Calculation Of Genetic Distances Research Articles

The Genetic Closeness of the Finnish Ugric, Slav and Germanic Populations According To Anthropological and Genetical Data

The calculation of genetic distances of 55 human populations belonging to four great human races considering loci of proteins, enzymes and blood groups, and construction the dendrogram of this population distinguished some relationship of German, Slavic and Finnish-Ugric populations. So, Russians are in one subcluster with Poles, Iranians, Komi, Chuvashes, Udmurtians, Nentses and Ossetians. Germans are in one subcluster with Serbs, Moldavians, Hungarians, Croatians and Czechs. Greecs are in closeness with Slavic populations on this dendrogram, too. There were common migrations of this populations from places of first differentiation in Asia. In Europe German populations were migrated by another way than ancestors of Russians, which were migrated in Europe across North of Siberia. The ancestors of Germans probably migrated by the same way as Hunnu. Now are investigated settlements of ancient Caucasoids in Central Asia. The studying of mt DNA of rural Russian population in Yaroslavsky region discovered all haplogroups of Russians and even Caucasoid (H, W, I, U, X, T1). The last decoding of petrogliphs in Baical region discovered the presence of ancestors of Caucasoids in Siberia in paleolithic.

New status for two African giant forest shrews, Crocidura goliath goliath and C. goliath nimbasilvanus (Mammalia: Soricomorpha), based on molecular and geometic morphometric analyses

Crocidura goliath nimbasilvanus Hutterer, 2003 (replacement name for C. odorata guineensis Heim de Balsac, 1968) from West Africa (Guinea, Liberia, Ivory Coast) and Crocidura goliath goliath Thomas, 1906 from Central Africa (Cameroon, Central African Republic, Gabon, Republic of Congo, Democratic Republic of Congo) were regarded as members of a single species until recently. A phylogenetic analysis including three mitochondrial (16S, cytb and COI) and one nuclear marker (BRCA) shows that C. g. nimbasilvanus is the sister taxon of C. nimbae, a species also endemic to West Africa. Crocidura g. goliath is part of the C. olivieri group and closely related to C. olivieri, C. viaria and C. fulvastra . Calculation of genetic distances between cytb sequences confirms this pattern (divergence of 13.5% between C. G. nimbasilvanus and C. G. goliath ). An analysis of 112 skulls using morphometric geometrics provides evidence of marked shape differences between the two taxa. Despite close external morphological resemblances, we found diagnostic external and craniodental characters between these two forms. We therefore propose to treat C. nimbasilvanus and C. goliath as distinct species. Similar morphological features exhibited by these two African giant forest shrews, especially their large size, may be the result of homoplasy due to convergent evolutionary pressure. We also investigated the phenotypic diversification in size and skull shape within C. goliath and discovered strong intraspecific variability.

New Status for Two African Giant Forest Shrews,Crocidura goliath goliathandC. goliath nimbasilvanus(Mammalia: Soricomorpha), Based on Molecular and Geometic Morphometric Analyses

Crocidura goliath nimbasilvanus Hutterer, 2003 (replacement name for C. odorata guineensis Heim de Balsac, 1968) from West Africa (Guinea, Liberia, Ivory Coast) and Crocidura goliath goliath Thomas, 1906 from Central Africa (Cameroon, Central African Republic, Gabon, Republic of Congo, Democratic Republic of Congo) were regarded as members of a single species until recently. A phylogenetic analysis including three mitochondrial (16S, cytb and COI) and one nuclear marker (BRCA) shows that C. g. nimbasilvanus is the sister taxon of C. nimbae, a species also endemic to West Africa. Crocidura g. goliath is part of the C. olivieri group and closely related to C. olivieri, C. viaria and C. fulvastra. Calculation of genetic distances between cytb sequences confirms this pattern (divergence of 13.5% between C. g. nimbasilvanus and C. g. goliath). An analysis of 112 skulls using morphometric geometrics provides evidence of marked shape differences between the two taxa. Despite close external morphological resemblances, we found diagnostic external and craniodental characters between these two forms. We therefore propose to treat C. nimbasilvanus and C. goliath as distinct species. Similar morphological features exhibited by these two African giant forest shrews, especially their large size, may be the result of homoplasy due to convergent evolutionary pressure. We also investigated the phenotypic diversification in size and skull shape within C. goliath and discovered strong intraspecific variability.

