Mean Genetic Divergence Research Articles

DNA barcoding reveals high levels of genetic diversity in the fishes of the Itapecuru Basin in Maranhão, Brazil

DNA barcoding is a useful complementary tool for use in traditional taxonomic studies due to its ability to detect cryptic species, and may be particularly efficient in the identification of fish species. The fish fauna of the Itapecuru River represents an important fishery resource in the Brazilian State of Maranhão, although it is currently suffering increasing degradation as a result of anthropogenic impacts. Therefore, DNA barcoding was used in the present study to identify fish species and establish a database of the rich freshwater fish fauna of Maranhão. A total of 440 specimens were analyzed, corresponding to 64 species belonging to 59 genera, 31 families, and 10 orders. Overall, 92.19% of these species could be identified by DNA barcoding, and were characterized by low levels (average 0.80%) of intra-specific divergence. However, five species (Anableps anableps, Gymnotus carapo, Sciades couma, Pseudauchenipterus nodosus, and Leporinus piau) presented values of mean genetic divergence above 3%, indicating the existence of cryptic diversity in these fishes. The DNA barcoding approach permitted the analysis of a large number of specimens and facilitated the discrimination and identification of closely related fish species in the Itapecuru Basin.

Divergência em QTLs e variância genética para teores de proteína e óleo em soja

Resumo: O objetivo deste trabalho foi avaliar a relação entre os parâmetros de divergência em regiões de QTLs e a variância genética em genótipos de soja, quanto aos teores de proteína e óleo nos grãos. Dois grupos de genótipos foram avaliados, em diferentes ambientes, quanto aos teores de proteína e óleo e genotipados com marcadores moleculares de regiões de QTLs. A partir de cada grupo, estabeleceram-se subgrupos por critérios pré-definidos e avaliou-se a relação entre os parâmetros, tendo-se comparado a divergência média e a variância genética entre os subgrupos. Os subgrupos foram definidos com base nos critérios de diferença em divergência média, homogeneidade e heterogeneidade nos subgrupos e proximidade em uma projeção tridimensional da matriz de distância. As percentagens de concordância entre maiores valores de divergência média e de variância genética para o total de subgrupos de cada grupo inicial foram de 72,5 e de 73,4%, respectivamente. Portanto, nestes genótipos, há relação positiva entre as estimativas de divergência em regiões de QTL e variância genética para os teores de proteína e de óleo dos grãos. As distâncias genéticas com base nos marcadores moleculares de regiões de QTLs são eficientes para a predição da variabilidade genética em genótipos de soja para os teores de proteína e de óleo dos grãos.

DNA barcoding of Nilssonia congeners corroborates existence of wild N. nigricans in northeast India

DNA barcode data of soft-shell turtles is limited in global DNA database while it is completely lacking for the highly debated species Nilssonia nigricans. We employed DNA barcoding technique to discriminate the species cluster for Nilssonia congeners, especially for the highly debated N. nigricans from different localities of northeast India. Sampling across the region included a few live specimens from wild, market sold carcass specimens, and a few dry carapaces meant for home decoration purpose. The generated sequences (621 bp of mtCOI) of dry carapaces showed 99–100% homology with the generated sequences of morphologically identified N. nigricans. The COI barcode sequences of N. nigricans (n = 12) showed 3.8% mean genetic divergence with N. hurum (n = 3), 10% with N. gangetica (n = 4), and 9.2% with N. formosa (GenBank sequences). Similarly, the mtCytb sequences of the dry carapace and live specimens of N. nigricans were 99–100% homologous with the conspecific database sequences and formed specific clusters. The inferred Neighbor-Joining (NJ), Maximum Likelihood (ML), and Bayesian (BA) phylogeny based on partial mtCOI gene efficiently discriminated all the congeners of Nilssonia into specific clusters and, therefore, it was helpful to detect the existence of N. nigricans.

Multispecies coalescent analysis of the early diversification of neotropical primates: phylogenetic inference under strong gene trees/species tree conflict.

