Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?

The phylogenetic profile method has been widely applied in the prediction of protein-protein interactions (PPIs). Studies often use all of the available complete genomes for this method. With more than 400 genomes complete and new ones on the horizon, it remains unclear how to select reference organisms for profile construction and then influence the PPI prediction. Here, we performed a systematic assessment of reference organism selection from 225 complete genomes with their evolutionary tree. Our results suggest that reference organisms should be selected from moderately and highly genetically distant organisms, from all three domains (Bacteria, Archaea, and Eukarya), and by their even distribution at the fifth hierarchical level in the evolutionary tree. Our study provides important guidance on the construction of phylogenetic profiles for PPI prediction and functional genomics, which has become challenging due to the large and increasing number of available candidate organisms.     

Anatomical and ITS rDNA-based phylogenetic identification of two new West African resupinate thelephoroid species

An anatomical approach coupled with molecular phylogeny of 84 sequences of thelephoroid taxa have been used to describe two new West African resupinate Thelephorales, namely, Tomentella agereri and Tomentella maroana. T. agereri presents a maximal sequence similarity of 94% with its genetically closest species, Tomentalla pilosa, according to a Blastn search in public GenBanks. By molecular phylogenetics, it is nested within the T. pilosa complex, a well-supported (bootstrap support of 100%) monophyletic clade composed of cystidiate and differentiated rhizomorphic species, although it presents contrasting anatomical features including the lack of cystidia, the presence of undifferentiated rhizomorphs, and basidiospores with very short aculei, up to 0.5 μm. Tomentalla maroana is close, by molecular phylogenetic study, to T. ellisii, T. pisoniae, and T. hjortstamiana. The phylogenetic proximity between T. maroana and T. ellisii is supported by morphological characters between the two species, namely, a crustose adherent basidiocarp, a differentiated sterile margin, and a granular hymenium. The two species deviate from each other by 11.38–12.37% with regard to the ITS rDNA sequences, whereas the intraspecific genetic distances vary from 1.68% to 2.9% among the three specimens assigned to T. maroana. Discriminating characters as well as genetic distance between the new species and the closely related species are discussed in detail.     

Construction of phylogenetic tree forNicotiana species based on RAPD markers

To apply random amplified polymorphic DNA for analysis of phylogenetic relationships, we used 34 synthetic oligonucleotides as primers to examine interspecific and intraspecific variations among 18 genotypes, nine species ofNicotiana. The nine species used in this study belong to sectionsTomentosae andAlatae. In addition, we attempted to clarify the taxonomic position ofN. sylvestris. A total of 354 distinct DNA fragments were obtained by polymerase chain reaction. Pair-wise comparisons of unique and shared amplification products were used to generate Jaccard's similarity coefficients and Nei and Li's similarity coefficients with the computer software of numerical taxonomy and multivariate analysis system. On the basis of the dendrogram constructed with the similarity coefficients, the 18Nicotiana genotypes were divided into two clusters. The classification analyzed by RAPD markers is in accordance with the classification of Goodspeed thatN. sylvestris is a member of sectionAlatae.     

The success of sequence capture in relation to phylogenetic distance from a reference genome: a case study of avian haemosporidian parasites

Genomic sequencing of avian haemosporidian parasites (Haemosporida) has been challenging due to excessive contamination from host DNA. In this study, we developed a cost-effective protocol to obtain parasite sequences from naturally infected birds, based on targeted sequence capture and next generation sequencing. With the genomic data of Haemoproteus tartakovskyi as a reference, we successfully sequenced up to 1000 genes from each of the 15 selected samples belonging to nine different cytochrome b lineages, eight of which belong to Haemoproteus and one to Plasmodium. The targeted sequences were enriched to ～10⁴-fold, and mixed infections were identified as well as the proportions of each mixed lineage. We found that the total number of reads and the proportions of exons sequenced decreased when the parasite lineage became more divergent from the reference genome. For each of the samples, the recovery of sequences from different exons varied with the function and GC content of the exon. From the obtained sequences, we detected within-lineage variation in both mitochondrial and nuclear genes, which may be a result of local adaptation to different host species and environmental conditions. This targeted sequence capture protocol can be applied to a broader range of species and will open a new door for further studies on disease diagnostics and comparative analysis of haemosporidians evolution.     

