High Level Of Genetic Similarity Research Articles

Genetic characterization of Nigerian indigenous pig using polyacrilamide gel electrophoresis

The genetic structure of Nigerian indigenous pigs (NIP) and crossbred pigs were investigated using polyacrylamide gel electrophoresis. A total of 79 NIP blood samples were collected from three different locations within South-western Nigeria namely, Igbara Odo, Ekiti State (33 samples), Ogbooro, Oyo State (30 samples), and Institute of Agricultural Research and Training (IAR&T), Oyo State (16 samples). In addition, 41 crossbred pig blood samples were collected from the Teaching and Research Farm (T&R Farm), Obafemi Awolowo University, Ile-Ife. The blood serum samples obtained from the pigs were subjected to Sodium dodecyl sulphate (12%) SDS-PAGE gel electrophoresis. A total of 19 protein loci were scored for the NIP and 16 for crossbred samples. The SDS-PAGE electrophoretic profiles were analysed using PAST package (2005) to determine genetic similarity coefficients and construct phylogenetic dendrograms using Nei’s standard genetic distance. Ogbooro NIP samples showed a very high level of genetic similarity (91%) while IAR&T was 87% whereas Igbara Odo was 56%. The T&R Farm crossbred pigs showed 81%. The total local pig samples from the three locations gave a high genetic similarity coefficient of 84% confirming their genetic relatedness. The high genetic similarity observed in the indigenous pig samples in Ogbooro indicated a level of inbreeding of pig stocks in this locality which can be conserved as a genetic resource for breeding programmes for pure NIP in the future. Key words: Animal genetic resources, conservation, Nigeria indigenous pig, electrophoresis

Mycorrhizal specificity of Diuris fragrantissima (Orchidaceae) and persistence in a reintroduced population

This study investigated the diversity and specificity of mycorrhizal fungi associated with five Diuris (Orchidaceae) taxa in south-eastern Australia, as part of a reintroduction program for the endangered species Diuris fragrantissima. We compared fungi isolated from D. fragrantissima occurring naturally in the only remaining population with those from artificially cultivated plants and reintroduced plants 18 months after planting in a new field site west of Melbourne. Genetic similarity of nuclear internal transcribed spacer and nuclear large subunit DNA sequences showed that Diuris taxa associate with a narrow taxonomic range of fungi within the cosmopolitan family Tulasnellaceae in the Rhizoctonia alliance. All fungal isolates induced host seed germination and hence were considered mycorrhizal. Fungal isolates from naturally occurring D. fragrantissima plants showed a higher level of genetic similarity than fungi isolated from cultivated plants. This observation suggests that, historically, the species may have associated with a more genetically variable range of Tulasnella fungi. Artificially cultivated D. fragrantissima were propagated aseptically from seed and spontaneously formed mycorrhizal associations within 6 months of transfer to potting media. Wild collected D. fragrantissima plants maintained in cultivation for over 30 years were found to contain mycorrhizal fungi similar to those isolated from naturally occurring plants in 2004–2006. Mycorrhizal associations in artificially cultivated D. fragrantissima were present in 18 randomly sampled plants 18 months after reintroduction. Further, associations formed between several reintroduced plants and a fungus concurrently inoculated into site soil. We propose that future orchid reintroductions may benefit from the concurrent addition of suitable mycorrhizal fungi to site soil. Maintenance of orchid mycorrhizal relationships after reintroduction is essential to improve long-term viability of reintroduced populations.

Genomic microsatellites identify shared Jewish ancestry intermediate between Middle Eastern and European populations

BackgroundGenetic studies have often produced conflicting results on the question of whether distant Jewish populations in different geographic locations share greater genetic similarity to each other or instead, to nearby non-Jewish populations. We perform a genome-wide population-genetic study of Jewish populations, analyzing 678 autosomal microsatellite loci in 78 individuals from four Jewish groups together with similar data on 321 individuals from 12 non-Jewish Middle Eastern and European populations.ResultsWe find that the Jewish populations show a high level of genetic similarity to each other, clustering together in several types of analysis of population structure. Further, Bayesian clustering, neighbor-joining trees, and multidimensional scaling place the Jewish populations as intermediate between the non-Jewish Middle Eastern and European populations.ConclusionThese results support the view that the Jewish populations largely share a common Middle Eastern ancestry and that over their history they have undergone varying degrees of admixture with non-Jewish populations of European descent.

