell mineralization) prior to acquiring those currently known in placental mammals. [ABSTRACT FROM AUTHOR]

Enamelin (ENAM) plays an important role in the mineralization of the forming enamel matrix. We have performed an evolutionary analysis of mammalian ENAM to identify highly conserved residues or regions that could have important function (selective pressure), to predict mutations that could be associated with amelogenesis imperfecta in humans, and to identify possible adaptive evolution of ENAM during 200 million years ago of mammalian evolution. In order to fulfil these objectives, we obtained 36-ENAM sequences that are representative of the mammalian lineages. Our results show a remarkably high conservation pattern in the region of the 32-kDa fragment of ENAM, especially its phosphorylation, glycosylation, and proteolytic sites. In primates and rodents we also identified several sites under positive selection, which could indicate recent evolutionary changes in ENAM function. Furthermore, the analysis of the unusual signal peptide provided new insights on the possible regulation of ENAM secretion, a hypothesis that should be tested in the near future. Taken together, these findings improve our understanding of ENAM evolution and provide new information that would be useful for further investigation of ENAM function as well as for the validation of mutations leading to amelogenesis imperfecta. [ABSTRACT FROM AUTHOR]

Period ( Per) is a canonical circadian clock gene. The fruit fly, an invertebrate, has one per gene, while the human, a tetrapod vertebrate, has three Per genes. Per1, Per2, and Per3 of the tetrapods were generated from two rounds of ancient genome duplications from the ancestral chordate Per gene. Searching for five teleost fish genomes in a combination of phylogenetic, splicing site, and syntenic analyses revealed that zebrafish have two per1 genes, per1a and per1b, one per2, and one per3; medaka, fugu, and tetraodon each have two per2 genes, per2a and per2b, one per1, and one per3; sticklebacks also have per2a, per2b, and one per1 but lack per3; and per1a/ per1b in zebrafish and per2a/ per2b in madaka, fugu, tetraodon, and stickleback are ancient duplicates. While the dN/dS ratios of the five fish per duplicates are all <1, suggesting that they likely have been subject to purifying selection, the Tajima relative rate test showed that zebrafish per1a/ per1b and fugu and medaka per2a/ per2b have asymmetric evolutionary rates, implicating that one of these duplicates might have been under positive selection or relaxed functional constraint. Further, in situ hybridization showed that zebrafish per1a and per1b clearly have distinct patterns of temporal and spatial expression. These results support the notion that extra copies of teleost per genes were generated from the fish-specific genome duplication, and divergent resolution after the duplication resulted in retention of different per duplicates in different fish, most of which have diverged significantly. [ABSTRACT FROM AUTHOR]

The class II genes of the major histocompatibility complex encode proteins which play a crucial role in antigen presentation. They are among the most polymorphic proteins known, and this polymorphism is thought to be the result of natural selection. To understand the selective pressure acting on the protein and to examine possible differences in the evolutionary dynamics among species, we apply maximum likelihood models of codon substitution to analyze the DRB genes of six mammalian species: human, chimpanzee, macaque, tamarin, dog, and cow. The models account for variable selective pressures across codons in the gene and have the power to detect amino acid residues under either positive or negative selection. Our analysis detected positive selection in the DRB genes in each of the six mammals examined. Comparison with structural data reveals that almost all amino acid residues inferred to be under positive selection in humans are in the peptide binding region (PBR) and are in contact with the antigen side chains, although residues outside of but close to the PBR are also detected. Strong purifying selection is also detected in the PBR, at sites which contact the antigen and at sites which may be involved in dimerization or T cell binding. The analysis demonstrates the utility of the random-sites analysis even when structural information is available. The different mammalian species are found to share many positively or negatively selected sites, suggesting that their functional roles have remained very similar in the different species, despite the different habitats and pathogens of the species. [ABSTRACT FROM AUTHOR]