Neotropical primates (NP) are presently distributed in the New World from Mexico to northern Argentina, comprising three large families, Cebidae, Atelidae, and Pitheciidae, consequently to their diversification following their separation from Old World anthropoids near the Eocene/Oligocene boundary, some 40 Ma. The evolution of NP has been intensively investigated in the last decade by studies focusing on their phylogeny and timescale. However, despite major efforts, the phylogenetic relationship between these three major clades and the age of their last common ancestor are still controversial because these inferences were based on limited numbers of loci and dating analyses that did not consider the evolutionary variation associated with the distribution of gene trees within the proposed phylogenies. We show, by multispecies coalescent analyses of selected genome segments, spanning along 92,496,904 bp that the early diversification of extant NP was marked by a 2-fold increase of their effective population size and that Atelids and Cebids are more closely related respective to Pitheciids. The molecular phylogeny of NP has been difficult to solve because of population-level phenomena at the early evolution of the lineage. The association of evolutionary variation with the distribution of gene trees within proposed phylogenies is crucial for distinguishing the mean genetic divergence between species (the mean coalescent time between loci) from speciation time. This approach, based on extensive genomic data provided by new generation DNA sequencing, provides more accurate reconstructions of phylogenies and timescales for all organisms.

428 VERTICAL HEPATITIS B VIRUS TRANSMISSION DESPITE SEROVACCINATION OF THE NEWBORN IN HIGHLY VIRAEMIC MONO-INFECTED MOTHERS FROM VARIOUS ETHNIC ORIGINS: A RETROSPECTIVE STUDY IN PARIS, FRANCE

4/8 (50%) rapidly developed lamivudine-resistance mutations. Patients with HBV-reactivation were characterized by a degree of HBsAg-variability higher than that in stably-HBV-infected patients, particularly in a-determinant critical for modulating HBVinfectivity and evasion from neutralizing-antibodies (mean geneticdivergence: 0.058 versus 0.017, P < 0.001). Furthermore, both the percentage of patients with at least 1 immune-escape mutation, and the median number of immune-escape mutations in a-determinant, were significantly higher in patients with HBV-reactivation than in controls (64.3%[9/14] versus 27%[27/100], P = 0.008; and 1[IQR: 0–2] versus 0[IQR: 0–2], P = 0.002, respectively). Moreover, ≥1 specific HBsAg-mutation (M103I-T123N-S143L-D144E-S154L-V190A) was present in 8/14 (57.1%) patients with HBV-reactivation status (independently from the presence of drug-resistance mutations), while in controls they were absent (0/100 for M103I-T123ND144E-S154L), or nearly absent (1/100 for S143L and 2/100 for V190A). All the identified mutations (except for V190A, situated in the membrane-embedded C-terminal domain) are localized in a-determinant, and are known to be associated with decreased HBsAg-antigenicity. T123N introduces an N-linked glycosylationsite, thus potentially reducing HBsAg immunogenic-surface. Conclusions: HBV-reactivation correlates with an increased HBV ability to evade the pressure imposed by humoral immuneresponse. This highlights the need of a careful monitoring, and of establishing an adequate, high-genetic-barrier therapy (if required) in order to prevent HBV-reactivation and consequent liver damage in the setting of immune-suppression.

High resolution melting of trnL amplicons in fruit juices authentication

Fruit juices labeled as 100% fruit are a growing market in the EU representing two-thirds of total sales in 2011. These usually have premium prices representing favored targets for adulteration. Herein our main objective was to evaluate the effectiveness of High Resolution Melting Analysis applied to fruit species discrimination (orange, mango, peach, pear and pineapple) in fruit juices using the DNA barcode trnL. Three DNA extraction procedures (CTAB, membrane and resin based) were tested. The locus trnL proved to be appropriate being the mean genetic divergence estimated at 27.7%. Results provided a very clear discrimination of the 5 species easily visualized throughout the melt curve difference graphs. Mixed juices of orange and mango were also assayed. The complete discrimination of the mixtures was achieved proving the efficiency of the method as an authenticity test. The proposed methodology proved its efficiency in the genetic-based discrimination of species in juices with the advantages of single-tube analysis.