Duplication of the class I cytosolic small heat shock protein gene and potential functional divergence revealed by sequence variations flanking the α-crystallin domain in the genus Rhododendron (Ericaceae)

Positive selection in the -crystallin domain (ACD) of the chloroplast small heat shock protein (CPsHSP) gene was found in a previous study and was suggested to be related to the ecological adaptation of Rhododendron species in the subgenus Hymenanthes. Consequently, it was of interest to examine whether gene duplication and subsequent divergence have occurred in other sHSP genes, for example class I cytosolic sHSP genes (CT1sHSPs) in Rhododendron in Taiwan, where many endemic species have evolved as a result of habitat differentiation. A phylogeny of CT1sHSP amino acid sequences was built from Rhododendron, Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Vitis vinifera and other species for elucidation of the phylogenetic relationships among CT1sHSPs. Phylogenies of Rhododendron CT1sHSP nucleotide and amino acid sequences were generated for positive selection and functional divergence analysis, respectively. Positively selected sites and amino acid differences between types of Rhododendron CT1sHSPs were mapped onto the wheat sHSP16.9 protein structure. Average genetic distance (Dxy) and dN/dS ratios between types of Rhododendron CT1sHSP genes were analysed using sliding window analysis. Gene conversion was also assessed between types of Rhododendron CT1sHSPs. Two types of Rhododendron CT1sHSP were identified. A high level of genetic similarity and diversity within and flanking the ACD, respectively, between types of Rhododendron CT1sHSP were found. Main differences between the two types of Rhododendron CT1sHSPs were: (1) increased hydrophobicity by two positively selected amino acid sites and a seven-amino-acid insertion in the N-terminal arm; and (2) increased structural flexibility and solubility by a seven-amino-acid insertion in the N-terminal arm and one positively selected amino acid site in the C-terminal extension. Functional conservation of the ACD of Rhododendron CT1sHSP genes was inferred b

Genetic variability in Asparagus racemosus (Willd.) from Madhya Pradesh, India by random amplified polymorphic DNA

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Asparagus racemosus (Willd.) an important medicinal plant collected from 7 different locations covering Madhya Pradesh. High level of genetic similarity was observed in the collected accessions. 4 random primers generated a total 39 polymorphic bands out of the total 71 bands. A low genetic diversity among the A. racemosus samples was revealed by RAPD analysis. Cluster analysis based on dice coefficient showed 2 major groups. This distributive pattern of genetic variation of A. racemosus accessions provides important baseline data for conservation and collection strategies for this species.

Genetic structure of natural populations of the relict species Aristolochia manshuriensis (Aristolochiaceae) in disturbed and intact habitats

Genetic structure of natural populations of the rare relict plant Manchurian birthwort (Aristolochia manshuriensis Kom.) in the Russian part of its area was analyzed using allozyme markers. The studied A. manshuriensis populations differed in the degree of their intrapopulation differentiation. The populations Nezhinka and Anan'evka were more differentiated (F(ST) = 0.1209 and 0.0576, respectively); these populations are located close in the regions of intense economic activity and are exposed to the strongest anthropogenic impact. A low degree of differentiation was detected in the population Malaya Borisovka (F(ST) = 0.0393), localized to intact habitats. The overall heterogeneity test has demonstrated that the population Malaya Anan'evka, exposed at present to small anthropogenic stress yet growing in disturbed habitats, displays no differentiation. These results suggest that at least three populations are influenced by genetic drift connected with a decrease in the reproductive and effective population sizes, which is caused, in particular, by anthropogenic impact. A high level of genetic similarity between the A. manshuriensis populations in Primor'e is discussed in connection with the evolutionary history of this species.