Two complementary perspectives on inter-individual genetic distance

This paper examines population structure through the prism of pairwise genetic distances. Two complementary perspectives, framed as two simple questions, are explored: Q1: What is the probability that a random pair of individuals from the same local population is more genetically dissimilar than a random pair from two distinct populations? Q2: On average, how genetically different are two individuals from the same local population, in comparison with two individuals chosen from any two distinct populations? Models are developed to provide quantitative answers for the two questions, given allele frequencies across any number of markers from two diploid populations. The probability from Q1 is shown to drop to zero with increasing number of genetic markers even for very closely-related populations and rare alleles. The average genetic dissimilarity of two individuals from distinct populations diverges from the average dissimilarity of two individuals from the same population by a percentage dependent on estimates of population differentiation. This perspective also suggests a measure of population distance based on the intuitive notion of pairwise genetic distance, along with a simple method of estimation. Results from recent empirical research on inter-individual genetic distance in human populations are analyzed in the context of the theoretical framework.     

Aminoacid profiles in the study of phylogenetic relationships in the genusOryza

Summary The amino acid profiles in seeds of thirteen different species ofOryza, including two cultivated rices,O. glaberrima andO. sativa and the two major geographical racesindica andjaponica were studied using an automatic amino acid analyser to assess differences in the profiles of cultivated species and their wild progenitors. The polygon graphic method was employed to envision the species relationship. Essential amino acid profiles in different species were also compared with those of the Food and Agriculture Organization (FAO) standards. The results suggest a wide range of variability amongOryza species for lysine (up to 4.4% as against 3.5% in cultivated rices) and other essential amino acids. This will be of considerable interest to rice breeders, when after overcoming genetic barriers, the possible utilization of these species in rice breeding becomes feasible.     

Anthropometric and genetic distance between Gonds of Central India

A morphological and genetic study was undertaken on five Gondi-speaking populations of Central India (Andhra Pradesh and Maharashtra States). There has been no systematic biological study on this large Dravidian-speaking tribal group, 4 million in number, amounting to 13% of the total tribal population of India. Data was collected on 16 anthropometric measurements and seven genetic markers (blood groups, hemoglobin, G6PD and plasma protein polymorphisms) on the Raj Gonds, Kolams, Manne, Koyas and Plains Maria Gonds. Various genetic distance measures such as Mahalanobis's D2 and Nei's and Sanghvi's measures and cluster analysis techniques were used to determine the relationship between these groups based on anthropometrics and genetic variables. The statistical analysis revealed the Gonds to be a heterogenous group in both morphology and genetic characteristics. The morphological and genetic distances between these five groups when projected graphically revealed that the spatial distribution of these Gonds generally corresponds to their present geographical distribution. However, the actual relationships among each of the Gond populations show differences when based on these two biological variables, the possible reasons for this being discussed in the paper. The emphasis of this study is on the importance of geographical proximity in producing morphological and genetic similarity between populations, brought about by a short distance as well as similar geographical factors (such as soil, terrain, flora, etc.) drawing these populations together under a common ecocultural umbrella.     

Studying the evolutionary relationships and phylogenetic trees of 21 groups of tRNA sequences based on complex networks

To find out the evolutionary relationships among different tRNA sequences of 21 amino acids, 22 networks are constructed. One is constructed from whole tRNAs, and the other 21 networks are constructed from the tRNAs which carry the same amino acids. A new method is proposed such that the alignment scores of any two amino acids groups are determined by the average degree and the average clustering coefficient of their networks. The anticodon feature of isolated tRNA and the phylogenetic trees of 21 group networks are discussed. We find that some isolated tRNA sequences in 21 networks still connect with other tRNAs outside their group, which reflects the fact that those tRNAs might evolve by intercrossing among these 21 groups. We also find that most anticodons among the same cluster are only one base different in the same sites when S ≥ 70, and they stay in the same rank in the ladder of evolutionary relationships. Those observations seem to agree on that some tRNAs might mutate from the same ancestor sequences based on point mutation mechanisms.     