Morphological and molecular analyses of larval trematodes in the intertidal bivalve Perumytilus purpuratus from central Chile

The bivalve Perumytilus purpuratus is a common species that is widely distributed throughout rocky intertidal zones in Chile. This bivalve is the first intermediate host for three trematode species: one bucephalid (an undetermined species) and two fellodistomids (Proctoeces lintoni and one undetermined species). A few studies based on morphological comparisons, experimental infection and molecular analyses have been performed to ascertain the taxon (at least at the family level) to which these trematodes belong; yet, there remains no clarification about the specific identity of these trematodes. Therefore, in this study, we compared the V4 region nucleotide sequences of the 18S rRNA of these three sporocyst species, classified as morphotypes, found in P. purpuratus and nine adult trematode species from intertidal fishes that are likely definitive hosts for these parasites. The sequences from two of the sporocyst morphotypes matched with adult trematodes from the intertidal fish: type 1 sporocyst was similar to Prosorhynchoides carvajali (Bucephalidae), with a mean genetic divergence of 0.78%, and type 2 sporocyst was similar to Proctoeces sp. (but not P. lintoni), with 0% genetic divergence. The third species (type 3 sporocyst) was classified to the family Fellodistomidae; however, the sequence from this species differed greatly from the three other fellodistomid species documented in the marine fish of Chile and from other fellodistomids in public databases. Moreover, this morphotype has a particular cercarial morphology that greatly differs from other fellodistomid species described thus far. Therefore, this intriguing trematode remains a mystery.

Profile of T cell recognition of HIV type 1 consensus group M Gag and Nef peptides in a clade A1- and D-infected Ugandan population.

Reagents for evaluating non-clade B HIV-specific T cell responses are uncommon. Peptides based on highly conserved HIV-1 consensus group M sequences that are phylogenetically closer to most circulating strains may provide potential alternative reagents in populations with diverse infections, and may be relevant for vaccine design. Recognition of such reagents in clade A1-and D-infected populations has not been previously evaluated. Interferon (IFN)-γ ELISpot assay was used to evaluate T cell recognition of Gag and Nef peptides based on consensus group M sequences in 50 treatment-naive adults predominantly infected with HIV-1 clades A1 and D. Gag-induced T cell responses were correlated with gag sequence diversity. Infecting clades were determined from gag sequences for 45 of the 50 subjects as 40% clade A1 (18/45), 45% clade D (20/45), 2% clade C (1/45), 2% A1/C recombinant (1/45), 2% A1/D (1/45), 7% CRF10_CD (3/45), and 2% U (unclassifiable) (1/45). The mean genetic divergence and diversity of clade A and D gag region compared to group M consensus sequences at synonymous and nonsynonymous nucleotide and amino acid levels were not always significant. Gag peptides were targeted at significantly higher frequency [88% (44/50)] than Nef [64% (32/50)]; p=0.014, although their mean IFN-γ magnitudes were comparable ([3703 (95% CI 2567-4839)] vs. [2120 (95% CI 478-3762)]), respectively. Measurable virus-induced IFN-γ responses were detected in 96% (48/50) individuals, primarily targeting the more conserved Gag p24 and Nef central core regions. Use of these reagents to screen for HIV-specific IFN-γ responses may mitigate the challenge of viral diversity; although this targeting is apparently biased toward a few highly conserved epitopes.