We found that the Black grouse ( Tetrao tetrix) possess low numbers of Mhc class II B ( BLB) and Y ( YLB) genes with variable diversity and expression. We have therefore shown, for the first time, that another bird species (in this case, a wild lek-breeding galliform) shares several features of the simple Mhc of the domestic chicken ( Gallus gallus). The Black grouse BLB genes showed the same level of polymorphism that has been reported in chicken, and we also found indications of balancing selection in the peptide-binding regions. The YLB genes were less variable than the BLB genes, also in accordance with earlier studies in chicken, although their functional significance still remains obscure. We hypothesize that the YLB genes could have been under purifying selection, just as the mammal Mhc- E gene cluster. [ABSTRACT FROM AUTHOR]

The Odysseus ( OdsH) gene was duplicated from its ancestral neuron-expressed gene, unc-4, and then evolved very rapidly under strong positive Darwinian selection as a speciation gene causing hybrid-male sterility between closely related species of the Drosophila simulans clade. Has OdsH also experienced similar positive selection between Drosophila sibling species other than those of the simulans clade? We cloned and sequenced OdsH and unc-4 from two clades of the Drosophila montium species subgroup, the Drosophila lini and the Drosophila kikkawai clades. The ratios of Ka/Ks for OdsH were remarkably low between sibling species of these two clades, suggesting that OdsH has been subjected to strong purifying selection in these two clades. [ABSTRACT FROM AUTHOR]

The HSP70 protein family consists one of the most conserved and important systems for cellular homeostasis under both stress and physiological conditions. The genes of this family are poorly studied in Mollusca, which is the second largest metazoan phylum. To study these genes in Mollusca, we have isolated and identified five HSP70 genes from Mytilus galloprovincialis (Mediterranean mussel) and investigated their short-term evolution within Mollusca and their long-term evolution within Metazoa. Both sequence and phylogenetic analyses suggested that the isolated genes belong to the cytoplasmic (CYT) group of the HSP70 genes. Two of these genes probably represent cognates, whereas the remaining probably represent heat-inducible genes. Phylogenetic analysis including several molluscan CYT HSP70s reveals that the cognate genes in two species have very similar sequences and form intraspecies phylogenetic clades, differently from most metazoan cognate genes studied thus far, implying either recent gene duplications or concerted evolution. The M. galloprovincialis heat-inducible genes show intraspecies phylogenetic clustering, which in combination with the higher amino acid than nucleotide identity suggests that both gene conversion and purifying selection should be responsible for their sequence homogenization. Phylogenetic analysis including several metazoan HSP70s suggests that at least two types of CYT genes were present in the common ancestor of vertebrates and invertebrates, the first giving birth to the heat-inducible genes of invertebrates, whereas the other to both the heat-inducible genes of vertebrates and the cognate genes of all metazoans. These analyses also suggest that inducible and cognate genes seem to undergo divergent evolution. [ABSTRACT FROM AUTHOR]

The H1 histone multigene family shows the greatest diversity of isoforms among the five histone gene families, including replication-dependent (RD) and replication-independent (RI) genes, according to their expression patterns along the cell cycle and their genomic organization. Although the molecular characterization of the RI isoforms has been well documented in vertebrates, similar information is lacking in invertebrates. In this work we provide evidence for a polyadenylation signature in the Mytilus “orphon” H1 genes similar to the polyadenylation characteristic of RI H1 genes. These mussel genes, together with the sea urchin H1δ genes, are part of a lineage of invertebrate “orphon” H1 genes that share several control elements with vertebrate RI H1 genes. These control elements include the UCE element, H1-box and H4-box. We provide evidence for a functional evolution of vertebrate and invertebrate RI H1 genes, which exhibit a clustering pattern by type instead of by species, with a marked difference from the somatic variants. In addition, these genes display an extensive silent divergence at the nucleotide level which is always significantly larger than the nonsilent. It thus appears that RI and RD H1 isoforms display similar long-term evolutionary patterns, best described by the birth-and-death model of evolution. Notably, this observation is in contrast with the theoretical belief that clustered RD H1 genes evolve in a concerted manner. The split of the RI group from the main RD group must therefore have occurred before the divergence between vertebrates and invertebrates about 815 million years ago. This was the result of the transposition of H1 genes to solitary locations in the genome. [ABSTRACT FROM AUTHOR]