HIV-1 envelope diversity 1 year after seroconversion predicts subsequent disease progression

Recent studies have suggested that the dynamics of HIV-1 evolutionary rate reflect the rate of disease progression. We wished to determine whether viral diversity early in infection is predictive of the subsequent disease course. HIV-1 envelope diversity at seroconversion and 1 year thereafter from 89 homosexual participants of the Amsterdam Cohort Studies on HIV infection and AIDS was correlated with clinical endpoints and markers of disease progression. Heteroduplex mobility assay (HMA) and sequencing followed by calculation of pairwise genetic distances were applied to determine HIV-1 envelope diversity. The HMA pattern (presence or absence of heteroduplexes) and sequence diversity were each tested for correlation with the clinical course of infection. HMA pattern at 1-year postseroconversion was significantly associated with progression to AIDS and AIDS-related death, with presence of heteroduplexes associated with accelerated disease progression. Moreover, not only this dichotomous measure of viral diversity (absence or presence of heteroduplexes), but also genetic diversity itself was associated with disease course. HMA pattern was an independent predictor of accelerated disease progression, also when CCR5 genotype, human leukocyte antigen (HLA)-type, viral load, CD4 T-cell counts, and coreceptor use at viral load set point were included in the analysis. Viral diversity early in HIV-1 infection is predictive of the subsequent disease progression. It remains to be established whether viral diversity itself plays a causal role in the increased damage to the immune system or whether it is a reflection of immune pressure or other selective forces.

Protein map: An alignment-free sequence comparison method based on various properties of amino acids

In this paper, we propose a new protein map which incorporates with various properties of amino acids. As a powerful tool for protein classification, this new protein map both considers phylogenetic factors arising from amino acid mutations and provides computational efficiency for the huge amount of data. The ten amino acid physico-chemical properties (the chemical composition of the side chain, two polarity measures, hydropathy, isoelectric point, volume, aromaticity, aliphaticity, hydrogenation, and hydroxythiolation) are utilized according to their relative importance. Moreover, during the course of calculation of genetic distances between pairs of proteins, this approach does not require any alignment of sequences. Therefore, the proposed model is easier and quicker in handling protein sequences than multiple alignment methods, and gives protein classification greater evolutionary significance at the amino acid sequence level.

Calculation of interpopulation genetic distances at different sample sizes

A new method for comparison of interpopulation genetic distances is proposed. The method allows a more precise location of populations in the space of genetic characters relative to one another at considerably different sample sizes. The method consists in multiple reduction of the sample sizes to the size of the smallest sample followed by averaging the calculated genetic distances between the reduced samples. Software for calculation of genetic distances by this method is presented.

Caracterización molecular de poblaciones venezolanas de Sigmodon hirsutus (Rodentia: Cricetidae)

Recent phylogenetic studies based on cytochrome b gene sequence, have determined that the species historically known as Sigmodon hispidus (Rodentia) from South America comprises a species S. hirsutus of paraphyletic origin. The aim of this study was to test the hypothesis that populations from Venezuela, represent the sensu strict form, ancestral haplotypes, and monophyletic subspecieS. For this, 12 individual sequences from three localities of different biogeographic regions in Venezuela were evaluated and sequenced based on cyto b. Additionally, the sequences were used to develop a cladistic analysis and genetic distance calculations, and to compare this information with two individual sequences of Sigmodon specimens available in Genbank. Phylogenetic analyses show that the three populations of S. hirsutus of Venezuela form an ancestral and monophyletic subclade supported by high bootstrap values and significant genetic distance between subclade within the S. hirsutus. Besides, the existence of two lineages suggests two subspecies, S. hirsutus hirsutus from Venezuela, and S. hirsutus mexicanus from Mexico-Central America, but, both species need formal description.