Are there two cryptic species of the lesser jerboa Jaculus jaculus (Rodentia: Dipodidae) in Tunisia? Evidence from molecular, morphometric, and cytogenetic data

Jerboas belonging to the genus Jaculus are widely distributed rodents inhabiting Palearctic desert and semi-desert areas. Previous studies on the lesser Egyptian jerboa Jaculus jaculus showed the existence of various morphological forms of controversial taxonomic status. They were sometimes related to two different species, J. jaculus and Jaculus deserti, although this has not been recognized in recent taxonomic updates. To clarify the systematic status of J. jaculus in Tunisia, we performed molecular (phylogenetic analyses of cytochrome b sequences), morphological (multivariate analyses of 13 skull measurements) and karyotypic (standard preparations from bone marrow cells) analyses on a number of specimens collected from ten localities. Our analyses revealed two monophyletic, well differentiated clades, with a mean genetic divergence value (K2P = 10.9 ± 0.01%), which is within the range of distances generally observed between rodent species. Morphometric analyses clearly separated populations of the two genetic clades from each other. However, karyotypes of individuals from both clades appeared similar. Individuals from both molecular clades/morphometric groups were found in sympatry in most of the localities sampled. These results, as obtained from a restricted area of the total distribution, suggest that there are two separate species within the currently accepted J. jaculus in Tunisia. Alternative hypotheses such as the occurrence of a strong, ancient phylogeographic structure, or the presence of pseudogenes, are also considered to account for the results obtained. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99, 673–686.

The genetic divergence of prehistoric populations of the south‐central Andes as established by means of craniometric traits

The peopling of the south-central Andean region can be determined by exploring a combination of cultural, economic, and biological factors that influence the structure of populations and determine particular dispersals of gene frequencies. Quantitative characters from 1,586 adult crania of both sexes from northern Chile, northwestern Argentina, and the Cochabamba valleys in Bolivia were analyzed employing multivariate statistical analyses. Biological distances, representing phenotypic variation between these regions and their subregions, were studied within a population genetics framework. An analysis of Mahalanobis D(2) distances establishes two principle directions of interaction: the first between the Cochabamba valleys and northern Chile, and the second between the Cochabamba region and northwestern Argentina. The Chile and Argentina regions are shown to be less related to each other than each is to the Bolivian region. A higher mean genetic divergence is found for the entire region (F(ST) = 0.195); with northwestern Argentina having the highest spatial isolation (F(ST) = 0.143) and northern Chile the lowest (F(ST) = 0.061). These results allow us to propose a populating model based on the dispersion of several lines from a common ancestral population similar to those who inhabited the Cochabamba valleys. These lines differentiated themselves in time and space according to the effective size and the rate of gene flow, eventually producing the human groups which inhabited the valleys of northern Chile and northwestern Argentina.

A review of the Tripterygion tripteronotus (Risso, 1810) complex, with a description of a new species from the Mediterranean Sea (Teleostei: Tripterygiidae)

We compared specimens of Tripterygion tripteronotus from 52 localities of the Mediterranean Sea and adjacent waters, using four gene sequences (12S rRNA, tRNA-valine, 16S rRNA and COI) and morphological characters. Two well-differentiated clades with a mean genetic divergence of 6.89±0.73% were found with molecular data, indicating the existence of two different species. These two species have disjunctive geographic distribution areas without any molecular hybrid populations. Subtle but diagnostic morphological differences were also present between the two species. T. tripteronotus is restricted to the northern Mediterranean basin, from the NE coast of Spain to Greece and Turkey, including the islands of Malta and Cyprus. T. tartessicum n. sp. is geographically distributed along the southern coast of Spain, from Cape of La Nao to the Gulf of Cadiz, the Balearic Islands and northern Africa, from Morocco to Tunisia. According to molecular data, these two species could have diverged during the Pliocene glaciations 2.7-3.6 Mya.