Amplified fragment length polymorphism used for inter- and intraspecific differentiation of screwworms (Diptera: Calliphoridae)

Morphologically, early immature stages of the economically important pest called screwworms, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), and non-pest secondary screwworms, Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae), are nearly indistinguishable. Correct identification is crucial to the ongoing eradication and exclusion program protecting the United States, Mexico and Central America from reinvasion of screwworms persistent in South America and the Caribbean. Amplified fragment length polymorphism (AFLP) polymerase chain reaction was used to differentiate populations of C. hominivorax and to discriminate them from C. macellaria. Ten primer pairs screened for interspecific discrimination of C. hominivorax from C. macellaria showed 52 discrete bands, allowing the two species to be readily distinguished; divergent branches on resulting dendrograms showed 100% bootstrap support. C. macellaria populations grouped at the 92% level; C. hominivorax populations grouped at the 68% level. Of the 52 bands, seven were monomorphic for both species, 22 were specific to C. macellaria, ten were present only in C. hominivorax and the remaining 13 bands differentiated C. hominivorax populations. Separate studies using ten strains of C. hominivorax showed a higher level of genetic similarity within than between populations. Analyses using 72 bands (19 monomorphic bands, 53 bands grouped all ten strains at the 58% similarity level) resolved seven mutant strains from Mexico (85% similarity level); all ten strains were resolved at the 72% similarity level. Diagnostic bands were identified for species and strain identification. We conclude that AFLP can be a valuable tool for studies of interspecific and intraspecific genetic variation in screwworm populations.

Morphometric and Genetic Variation of Six Seed Sources of Azadirachta excelsa (Jack) Jacobs

Isozyme variability was examined in six seed sources representing the Azadirachta excelsa on two provenance trials in Batu Arang (Selangor, Malaysia) and Merchang (Terengganu, Malaysia). A concomitant study of morphometric variation revealed a slight variation in leaf morphology extending from quantitative to qualitative characteristics. The existence of this small variation presented an ideal opportunity to examine the genetic variation of these seed sources collected in Bukit Lagong and Manong (West Coast of P. Malaysia), Pengkalan Arang and Pasir Mas (East Coast of P. Malaysia), Semengoh (East Malaysia) and Narathiwat (Thailand). Nineteen enzyme systems were used to determine the genetic variation among seed sources using isozyme analysis. Allelic frequency data indicated little differentiation between seed sources. The mean values of observed heterozygosity (Ho) varied from 0.0229 (Pengkalan Arang) to 0.0451 (Bukit Lagong) whereas the mean values expected heterozygosity (He) varied from 0.0575 (Pengkalan Arang) to 0.0983 (Manong). The percentages of proportion polymorphic loci were found to vary between 31.43% (Pengkalan Arang and Pasir Mas) and 42.86% (Bukit Lagong and Manong). Genetic identities according to Nei ranged from 0.7727 to 0.9999. Despite these high levels of genetic similarity, the populations appeared to be highly inbred as indicated by positive mean of FIS and FIT values with the mean values of 0.5643 and 0.8038.

Genetic diversity in Oroxylum indicum (L.) Vent. (Bignoniaceae), a vulnerable medicinal plant by random amplified polymorphic DNA marker

Random amplified polymorphic DNA (RAPD) markers were used to assess genetic diversity in Oroxylum indicum (L.) Vent (Bignoniaceae) a vulnerable medicinal plant collected from eight locations in Andhra Pradesh, India. High level of genetic similarity was observed in the collected accessions. Forty random primers, each with 10 bases generated a total of 188 polymorphic bands out of the 387 total bands, that is, polymorphism of 49.61% was observed. Overall genetic similarity based on 40 random primers was 87%. Cluster analysis based on Dice coefficient showed two major groups. The results show that the genetic diversity of this species is low, possibly depicting a difficulty in adapting to environmental variations. This distributive pattern of genetic variation of O. indicum accessions provides important baseline data for conservation and collection strategies for this species. The collected accessions were introduced to University of Hyderabad field gene bank along with other redlisted plants of Deccan ecoregion.

Determination of genetic stability of grafted marula trees using AFLP markers

Genetic stability of grafted marula trees within seven lines, some of which exhibiting interline phenotypic variations, was evaluated using the AFLP technique. The study was conducted in two-fold using samples from the DR, LP, MR, OS, PH, SW and TR lines. The genetic analysis using leaf materials indicated varying levels of genetic variations between genotypes within the OS, MR, LP and PH lines. The genotypes of the DR, TR and SW lines showed high intraspecific genetic similarity and formed tight clusters on the UPGMA-based dendrogram. The genetic analysis using a subset of the initial sample set constituting both leaf and bark materials which represented the scion and the rootstock components of grafted trees showed high genetic similarities between the graft partners of some genotypes within the OS and PH lines. These high levels of genetic similarity between scion and rootstock partners of a grafted tree suggested that the rootstock graft developed shoots and grew into a tree following graft failure. The observed results imply that grafting is not always successful even within compatible species, however, it can be reliably monitored using molecular markers.

