Mean Pairwise Genetic Distance Research Articles

Successful expansion of Mycobacterium tuberculosis Latin American and Mediterranean sublineage (L4.3/LAM) in Tunisia mainly driven by a single, long-established clonal complex

ObjectivesTo explore the evolutionary history of Mycobacterium tuberculosis Latin American and Mediterranean (L4.3/LAM) sublineage in Tunisia, where it predominates. MethodsHigh-resolution genotyping of 252 L4.3/LAM clinical strains was undertaken, and whole-genome sequencing was performed on 31 representative isolates. ResultsGenotyping data coupled with Bayesian analyses split the Tunisian L4.3/LAM strain collection into two divergent entities (65.07% vs 34.92%): a major subpopulation, dominated by a single clonal complex (CC), TUN4.3_CC1 (94.51%); and a minor subpopulation, dominated by TUN4.3_CC2 (42.04%). TUN4.3_CC1 is clearly thriving in Tunisia, accounting for 61.5% of the L4.3/LAM sublineage. TUN4.3_CC1 displayed higher mean allelic richness compared with TUN4.3_CC2 and predominated throughout the entire region, indicating a long-established history. The very low proportion of drug resistance among TUN4.3_CC1 isolates is indicative of their intrinsic ability to spread successfully in the host population. Genomic analyses further confirmed the clear genetic separation between the two main CCs (pairwise fixation index 0.56), and suggested the relatively ancient origin of TUN4.3_CC1. Consistent with its successful expansion, TUN4.3_CC1 showed reduced mean pairwise genetic distance between genomes. ConclusionsThese findings link the successful expansion of L4.3/LAM in Tunisia to a single long-established clone.

Study on genetic variations of the D-loop region in three Vietnamese ethnic groups Kinh, Lolo and Lahu

Mitochondrial DNA (mtDNA) sequence analysis has been widely used to investigate population genetic and evolutional history of different ethnic groups worldwide. In this study, the D-loop region of 119 Vietnamese individuals belonging to three different ethnic groups was sequenced and compared with reference mtDNA on rCRS for genetic variations. Total 218 genetic polymorphisms were found in this population, among which 48 variations appeared with frequencies of more than 0.1. Further statistical analysis showed that there were 23, 13 and 24 single nucleotide polymorphisms (SNP) distributed differently between Kinh vs. Lolo, Kinh vs. Lahu , and Lolo vs. Lahu groups, respectively. The mean pairwise genetic distances between each pair of ethnic groups were 0.0101, 0.0098 and 0.0092 for Kinh - Lolo, Kinh - Lahu, Lolo - Lahu, respectively. This indicated that although the Lolo and Lahu ethnic groups both belong to the Tibeto-Burman language group, the genetic distance between them was no closer than the genetic distances between them and the Kinh group of the Viet-Muong (Austroasiatic) language group. This study was the first research on the D-loop region of the Lolo and Lahu populations in Vietnam. These results provided more data for exploring the genetic background and the history of those ethnic groups as well as other minority ethnic groups in Vietnam.

How are transgender women acquiring HIV? Insights from phylogenetic transmission clusters in San Francisco.

We explored potential HIV transmission typologies that involve transgender women to obtain insights on sexual and needle-sharing networks as sources of HIV infection. San Francisco residents diagnosed with HIV in care at public facilities who had available viral pol sequences from June 2001 to January 2016 were included in the analysis. Viral sequence data were matched to the San Francisco HIV/AIDS Case Registry to obtain demographic and risk classification information. Transmission clusters with at least two cases were identified by bootstrap values at least 90% and mean pairwise genetic distances 0.025 or less substitutions per site. Transgender women represented 275 of 5200 patients; 86 were present in 70 clusters. Four typologies were hypothesized: first, transgender women in clusters with MSM; second, transgender women who inject drugs in clusters with cisgender women and men who inject drugs; third, multiple transgender women in clusters with one man; and fourth, multiple transgender women who do not inject drugs in clusters with men and cisgender women who inject drugs. Transmission patterns of transgender women may stand apart from MSM epidemics. Transgender women clustered with people who inject drugs, and with men who have sex with transgender women and cisgender women. Aggregation of transgender women into the category of MSM may obscure understanding of how they acquire HIV and to whom they may transmit infection. Phylogenetic insights strengthen the case that HIV prevention programs for MSM may not be applicable to transgender women or their partners.

Molecular phylogenetics of slit-faced bats (Chiroptera: Nycteridae) reveal deeply divergent African lineages.