Are hepatitis B virus “subgenotypes” defined accurately?

Background Recently, several novel hepatitis B virus (HBV) subgenotypes have been introduced that do not meet proper definition of “subgenotypes”. In particular for HBV genotype A, such novel subgenotypes have been reported. Objective To comprehensively reanalyse all HBV subgenotypes A, and to propose a novel, consistent alternative for HBV classification. Study design All HBV full-length genome subgenotypes A1–A6 were reanalysed using phylogenetic reconstruction and genetic distance calculation in order to study their evolutionary relationships. Results Phylogenetic analysis based on the complete genome sequence of subgenotype A strains revealed four distinct clusters supported by high bootstrap values, whereas only the three groups A1, A2 and A6 could be assigned as subgenotypes. Previously introduced subgenotype A3, “tentative A4” and A5 clustered together in one main branch and were designated as “quasi-subgenotypes”. Also genetic distances failed to classify these three groups as definite subgenotypes. These results advocate for a new classification of HBV genotype A into subgenotype A1, A2, “quasi-subgenotype A3” and A4. Conclusion Detailed phylogenetic analysis of the complete genome sequences demonstrates that some of available HBV genotype A strains may not be considered as definite “subgenotypes”. These strains, which are mainly of African origin, could be considered as “quasi-subgenotypes” which puts them in between the “clade” and “subgenotype” definition. Geographical origin may have a key role in further classification of HBV subgenotypes.

Exploiting a wheat EST database to assess genetic diversity

Expressed sequence tag (EST) markers have been used to assess variety and genetic diversity in wheat (Triticum aestivum). In this study, 1549 ESTs from wheat infested with yellow rust were used to examine the genetic diversity of six susceptible and resistant wheat cultivars. The aim of using these cultivars was to improve the competitiveness of public wheat breeding programs through the intensive use of modern, particularly marker-assisted, selection technologies. The F2 individuals derived from cultivar crosses were screened for resistance to yellow rust at the seedling stage in greenhouses and adult stage in the field to identify DNA markers genetically linked to resistance. Five hundred and sixty ESTs were assembled into 136 contigs and 989 singletons. BlastX search results showed that 39 (29%) contigs and 96 (10%) singletons were homologous to wheat genes. The database-matched contigs and singletons were assigned to eight functional groups related to protein synthesis, photosynthesis, metabolism and energy, stress proteins, transporter proteins, protein breakdown and recycling, cell growth and division and reactive oxygen scavengers. PCR analyses with primers based on the contigs and singletons showed that the most polymorphic functional categories were photosynthesis (contigs) and metabolism and energy (singletons). EST analysis revealed considerable genetic variability among the Turkish wheat cultivars resistant and susceptible to yellow rust disease and allowed calculation of the mean genetic distance between cultivars, with the greatest similarity (0.725) being between Harmankaya99 and Sönmez2001, and the lowest (0.622) between Aytin98 and Izgi01.

Assessing genetic diversity of some potato (Solanum tuberosum L.) genotypes grown in Turkey using the AFLP marker technique

In the present study, the level of polymorphism and the genetic relationships among 26 potato genotypes were studied by means of molecular markers using the amplified fragment length polymorphism (AFLP) technique. DNA was extracted from fresh leaves of the seedlings. Selective amplification products revealed a total of 191 polymorphic bands ranging from 8 to 45 for each combination. Scoring results were used to generate a tree in JMP software. The 26 samples formed six clades with varying number of members between one and eleven. Genetic distances among genotypes were calculated according to Jaccard’s formula, in Phylip 3.0 software. According to the results of genetic distance, dendrogram showed that genotypes 6/7-4 and 6/7-2 were the closest genotypes with a genetic distance of 0.13. On the other hand, genotypes Posof-10 and Marabel were the most distinct from each other with a genetic distance value of 0.55. The AFLP marker results showed a great consistency along with their pedigrees indicating the AFLP technique as a useful tool in the calculation of genetic distance of the potato genotypes.