Detecting Copy Number Variation in the Human Genome Using Comparative Genomic Hybridization

Among human beings, it was once estimated that our genomes were 99.9% genetically identical. While this high level of genetic similarity helps to define us as a species, it is our genetic variation that contributes to our phenotypic diversity. As genomic technologies evolve to provide genome-wide analyses at higher resolution, we are beginning to appreciate that the human genome has a lot more variation than was once thought. Array-based comparative genomic hybridization (CGH) is one of these technologies that has recently revealed a newly appreciated type of genetic variation: copy number variation, in which thousands of regions of the human genome are now known to be variable in number between individuals. Some of these copy number variable regions have already been shown to predispose to certain common diseases, and others may ultimately have a significant impact on how each of us reacts to certain foods (e.g., allergic reactions), medications (e.g., pharmacogenomics), microscopic infections (i.e., immunity), and other aspects of our ever-changing environment.

Assessment of Genetic Variability in Two North Indian Buffalo Breeds Using Random Amplified Polymorphic DNA (RAPD) Markers

Murrah and NiliRavi are the important North Indian buffalo breeds occupying the prominent position of being the highest milk producers. These breeds are more or less similar at morphological as well as physiological levels. The technique of RAPD-PCR was applied in the present study to identify a battery of suitable random primers to detect genetic polymorphism, elucidation of the genetic structure and rapid assessment of the differences in the genetic composition of these two breeds. A total of 50 random primers were screened in 24 animals each of Murrah and NiliRavi buffaloes to generate RAPD patterns. Of these, 26 (52%) primers amplified the buffalo genome generating 263 reproducible bands. The number of polymorphic bands for the 26 chosen RAPD primers varied from 3 (OPG 06 and B4) to 26 (OPJ 04) with an average of 10.1 bands per primer and size range of 0.2 to 3.2 kb. DNA was also pooled and analyzed to search for population specific markers. Two breed specific RAPD alleles were observed in each of Murrah (OPA02 and OPG16) and NiliRavi (OPG09) DNA pools. RAPD profiles revealed that 11 (4.2%) bands were common to all the 48 individuals of Murrah and NiliRavi buffaloes. Pair-wise band sharing calculated among the individual animals indicated considerable homogeneity of individuals within the breeds. Within breed, band sharing values were relatively greater than those of interbreed values. The low genetic distance (Nei's) value (0.109) estimated in this study is in accordance with the origin and geographical distribution of these breeds. The RAPD analysis indicated high level of genetic similarity between these two important North Indian buffalo breeds.

Enteroviral Infection Outbreak in the Republic of Belarus: Principal Characteristics and Phylogenetic Analysis of Etiological Agents

For the last decade enterovirus outbreaks were registered in all of six districts of Belarus. Two of them, reported in 1997 (in Gomel) and in 2003 (in Minsk), were the most extensive and involved 461 and 1,351 patients respectively. Virus ECHO 30 was identified as the dominant etiologic agent of the outbreak in 1997 whereas co-circulation of ECHO 30, ECHO 6 and Coxsackievirus B5 took place in 2003. Analysis of clinical manifestations during the Minsk outbreak revealed unusually high rate of severe clinical forms of infection including aseptic meningitis, encephalitis and myocardial disorders. Epidemiologic observation was ordinary for enterovirus epidemics in temperate climates: the peak of the outbreak was recorded during summer-autumn period of 2003, and 0-14 years old children predominated. Data from the case-control study indicated that illness was associated with drinking water from community water system. Also the laboratory examination demonstrated contamination of different water samples with the epidemic virus serotypes and sequence analysis showed high level of genetic similarity between waterborne and clinical isolates. For these reasons the outbreak should be classified as a waterborne one. Phylogenetic reconstruction showed that all Belarusian ECHO 30 isolates belong to the major genotype of ECHO 30 which has been circulating for last 15 years in Europe and North America. Viral agents of 2003 were very similar and substantially differed from isolates of 1997. Comparison of nucleotide sequences of isolates from myocarditis patients revealed their considerable genetic similarity with ECHO 30 isolates from patients with aseptic meningitis and from water. The results of the study draw attention to the importance of virological control of tap and bottled water as a relevant measure aimed at reduction of epidemiological risks.