The bat family Nycteridae contains only the genus Nycteris, which comprises 13 currently recognized species from Africa and the Arabian Peninsula, one species from Madagascar, and two species restricted to Malaysia and Indonesia in South‐East Asia. We investigated genetic variation, clade membership, and phylogenetic relationships in Nycteridae with broad sampling across Africa for most clades. We sequenced mitochondrial cytochrome b (cytb) and four independent nuclear introns (2,166 bp) from 253 individuals. Although our samples did not include all recognized species, we recovered at least 16 deeply divergent monophyletic lineages using independent mitochondrial and multilocus nuclear datasets in both gene tree and species tree analyses. Mean pairwise uncorrected genetic distances among species‐ranked Nycteris clades (17% for cytb and 4% for concatenated introns) suggest high levels of phylogenetic diversity in Nycteridae. We found a large number of designated clades whose members are distributed wholly or partly in East Africa (10 of 16 clades), indicating that Nycteris diversity has been historically underestimated and raising the possibility that additional unsampled and/or undescribed Nycteris species occur in more poorly sampled Central and West Africa. Well‐resolved mitochondrial, concatenated nuclear, and species trees strongly supported African ancestry for SE Asian species. Species tree analyses strongly support two deeply diverged subclades that have not previously been recognized, and these clades may warrant recognition as subgenera. Our analyses also strongly support four traditionally recognized species groups of Nycteris. Mitonuclear discordance regarding geographic population structure in Nycteris thebaica appears to result from male‐biased dispersal in this species. Our analyses, almost wholly based on museum voucher specimens, serve to identify species‐rank clades that can be tested with independent datasets, such as morphology, vocalizations, distributions, and ectoparasites. Our analyses highlight the need for a comprehensive revision of Nycteridae.

A51 Genetic variability of small ruminant lentiviruses in sheep and goats from single-species flocks from Poland

Previous phylogenetic analyses of small ruminant lentivirus (SRLV) sequences found in Poland revealed the circulation of subtype A1 in both sheep and goats, subtypes B1 in goats, and subtypes B2, A12, and A13 in sheep only. This study aimed to analyze the genetic nature of SRLV circulating in sheep and goats from single-species flocks. In order to analyze the degree of genetic variability, the fragments of gag and env genes of 24 SRLV strains were amplified by PCR, cloned into plasmid vectors, sequenced, and consensus sequences were aligned to each other and to reference sequences available from GenBank. Phylogenetic analysis was performed using the Geneious tree-builder tool, and phylogenetic trees were constructed using Mr Bayes (using the general time reversible substitution model) within Geneious Pro 5.3. Pairwise genetic distances were calculated in MEGA 6. Phylogenetic analysis revealed that the strains were highly heterogeneous and represented ovine strains belonging to subtypes A12 and B2 and caprine strains grouped in subtypes B1, B2, A1, and A12. In addition, two novel subtypes, A16 and A17, were found in goats. The mean pairwise genetic distances of gag and env sequences of both clusters were above 15 per cent nucleotide divergence when compared to all other subtypes within group A, which is a criterion required to distinguish a new subtype. Additionally, the existence of two separated clusters was confirmed by high bootstrap values. Co-infections with strains belonging to different subtypes within A and B groups were detected in one sheep and four goats originating from four flocks. Since the co-infection with more than one lentivirus genotype offers an opportunity for viral recombination, the possible recombination events were tested based on RDP analysis. For all co-infected animals, no evidence of recombination was found within the gag gene; however, env sequences showed some recombination patterns in three samples. In conclusion, we have demonstrated extended genetic variability of SRLV in sheep and goats from Poland with the existence of co-infection and recombination events.

Factors affecting interspecific differences in genetic divergence among populations of Anolis lizards in Cuba

BackgroundGeographical patterns and degrees of genetic divergence among populations differ between species, reflecting relative potentials for speciation or cladogenesis and differing capacities for environmental adaptation. Identification of factors that contribute to genetic divergence among populations is important to the understanding of why some species exhibit greater interpopulation genetic divergence. In this study, we calculated the mean pairwise genetic distances among populations as species’ average genetic divergence by a phylogeny using nuclear and mitochondrial genes of 303 individuals from 33 Cuban Anolis species and estimated species ages by another phylogeny using nuclear and mitochondrial genes of 51 Cuban and 47 non-Cuban Anolis species. We identified factors that influence species’ differences in genetic divergence among 26 species of Anolis lizards from Cuba. Species ages, environmental heterogeneity within species ranges, and ecomorph types were considered as factors affecting average genetic divergences among populations.ResultsThe phylogenies presented in this study provide the most comprehensive sampling of Cuban Anolis species to date. The phylogeny showed more conservative evolution of Anolis ecomorphs within Cuba and identified twig anoles as a monophyletic group. Subsequent Phylogenetic Generalized Least Squares (PGLS) analyses showed that species age was positively correlated with species’ average genetic divergence among populations.ConclusionAlthough previous studies have focused on factors affecting genetic divergence within species, the present study showed for the first time that species differences in genetic divergence could be largely affected by species age.