New method for comparing DNA primary sequences based on a discrimination measure

We introduce a new approach to compare DNA primary sequences. The core of our method is a new measure of pairwise distances among sequences. Using the primitive discrimination substrings of sequence S and Q, a discrimination measure DM(S, Q) is defined for the similarity analysis of them. The proposed method does not require multiple alignments and is fully automatic. To illustrate its utility, we construct phylogenetic trees on two independent data sets. The results indicate that the method is efficient and powerful.     

Efficiencies of maximum likelihood methods of phylogenetic inferences when different substitution models are used

Choice of a substitution model is a crucial step in the maximum likelihood (ML) method of phylogenetic inference, and investigators tend to prefer complex mathematical models to simple ones. However, when complex models with many parameters are used, the extent of noise in statistical inferences increases, and thus complex models may not produce the true topology with a higher probability than simple ones. This problem was studied using computer simulation. When the number of nucleotides used was relatively large (1000 bp), the HKY+Gamma model showed smaller d(T) topological distance between the inferred and the true trees) than the JC and Kimura models. In the cases of shorter sequences (300 bp) simpler model and search algorithm such as JC model and SA+NNI search were found to be as efficient as more complicated searches and models in terms of topological distances, although the topologies obtained under HKY+Gamma model had the highest likelihood values. The performance of relatively simple search algorithm SA+NNI was found to be essentially the same as that of more extensive SA+TBR search under all models studied. Similarly to the conclusions reached by Takahashi and Nei [Mol. Biol. Evol. 17 (2000) 1251], our results indicate that simple models can be as efficient as complex models, and that use of complex models does not necessarily give more reliable trees compared with simple models.     

Patterns of phylogenetic beta diversity in China's grasslands in relation to geographical and environmental distance

Patterns and determinants of beta (β-) diversity can be used to explore the underlying mechanisms regulating community assembly. Despite being the most commonly used measure of β-diversity, species turnover does not consider the evolutionary differences among species, treating all species equally. Incorporating information on phylogenetic non-independence or relatedness among species in the calculation of β-diversity may substantially advance our understanding of the ecological and evolutionary mechanisms structuring communities. Here, we investigate the relative influence of geographical distance and differences in environmental conditions (environmental distance) on the phylogenetic β-diversity between grassland communities expanding 4000 km across the Tibetan Plateau, the Inner Mongolia Plateau and the Xinjiang Autonomous Region in China. Both observed and standardized effect size of phylogenetic β-diversity were significantly correlated with geographical and environmental distance across all regions. However, the effect of geographical distance on the standardized effect size of phylogenetic β-diversity disappeared when environmental distance was controlled. We also found that within different regions, the effect of environmental distance on both observed and standardized effect size of phylogenetic β-diversity was more significant than geographical distance. Among environmental variables, climate played a more important role in shaping observed phylogenetic β-diversity across and within regions, and standardized effect size of phylogenetic β-diversity across regions. Soil properties played a more important role in shaping standardized effect size of phylogenetic β-diversity within regions. The phylogenetic β-diversity of species from dicot and monocot clades exhibited similar patterns along environmental and geographical distance. The results suggest that at the study scale, phylogeny of grassland communities in China is predominantly structured by environmental filtering, and the dominant environmental factors may be scale-dependent.     