A molecular phylogeny of the genus Echinococcus inferred from complete mitochondrial genomes

Taxonomic revision by molecular phylogeny is needed to categorize members of the genus Echinococcus (Cestoda: Taeniidae). We have reconstructed the phylogenetic relationships of E. oligarthrus, E. vogeli, E. multilocularis, E. shiquicus, E. equinus, E. ortleppi, E. granulosus sensu stricto and 3 genotypes of E. granulosus sensu lato (G6, G7 and G8) from their complete mitochondrial genomes. Maximum likelihood and partitioned Bayesian analyses using concatenated data sets of nucleotide and amino acid sequences depicted phylogenetic trees with the same topology. The 3 E. granulosus genotypes corresponding to the camel, pig, and cervid strains were monophyletic, and their high level of genetic similarity supported taxonomic species unification of these genotypes into E. canadensis. Sister species relationships were confirmed between E. ortleppi and E. canadensis, and between E. multilocularis and E. shiquicus, regardless of the analytical approach employed. The basal positions of the phylogenetic tree were occupied by the neotropical endemic species, E. oligarthrus and E. vogeli, whose definitive hosts are derived from carnivores that immigrated from North America after the formation of the Panamanian land bridge. Host-parasite co-evolution comparisons suggest that the ancestral homeland of Echinococcus was North America or Asia, depending on whether the ancestral definitive hosts were canids or felids.

Legal Constraints on the Use of Race in Biomedical Research: Toward a Social Justice Framework

This article addresses three questions concerning the legal regulation of the use of race as a category in biomedical research: how does the law currently encourage the use of race in biomedical research?; how might the existing legal framework constrain its use?; and what should be the law's approach to race-based biomedical research? It proposes a social justice approach that aims to promote racial equality by discouraging the use of "race" as a biological category while encouraging its use as a socio-political category to understand and investigate ways to eliminate disparities in health status, access to health care, and medical treatment.

Presence of Ecophysiologically Diverse Populations within Cobetia marina Strains Isolated from Marine Invertebrate, Algae and the Environments

Over the last decade, taxonomic surveys have recovered sixteen strains of Halomonas-like marine heterotrophic bacteria from different ecological habitats. The sixteen strains were isolated from three N.W. Pacific Ocean habitats: seawater, the mussel Crenomytilus grayanus and the degraded thallus of brown alga Fucus evanescens. These strains were subjected to a taxonomic investigation of their phenotypic/physiological, genetic, and phylogenetic features. Analysis indicates these bacteria belong to Cobetia marina. The study found all strains tolerated CdCl2 concentrations up to 875 mM. Taxonomically, the sixteen strains belong to the same species, nevertheless, their physiological features revealed distinguishing characteristics. For instance, strain KMM 296, recovered from the mussel Crenomytilus grayanus, was distinct from other C. marina strains by its ability to produce highly active alkaline phosphatase. The majority of C. marina strains that were isolated from degraded alga thallus appeared to have a particular metabolic specialisation by utilizing a range of easily assimilable monosaccharides. Notably, despite a high level of genetic similarity (80% of DNA relatedness), the phenotypic features of the strains isolated from degraded alga thallus differed with the type strain C. marina LMG 2217T. These differences suggest an ecologically adapted population of C. marina at a subspecies level.