Polymorphic DNA fingerprinting patterns in distinct Chromobacterium violaceum strains using ERIC-PCR analysis

In the present study, distinct Chromobacterium violaceum strains were genetically characterized from polymorphicDNA fi ngerprinting patterns. Such assays were performed in presence of primer ERICII,originally designed from enterobacterial intergenic repetitive element sequences. Clustering analysis ofthe ERIC-PCR products and genetic similarity phenogram were estimated by using the coeffi cient ofSorensen-Dice and the UPGMA algorithm in the NTSYS-pc computer program. Genotypic diversityand the Shannon gene diversity indexes among the bacterial strains were calculated using the populationgenetics package POPGENE. Four main groups including individuals belonged to specifi c strainswere defi ned by clustering analysis of ERIC-PCR products, in which similarity coeffi cients varied from0.57 to 1 The inter-strain genetic distance and identity calculations revealed that the largest distancewas observed between C. violaceum ATCC12472 and 07.1 strains (0.6414) and that the greatest identitybetween those identifi ed as C. violaceum ATCC12472 and CBM strains (0.7622), confi rming the patterngenerated in the similarity phenogram. Considering the accentuated reproducibility in amplifi cation reactions and the highly polymorphic DNA fi ngerprinting profi le observed for each bacterial strain,these fi ndings create real possibilities for the detection of C. violaceum strains in microbial mixed culturesthrough ERIC-PCR assays.

Novel hepatitis B virus subgenotype A6 in African-Belgian patients

Background Genome diversity of hepatitis B virus (HBV) is prominent among DNA viruses; which, allowed the virus to be genetically classified into eight genotypes and several subgenotypes. Objective To introduce and to characterize a novel subgenotype HBV, classified as A6. Study design HBV full-length genomes were isolated and sequenced from three African-Belgian patients chronically infected with the virus. Using phylogenetic reconstruction and genetic distance calculation, the evolutionary relationships of the novel strains were investigated. Results Phylogenetic analysis based on complete genome sequences of genotype A strains revealed distinct clusters supported by high bootstrap values. The three African-Belgian strains clustered separately from the other known A subgenotypes (A1–A5) with maximal bootstrap support (100%). The mean inter-subgenotypic nucleotide divergence over the complete genome sequence between the novel A6 strains and A1–A5 was higher than 4%. Conclusion Phylogenetic analysis of the complete genome sequences yielded maximal bootstrap value support for nodes that establish the new lineage as a novel subgenotype. In addition, nucleotide divergence more than 4% based on full-length genome of the virus, clearly demonstrated that the three African-Belgian strains belonged to a novel subgenotype of HBV, which was assigned as “A6”. Noteworthy, the phylogeny of genotype A demonstrated that the A6 is a basal lineage that diverged earlier from the other African subgenotypes of genotype A.

Phylogenetic analysis of the pathogenic bacteria Spiroplasma penaei based on multilocus sequence analysis