Reconstruction of certain phylogenetic networks from the genomes at their leaves

A network N is a rooted acyclic digraph. A base-set X for N is a subset of vertices including the root (or outgroup), all leaves, and all vertices of outdegree 1. A simple model of evolution is considered in which all characters are binary and in which back-mutations occur only at hybrid vertices. It is assumed that the genome is known for each member of the base-set X. If the network is known and is assumed to be “normal,” then it is proved that the genome of every vertex is uniquely determined and can be explicitly reconstructed. Under additional hypotheses involving time-consistency and separation of the hybrid vertices, the network itself can also be reconstructed from the genomes of all members of X. An explicit polynomial-time procedure is described for performing the reconstruction.     

Mutant allele frequencies and genetic distance relationships in domestic cat populations of lower Egypt and the eastern Mediterranean

Summary Gene frequency surveys conducted in Alexandria and Cairo reveal genetic profiles which are extensions of those that characterize the cat populations of European cities. For nine selected comparisons with Alexandria, regression analysis indicates that a linear function best describes the relationship between Nei's and Cavalli-Sforza's genetic distance indices and geographic distance.     

Evolutionary aspects of the synuclein super-family and sub-families based on large-scale phylogenetic and group-discrimination analysis

Over the last decade, many genetic studies have suggested that the synucleins, which are small, natively unfolded proteins, are closely related to Parkinson’s disease and cancer. Less is known about the molecular basis of this role. A comprehensive analysis of the evolutionary path of the synuclein protein family may reveal the relationship between evolutionarily conserved residues and protein function or structure. The phylogeny of 252 unique synuclein sequences from 73 organisms suggests that gamma-synuclein is the common ancestor of alpha- and beta-synuclein. Although all three sub-families remain highly conserved, especially at the N-terminal, nearly 15% of the residues in each sub family clearly diverged during evolution, providing crucial guidance for investigations of the different properties of the members of the superfamily. His50 is found to be an alpha-specific conserved residue (91%) and, based on mutagenesis, evolutionarily developed a secondary copper binding site in the alpha synuclein family. Surprisingly, this site is located between two well-known polymorphisms of alpha-synuclein, E46K and A53T, which are linked to early-onset Parkinson’s disease, suggesting that the mutation-induced impairment of copper binding could be a mechanism responsible for alpha-synuclein aggregation.     

Impact of scoring error and reproducibility RAPD data on RAPD based estimates of genetic distance

RAPD band reproducibility and scoring error were evaluated for RAPDs generated by 50 RAPD primers among ten snap bean (Phaseolus vulgaris L.) genotypes. Genetic distances based on different sets of RAPD bands were compared to evaluate the impact of scoring error, reproducibility, and differences in relative amplification strength on the reproducibility of RAPD based genetic distance estimates. The measured RAPD data scoring error was 2%. Reproducibility, expressed as the percentage of RAPD bands scored that are also scored in replicate data, was 76%. The results indicate that the probability of a scored RAPD band being scored in replicate data is strongly dependent on the uniformity of amplification conditions between experiments, as well as the relative amplification strength of the RAPD band. Significant improvement in the reproducibility of scored bands and some reduction in scoring error was achieved by reducing differences in reaction conditions between replicates. Observed primer variability for the reproducibility of scored RAPDs may also facilitate the selection of primers, resulting in dramatic improvements in the reproducibility of RAPD data used in germplasm studies. Variance of genetic distances across replicates due to sampling error was found to be more than six times greater than that due to scoring error for a set of 192 RAPD bands. Genetic distance matrices computed from the RAPD bands scored in replicated data and RAPD bands that failed to be scored in replicated data were not significantly different. Differences in the ethidium bromide staining intensity of RAPD bands were not associated with significant differences in resulting genetic distance matrices. The assumption of sampling error as the only source of error was sufficient to account for the observed variation in genetic distance estimates across independent sets of RAPD bands.     