In order to identify single-nucleotide polymorphisms (SNPs) and analyze their characteristics in a set of 111 genes, we resequenced exons and flanking regions in an average of 170 chromosomes from individuals of European origin. Genetic variability was decreased in noncoding regions highly conserved between human and rodents, indicating functional relevance of these regions. Furthermore, diversity of coding nonsynonymous SNPs was found lower in regions encoding a known protein sequence motif. SNPs predicted to be of functional significance were more common amongst rare variants. Despite the significant recent growth of SNP numbers in public SNP databases, only a small fraction of these rare variants is represented. This may be relevant in the investigation of the genetic causes of severe side effects, for which rare variants are plausible candidates. Estimation of htSNPs reduces the genotyping effort required in capturing common haplotypes, for certain genes, however, this accounts for only a small fraction of haplotype diversity.The Pharmacogenomics Journal (2005) 5, 183-192. doi:10.1038/sj.tpj.6500306 Published online 5 April 2005 [ABSTRACT FROM AUTHOR]

Toll-like receptors (TLRs) play an important role in the recognition of microbial components. Only chicken TLR2 and -4 have been reported in the literature. The objectives of this study were to identify new chicken TLRs and to evaluate evolutionary significance of these receptors. Searching chicken genomic databases and DNA sequencing revealed five new TLRs, TLR1 (type 1 and 2), -3, -5, and -7. No chicken orthologues of mammalian TLR8, -9, or -10 were found. As in mammals, all chicken TLRs (chTLRs) share identical protein secondary structure that consists of several leucine-rich domains, a transmembrane domain, and Toll/Interleukin-1 receptor domain(s). Phylogenetic analyses indicate that the identified chTLR genes are the orthologues of TLRs in mammals. Analyses of the number of synonymous substitutions per synonymous site and nonsynonymous substitutions per nonsynonymous site indicate that the nucleotide sequences coding for the leucine-rich repeats of chicken TLR1 type 1 and type 2 were significantly under positive Darwinian selection. In contrast, the sequences of other TLRs were under purifying selection. These results support the hypothesis that one of the major evolutionary strategies of the innate immune system is to recognize a few highly conserved microbial components with several conserved TLRs. The results also indicate that the sequence changes in the ligand-binding domains of TLR1 in chickens provide adaptive advantages during evolution. [ABSTRACT FROM AUTHOR]

Ninety-five genomic sequences of the ligand-binding domain of glutamate-gated chloride channel genes of three populations of the parasitic nematode H. placei were evaluated for patterns of diversity, demography, and selection. These genes code for subunits of ion channels, which are involved in the mode of action of the most commonly used antiparasitic drugs, the macrocyclic lactones. An extremely high frequency of unique segregating sites in exons and introns was observed, with significantly negative neutrality tests in each population for noncoding, synonymous, and nonsynonymous sites. Several tests indicated that support for balancing selection, positive selection, and hitchhiking was lacking. McDonald–Kreitman tests using H. contortus or C. elegans as an outgroup revealed an extreme excess of replacement polymorphism, consistent with weak purifying selection. Although these tests agree that negative selection may explain the excess of replacement changes, an alternative interpretation is required for the significantly negative Fu and Li’s D statistics based on silent and noncoding sites. These include homogeneous forces such as background selection and demographic expansion. The lack of population subdivision and the negative values of Tajima’s D for this outbreeding parasitic nematode render background selection less likely than demographic expansion. Comparison of D statistics based on different site types using neutral coalescent simulations supported this interpretation. Although this statistic was more negative for nonsynonymous sites than for synonymous sites, most comparisons of the D statistic were not significantly different between mutation classes. A few significant site comparisons were also consistent with demographic expansion, because the observed test statistic (Dneutral - Dselected) were low relative to the neutral expectations. Finally, previous mitochondrial studies also identified a demographic expansion of this parasitic nematode species, which lends further support to a scenario involving both demographic and purifying forces in the ligand-binding domain of H. placei. [ABSTRACT FROM AUTHOR]