A pathogenic Spiroplasma penaei strain was isolated from the hemolymph of moribund Pacific white shrimp, Penaeus vannamei. The shrimp sample originated from a shrimp farm near Cartagena, Colombia, that was suffering from high mortalities in ponds with very low salinity and high temperatures. This new emerging disease in a marine crustacean in the Americas is described as a systemic infection. The multilocus phylogenetic analysis suggests that S. penaei strain has a terrestrial origin. Evolutionary relationship trees, based on five partial DNA sequences of 16S rDNA, 23S rDNA, 5S rDNA, gyrB, rpoB genes and two complete DNA sequences of 16S–23S rDNA and 23S–5S rDNA intergenic spacer region, were reconstructed using the distance-based Neighboring-Joining (NJ) method with Kimura-2-parameter substitution model. The NJ trees based on all DNA sequences investigated in this study positioned S. penaei in the Citri–Poulsonii clade and corroborate the observations by other investigators using the 16S rDNA gene. Pairwise genetic distance calculation between sequences of spiroplasmas showed S. penaei to be closely related to Spiroplasma insolitum and distantly related to Spiroplasma sp. SHRIMP from China.

Phylogenetic analysis of hepatitis B virus full-length genomes reveals evidence for a large nosocomial outbreak in Belgium

Background Hepatitis B virus (HBV) is primarily transmitted from mother to child, by sexual contact, intravenous drug abuse, or unsafe health care-related injection practices. Despite increased safety efforts, nosocomial acquired hepatitis B infection remains problematic. Objectives A large HBV outbreak was investigated comprising 36 patients with acute HBV infection in a primary care physician's practice. Study design In a retrospective study (2003–2008), 36 serum samples from patients with acute HBV infection were collected. They had received several injections by the same physician at least 3 months before the onset of clinical symptoms. As a control group, sera were collected from HBV patients from other physicians from the same province. Full-length HBV genomes were amplified and were phylogenetically analysed. Results HBV complete genomes of 32 patients were successfully amplified and sequenced, and clustered together with the reference genotype A, subgenotype A2 strains. We also analysed 26 control HBV genotype A samples. All 32 HBV strains from the patient group clustered in a monophyletic branch with a bootstrap value of 100, whereas the control samples branched separately in another clade. The genetic distance value showed small differences within the patients group, whereas the rate within the control group was seven times higher. These observations confirm that the source of transmission was clearly different in both groups. Conclusion Maximum likelihood analysis and genetic distance calculations based on the full-length genomes of HBV strains isolated from patients and controls provided strong evidence for a common nosocomial source of infection for all 32 patient cases.

New aspects of an old discussion - phylogenetic relationships of Ammotragus and Pseudois within the subfamily Caprinae based on comparison of the 12S rDNA sequences

A mitochondrial 12S rDNA fragment was amplified by PCR and directly sequenced from eight members of the Caprinae (Ammotragus lervia, Capra aegagrus, Ovis ammon, O. musimon, O. nivicola, O. orientalis, O. vignei and Pseudois nayaur). Multiple alignment of the sequences and genetic distance calculation with the'distance of Taijama and Nei and the algorithms of Saitou and Nei (neighbour-joining - NJ) showed that Pseudois is grouped together with Capra and Ammotragus. All members of the genus Oxis formed a second cluster. Phylogenetic analyses supported these results. NJ-analyses and maximum parsimony (MP) trees did not support the present phylogenetic classification. Bootstrap values of 95% (NJ) and 96% (MP) confirms the grouping of P. nayaur and C. aegagrus. Another clade, O. ammon and O. orientalis supported weakly by bootstrap values of 65% (MP) and 70% (NJ) and the clade O. musimonand O. vignei had bootstrap values of 50% (MP) and 60% (NJ). So the phylogenetic relationship within the genus Oxis is still unsafe. But the parsimony analyses lead to the conclusion that Ammotragus represents an old lineage that diverged from ancestral caprines together with true sheep a long time ago and that both true goats and blue sheep forms represent one evolutionary lineage.

Inheritance pattern of microsatellite loci and their use for kinship analysis in the Japanese scallop Patinopecten yessoensis

The inheritance mode of seven microsatellite markers was investigated in Patinopecten yessoensis larvae from four controlled crosses, and the feasibility of using these markers for kinship estimation was also examined. All the seven microsatellite loci were compatible with Mendelian inheritance. Neither sex-linked barriers to transmission nor major barriers to fertilization between gametes from the parents were evident. Two of the seven loci showed the presence of null alleles in two families, suggesting the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. However, even if the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from four families were all unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers used may be capable of discriminating between related and unrelated scallop larvae in the absence of pedigree information, and of investigating the effective number of parents contributing to the hatchery population of the Japanese scallop.