喜马拉雅旱獭线粒体DNA控制区遗传多样性及系统发育

喜马拉雅旱獭是青藏高原的优势种,数量多、分布广,全面了解其遗传背景对该地区旱獭资源的保护与合理利用具有重要的意义。本研究以青藏高原云南、西藏和青海三省区共13个地理种群计258只旱獭为研究对象,PCR扩增获得线粒体DNA控制区基因部分序列(887 bp),并运用种群遗传学方法进行遗传多样性分析。结果显示:258份样品共发现了84个变异位点(9.40%),定义了68种单倍型,其单倍型多样性(h)平均值为0.968±0.003、核苷酸多样性(π)平均值为0.017 25±0.016 37,种群总体遗传多样性较高。AMOVA方差分析显示13个地理种群间存在着明显的遗传分化(Fst=0.620 67,P<0.001),种群间基因交流多数较低(Nm<1)。基于单倍型构建的系统发育树中13个地理种群的喜马拉雅旱獭聚为两支,其中来自青藏高原西南地区(西藏安多、青海格尔木、青海囊谦、云南迪庆)的18个单倍型聚成一个大的分支(A支),其余50个单倍型聚为一个大的分支(B支),在NETWORK网络图中也可见到相似网络拓扑结构。研究结果显示青藏高原喜马拉雅旱獭种群以唐古拉山脉为界分为两个大的种群,说明地理隔离是影响喜马拉雅旱獭种群动态变化的主要因素。     

Relationship between heterozygosity and genetic distance in the three major races of man

In pairwise comparisons of gene frequency data from the three major races of man, the single locus measures of the heterozygosity within and the genetic distance between races are shown to be strongly correlated across the loci coding for red cell proteins and enzymes. The intercept of the regression line of genetic distance on heterozygosity in protein enzyme loci is statistically insignificant. These findings suggest that the genetic variability at the enzyme and protein loci in man is probably maintained by a balance of mutation and random genetic drift. At the blood group loci, however, the observed relationship between genetic distance and heterozygosity does not follow the expectation of the neutral mutation hypothesis. These observations are discussed in terms of the changes in probability of identical monomorphism in two populations during the process of gene differentiation.     

Weighted relative entropy for phylogenetic tree based on 2-step Markov Model

The degree of similarity of DNA sequences can be concluded according to the comparison of DNA sequences, which helps to speculate their relationship in respect of the structure, function and evolution. In this paper, we introduce the fundamental of the weighted relative entropy based on 2-step Markov Model to compare DNA sequences. The DNA sequence, consisted of four characters A, T, C, G, can be considered as a Markov chain. By taking state space I = {A, T, C, G} and describe the DNA sequences with 2-step transition probability matrix we can get the eigenvalue of the DNA sequence to define the similarity metric. Therefore, we find a new method to compare the DNA sequences, which is used to classify chromosomes DNA sequences obtained from 30 species. The phylogenetic tree built by the alignment-free method of the distance matrix resulted from the weighted relative entropy has clearer and more accurate division.     

一种用于蛋白质相似性分析的新的相对距离

本文论述了一种新的相对距离,用于分析不同蛋白质序列的相似性分析和构造进化树．此种距离基于Lempel-Zip复杂度,不需要进行序列比对和复杂性算法．为了说明这种距离的合理性,本文对8个物种进行了相似性分析并构造了其进化树．     

Isolation by distance, linguistic similarity, and the genetic structure on Bougainville Island

Previous research has revealed extensive genetic variation among villages on Bougainville, in the Solomon Islands. Using previously published gene frequency data for seven loci, the role of isolation by distance in structuring genetic variation on Bougainville was reanalyzed. Newer methods of kinship estimation show that earlier estimates of the isolation by distance parameters were low. The fit of the model is highly significant (R2 = 0.409; P less than 0.001), and the parameter estimates indicate high isolation: a = 0.0538, b = 0.1978, L = -0.0057. Several methods of residual analysis were applied in order to determine factors affecting the fit of the model. Linguistic similarity has a significant effect on genetic variation once the effects of geographic distance are taken into account. Population-specific deviations from the expected model may be explained, in part, in terms of population history. Compared to other human populations, Bougainville Island shows an even greater among-group variation than has been suggested previously.