The polymeric ubiquitin (poly-u) genes are composed of tandem 228-bp repeats with no spacer sequences between individual monomer units. Ubiquitin is one of the most conserved proteins known to date, and the individual units within a number of poly-u genes are significantly more similar to each other than would be expected if each unit evolved independently. It has been proposed that the rather striking similarity among poly-u monomers in some lineages is caused by a series of homogenization events. Here we report the sequences of the polyubiquitin-C (Ubc) genes in two mouse strains. Analysis of these sequences, as well as those of the previously reported Chinese hamster and rat poly-u genes, supports the assertion that the homogenization of the ubiquitin-C gene in rodents is due to unequal crossing-over events. The sequence divergence of noncoding DNA was used to estimate the frequency of unequal crossing-over events (6.3 × 10-5 events per generation) in the Ubc gene, as well as to provide evidence of apparent selection in the poly-u gene. [ABSTRACT FROM AUTHOR]

The patterns of point mutation and nucleotide substitution are inferred from nucleotide differences in three coding and two noncoding regions of retroviral genomes. Evidence is presented in favor of the view that the majority of mutations accumulate at the reverse transcription stage. Purifying selection is apparently very weak at the amino acid level, and almost nonexistent between synonymous codons. The pattern of purifying selection obeys the rules previously established in vertebrates [Gojobori T, Li W-H, Graur D (1982) J Mol Evol 18:360-369]; i.e., the magnitude of purifying selection at the amino acid level is negatively correlated with Grantham's [Grantham R (1974) Science 185: 862-864] chemical distances between the amino acids interchanged. We refute Modiano et al.'s [Modiano G, Battistuzzi G, Motulsky AG (1981) Proc Natl Acad Sci USA 78:1110-1114] hypothesis, according to which the pattern of mutation is preadapted to buffer against deleterious mutations. On the contrary, the pattern of mutation reduces the level of conservativeness from that imposed on the amino acid substitution pattern by the structure of the genetic code. The extraordinarily high rate of nucleotide substitution in retroviruses in comparison with that in other organisms is apparently caused by an extremely high rate of mutation coupled with a lack of stringent purifying selection at both the codon and the amino acid levels. [ABSTRACT FROM AUTHOR]

The relative contribution of mutation and purifying selection to transition bias has not been quantitatively assessed in mitochondrial protein genes. The observed transition/transversion ( s/v) ratio is (μ P)/(μ P), where μ and μ denote mutation rate of transitions and transversions, respectively, and P and P denote fixation probabilities of transitions and transversions, respectively. Because selection against synonymous transitions can be assumed to be roughly equal to that against synonymous transversions, P/P ≈ 1 at fourfold degenerate sites, so that the s/v ratio at fourfold degenerate sites is approximately μ/μ, which is a measure of mutational contribution to transition bias. Similarly, the s/v ratio at nondegenerate sites is also an estimate of μ/μ if we assume that selection against nonsynonymous transitions is roughly equal to that against nonsynonymous transversions. In two mitochondrial genes, cytochrome oxidase subunit I (COI) and cytochrome b (cyt- b) in pocket gophers, the s/v ratio is about two at nondegenerate and fourfold degenerate sites for both the COI and the cyt- b genes. This implies that mutation contribution to transition bias is relatively small. In contrast, the s/v ratio is much greater at twofold degenerate sites, being 48 for COI and 40 for cyt- b. Given that the μ/μ ratio is about 2, the P/P ratio at twofold degenerate sites must be on the order of 20 or greater. This suggests a great effect of purifying selection on transition bias in mitochondrial protein genes because transitions are synonymous and transversions are nonsynonymous at twofold degenerate sites in mammalian mitochondrial genes. We also found that nonsynonymous mutations at twofold degenerate sites are more neutral than nonsynonymous mutations at nondegenerate sites, and that the COI gene is subject to stronger purifying selection than is the cyt- b gene. A model is presented to integrate the effect of purifying selection, codon bias, DNA repair and GC content on s/v ratio of protein-coding genes. [ABSTRACT FROM AUTHOR]

PolyAna (available at ) aids in the analysis of natural selection on protein-coding sequences by estimating sample gene diversity at individual polymorphic nucleotide sites, which are classified as synonymous, non-synonymous, or ambiguous. [ABSTRACT FROM AUTHOR]