Inheritance mode of microsatellite loci and their use for kinship analysis in the Pacific oyster (Crassostrea gigas)

Five full-sib families of the Pacific oyster (Crassostrea gigas) larvae were used to study the mode of inheritance at eight microsatellite loci, and the feasibility of these markers for kinship estimate was also examined. All eight microsatellite loci were compatible with Mendelian inheritance. Neither evidence of sex-linked barriers to transmission nor evidence of major barriers to fertilization between gametes from the parents was shown. Three of the eight loci showed the presence of null alleles in four families, demonstrating the need to conduct comprehensive species-specific inheritance studies for microsatellite loci used in population genetic studies. Although the null allele heterozygotes were considered as homozygotes in the calculation of genetic distance, offspring from five full-sib families were unambiguously discriminated in the neighbor-joining dendrogram. This result indicates that the microsatellite markers may be capable of discriminating between related and unrelated oyster larvae in the absence of pedigree information, and is applicable to the investigation of the effective number of parents contributing to the hatchery population of the Pacific oyster.

Genetic affinity of two south Indian ethnic groups with other populations

Humans appear to have spread to several parts of the Indian subcontinent by the middle Paleolithic period. It also provided a major passage for the distribution of modern humans. For the first time generic human leucocyte antigen (HLA) class II (DRB1) genotyping was performed using polymerase chain reaction-sequence-specific primer (PCR-SSP) (low-resolution) technique in two endogamous groups (Hindu-Brahmins and Sunni-Muslims) from the southern state of Andhra Pradesh in order to decipher the genetic affinity between them and with other populations. Calculation of genetic distances, construction of neighbour-joining dendograms and principal-component (P-C) maps were executed using HLA allelic frequencies. The present study reveals the genetic affinity of the Brahmin and Muslim populations from the state of Andhra Pradesh. The dendograms demonstrated that Indian populations form a separate cluster with oriental populations on one side and the eastern and the western Mediterranean populations on the other side. The principal component maps showed the clustering of Indian populations in the lower-right quadrant, where in the Sunni-Muslims occupied a position more closely to the north Indian Brahmins and the Bhargavas than to the geographically related south Hindu-Brahmin group. The study hypothesizes that unlike Brahmins who can be considered as an immediate stock of the Caucasians, the ancestors of Muslims might have been the result of an admixture between the Indo-Europeans and proto-Dravidians.

Leishmaniases in the Mediterranean in the era of molecular epidemiology

Molecular tools are used increasingly for descriptive epidemiological studies in different Mediterranean foci of visceral and cutaneous leishmaniases. Several molecular markers with different resolution levels have been developed to address key epidemiological questions related to the (re-)emergence and spread of leishmaniases, as well as its risk factors: environmental changes, immunosuppression and treatment failure. Typing and analytical tools are improving but are not yet addressing all epidemiological issues satisfactorily. There is an urgent need for better cooperation between laboratory scientists and epidemiologists and for regional epidemiological surveillance of these infectious diseases that affect all Mediterranean countries.

Genetic relationships among Chinese pigs and other pig populations from Hunan Province, China

In this study, protein-level polymorphisms of transferrin, pre-albumin, hemopexin, ceruloplasmin and amylase were investigated in Hunan native pigs and Large Yorkshire pigs collected from Hunan (a province of China), allowing calculations of allele frequencies, average heterozygosities, inbreeding coefficients and genetic distances. The genetic relationship between Southeast Asian native pigs and American pigs was more distant than those among Southeast Asian native pig breeds. The genetic relationship between Southeast Asian native pig breeds and Hampshire pigs was the most distant.