Similaridade genética entre raças bovinas brasileiras

A similaridade genética entre animais de duas raças bovinas brasileiras (Crioulo Lageano e Junqueira) foi estimada pela análise de polimorfismo de DNA amplificado ao acaso (RAPD), tendo como referência (outgroups) animais de raças comerciais das espécies Bos taurus e B. indicus. Estas duas raças possuem grande similaridade fenotípica, sugerindo uma origem genética comum. Uma matriz de similaridade genética baseada em polimorfismo de DNA foi obtida e representada graficamente por um dendrograma, definido após processo estatístico de reamostragem bootstrap. Ao contrário do que era previsto com base nas semelhanças morfológicas das duas raças, os animais das raças Crioulo Lageano e Junqueira não apresentaram similaridade elevada entre si quando comparados com animais de outras raças comerciais. Os dados indicam que as duas raças sofreram contribuições genéticas distintas no processo de formação racial.

Genetic variation among populations of the Antarctic toothfish: evolutionary insights and implications for conservation

Commercial fishing is having an increasingly negative impact on marine biodiversity, with over 70% of the world's fish stocks being fully exploited and, in many cases, overexploited. On top of this, the Commission for the Conservation of Antarctic Marine Living Resources (CCAMLR) has granted commercial fishing permits in the most remote marine environment on earth, the high-latitude Southern Ocean. The primary target of these new commercial fishing ventures is the large pelagic piscivorous predator, the Antarctic toothfish (Dissostichus mawsoni). Unfortunately, little information is available on the demography, genetics, or life history of this large fish. Without such information we have little idea as to the effects of commercial fishing on the population structure and survival of this species. In this study, we focus on patterns of genetic diversity within and between geographically disparate populations of the Antarctic toothfish, using randomly amplified polymorphic DNA markers. Results of our study showed high levels of genetic similarity within and between populations. Despite high levels of genetic similarity, genetic analyses detected significant population structure, including fixed differences among populations, a significant fixation index (Fst) and between-population differentiation via a Mantel test. From a conservation perspective, low levels of genetic diversity may be indicative of relatively small populations that would not be able to withstand heavy commercial fishing pressures. Given that there is evidence for significant genetic structure, it will be important to manage these fisheries in a manner that will help prevent the loss of unique genetic variation from regional overfishing.

Genetic relationships of endophytic Lophodermium nitens isolates from needles of Pinus strobus

The foliage of Pinus strobus (eastern white pine), as that of all other conifers examined, is occupied by endophytic fungi, the most frequent of which is Lophodermium nitens. The number and extent of endophytic infections and the genetic relationship of individual isolates within living needles as well as their relationship to isolates from forest floor needles is unknown. To examine these and related questions, forest floor isolates and foliar endophytes from needle segments were obtained for ribosomal DNA sequencing and randomly amplified polymorphic DNA (RAPD) analysis. Molecular and morphological data were compared and infection frequency determined as a function of position along the needle. Ribosomal DNA sequences of foliar and ascospore isolates showed high levels of genetic similarity (> 97% identity) for the internal transcribed spacer region. RAPD profiles were able to distinguish ascospore siblings from non-siblings, and also revealed that many needle isolates belonged to the same genotype as adjacent neighbour isolates, as would be expected from mycelial spread within the needle. Morphotype evaluation and RAPD profiles showed similar patterns: identical morphotypes grouped together and showed little or no genetic difference under RAPD analysis. Both morphological and molecular data indicated that the majority of infections were contained within 1 mm needle segments but could extend to about 4 mm in length. Infection frequency increased along the length of the needle from the proximal (shoot) end to the distal tip, with markedly higher rates in the distal quarter. Thus, endophytic infections of L. nitens in white pine needles consist of many localized, discrete infections, originating from ascospores and differentially distributed along the length of the needle. In the course of this work, it was found that GenBank accession no. AF203470 under the name Meloderma desmaszieresii appeared not to be that species but L. nitens on the basis of the ITS sequences.

Varietal diversity within grapevine accessions of cv. Tempranillo

Intra-varietal diversity of 31 accessions named as Tempranillo or described as synonyms of this representative Spanish grapevine variety was assessed using 48 morphological descriptors and 95 AFLP markers obtained using 2 primer combinations. We could identify homonyms as well as accessions belonging to varieties which, depending on their regional origin, are incorrectly cited as Tempranillo synonyms. Genetic analysis revealed a high level of genetic similarity between Tempranillo accessions (SG >0.97), which could correspond to three highly related genotypes. This narrow genetic variation supports a monophyletic origin of Tempranillo, and could be the result of rapid multiplication and distribution of a very low number of clones.