A Preliminary Comparative Evaluation of Genetic Diversity between Chinese and Japanese Wild Soybean (Glycine soja) Germplasm Pools using SSR markers

The wild soybean, an annual self-pollinating plant, is the progenitor of soybeans and is extensively distributed in the Far East of Russia, the Korea peninsula, China and Japan. Geographically, Japan is surrounded by sea and insulated from China. We preliminarily evaluate whether the Japanese and Chinese wild soybean germplasm pools are genetically differentiated from each other using SSR markers. The results showed that the two pools have great genetic differentiation. Some loci presented obvious differences in mean genetic divergence (GST) value between the two pools. The GST among the geographic regions in China was higher than that in Japan. The average within-geographic region gene diversity values (HS) in the two pools were completely identical and thus the genetic difference between the two pools was mostly attributed to the relatively high level of between-geographic region gene diversity (DST) in China. We suggest that Japanese and Chinese wild soybeans should be comparatively independently evolving in phylogeny.

Assessment of genetic diversity among 51 inbred sunflower lines

Genetic divergence of 51 inbreds and 3 checks of sunflower was assessed using the Mahalanobis D2 statistics. Fifty-one sunflower inbreds plus three checks, GAUSUF-15, TNASUF-7 and TNAU-1, of diverse geographical origin, were grouped into eight clusters which were not related to their geographic origin. Stem girth and seed yield per plant contributed the most to the total genetic divergence. Maximum inter-cluster distance was observed between the inbreds grouped in clusters I and V containing five and twelve inbreds, respectively, while the intra-cluster distance ranged from 0 to 2306.05. Based on mean performance, genetic divergence and clustering pattern, few inbreds namely CMS-234B, 7-1-B, CMS-597B, CMS-852B, ARM-250B, ARM-245B, HAM-69, ARM-284B, ARM-247B and HAM-174 were considered as potentially important for further breeding programs.

Delineation of genetic zones in the European Norway spruce natural range: preliminary evidence.

We applied geostatistics to previously reported chloroplast simple sequence repeats (cpSSR) haplotype frequency data from 95 European Norway spruce populations to provide preliminary evidence about the following issues: (i) delineation of genetically homogeneous regions ('genetic zones'); (ii) prediction of their haplotype frequencies and definition of related criteria to be applied for provenance identification and certification of seedlots; (iii) identification of putative allochthonous stands; and (iv) construction of a continental-scale 'availability map' of the intraspecific biodiversity for Norway spruce. Direct evidence of large-scale geographical structure over the European natural range was obtained, detecting both geographical clines and stationary patterns. The increase of the mean genetic divergence by geographical distance (up to approximately 1800 km apart) provided a strong hint that geographical distance is a major factor of differentiation in Norway spruce. Haplotype frequency surfaces were obtained by applying ordinary kriging to sampling frequency data. Cluster analysis carried out on haplotype frequency surfaces revealed a fair discrimination among 16 genetic zones, with an accuracy of 0.916. Dendrogram analysis carried out on the predicted mean haplotype frequency confirmed a fairly good separability of the genetic zones detected. Reclassification of populations by discriminant analysis confirmed the robustness of the genetic subdivision obtained. Combining the information from discriminant analysis and cross-validation of sampling points, three populations likely to be of nonlocal origin were identified. The application of geostatistical analysis to genetic marker data is discussed in relation to breeding activities and to the formulation of appropriate conservation strategies.

Intrafamilial transmission of hepatitis delta virus: molecular evidence

Background/Aims: Epidemiologic studies have suggested that transmission of hepatitis delta virus (HDV) occurs by intrafamilial routes in some populations in southern Italy, where HDV infection is endemic. To further evaluate intrafamilial transmission of HDV, we obtained the partial sequence of the viral genome from HDV-RNA positive members of families in which two or more immediate family members were positive for HDV-RNA. Methods: The region analyzed was the semi-conserved region from nucleotides 908 to 1265. Sequences obtained from family members were compared with those obtained from a control group of 20 unrelated patients. Results: The mean genetic divergence among HDV isolates was 2.8±1.7% within the 9 families analyzed, and 7.6±2.2% among the control group of unrelated individuals ( p Conclusions: The data indicate that in most family units, HDV-infected members harbored nearly identical strains of HDV, and provide molecular support that HDV infection can be transmitted within the family. Such spreading among family members highlights the role of inapparent transmission through personal contacts.