Palghat gap reveals presence of two diverged populations of Nilgiri tahr (Nilgiritragus hylocrius) in Western Ghats, India

Genetic analysis is an important tool in understanding population structure, genetic diversity, and phylogenetics of endangered species likely to be affected by microevolution and anthropogenic factors. Western Ghats landscape is one of the identified biodiversity hotspots in India, and micro-evolutionary processes are observed in this landscape due to the presence of the gaps in the mountain ranges. Nilgiri tahr is endemic to and distributed in this landscape while very little is known about genetic characteristics, population structure and impact of these gaps on the species. In the present study, two different populations of Nilgiri tahr from the north (NPG) and south (SPG) of Palghat gap (PG) were studied using the cytochrome b gene (Cyt b; 310 bp) of mtDNA genome in the Western Ghats, India. Two variable sites were observed in the Cyt b fragment while the mean pairwise genetic distance between these two populations was 0.007. All the samples phylogenetically clustered in either north or south of PG. The presence of shallow divergence indicates the presence of suitable habitat in past which may have facilitated movement between NPG and SPG. A subsequent change in Paleo-climatic conditions and gradual formation of PG may have resulted in population diversification during the Pleistocene. Besides, Forensically Informative Nucleotide Sequence (FINS) observed would help in geo-assigning any individual from NPG or SPG to understand the likely influences on population demography due to poaching.

Variance in estimated pairwise genetic distance under high versus low coverage sequencing: The contribution of linkage disequilibrium

The mean pairwise genetic distance among haplotypes is an estimator of the population mutation rate θ and a standard measure of variation in a population. With the advent of next-generation sequencing (NGS) methods, this and other population parameters can be estimated under different modes of sampling. One approach is to sequence individual genomes with high coverage, and to calculate genetic distance over all sample pairs. The second approach, typically used for microbial samples or for tumor cells, is sequencing a large number of pooled genomes with very low individual coverage. With low coverage, pairwise genetic distances are calculated across independently sampled sites rather than across individual genomes. In this study, we show that the variance in genetic distance estimates is reduced with low coverage sampling if the mean pairwise linkage disequilibrium weighted by allele frequencies is positive. Practically, this means that if on average the most frequent alleles over pairs of loci are in positive linkage disequilibrium, low coverage sequencing results in improved estimates of θ, assuming similar per-site read depths. We show that this result holds under the expected distribution of allele frequencies and linkage disequilibria for an infinite sites model at mutation–drift equilibrium. From simulations, we find that the conditions for reduced variance only fail to hold in cases where variant alleles are few and at very low frequency. These results are applied to haplotype frequencies from a lung cancer tumor to compute the weighted linkage disequilibria and the expected error in estimated genetic distance using high versus low coverage.

Molecular evidence of two colour morphs of northern snakehead (Channa argus) based on mitochondrial 12S rRNA

As an unclassified species, white-type Channa argus has existed for many years. In the present study, the relationships and genetic diversity in two colour morphs of northern snakehead were determined by the analysis of mitochondrial 12S rRNA gene, as well as other Channa species. The results of sequence analysis showed that the average genetic distance was 0.046 with the interspecies genetic distance ranging from 0.000 to 0.130; and the average interspecies genetic distance was estimated as 0.003 (range: 0.000–0.006). For the two colour morphs of Channa argus, the mean pair-wise genetic distance between them was also estimated as 0.003. Moreover, molecular phylogenetic tree was constructed using MEGA6.0, which showed that all the haploids gathered together as a branch and crossed each other. These results indicated that the white and biocolour-type Channa argus belonged to the same species, rather than subspecies at the molecular level, and the white-type Channa argus should be regard as an albino of biocolour type.

Genetic comparison of two color morphs of northern snakehead (Channa argus) and Chnannidae family

Relationships of two species of Channa argus (northern snakeheads) named “Bicolor type” and “White type”, as well as other six Channa species were investigated based on their partial sequence of mitochondrial DNA 16S rRNA genes in the present study. For the Channa family, the average genetic distance was 0.0863 with the inter-species genetic distance ranged from 0.0173 to 0.1384, and the average intra-species genetic distance in the genus channa was estimated as 0.00273 (range: 0.0019 to 0.0038). For the two C. argus species, the mean pair-wise genetic distance between “Bicolor type” and “White type” northern snakehead was estimated as 0.00218, which was within the intra-species genetic distance interval for Channa species, indicating that they belonged to the same species at molecular level. Moreover, these snakeheads can be divided into two distinct groups via 16S rRNA, which might be more accurate for Channa classification than traditional method based on the absence or presence of the pelvic fins of the fish.

Target region amplification polymorphism (TRAP) for assessing genetic diversity and marker-trait associations in chickpea (Cicer arietinum L.) germplasm

The effective utilization of crop diversity held in genebanks depends on our knowledge of useful traits and available markers associated with the target traits. Target region amplification polymorphism (TRAP) was used to evaluate the genetic diversity and underlying relationships among 263 accessions of chickpea landraces maintained by the USDA-ARS Western Regional Plant Introduction Station in Pullman, WA, USA. Two-hundred sixty-two TRAP markers were amplified by eight primer combinations. Altogether, 110 (42 %) markers were polymorphic, the other 152 (58 %) displayed no variation. These polymorphic markers revealed important differences among the accessions, with an estimated, mean pair-wise genetic distance of 25.82 %, ranging from 2.8 to 50.0 %. Genetic distance analysis divided the accessions into two major groups, with 113 and 150 accessions each, and substantial association between molecular diversity and geographic origin was evident. Bayesian analysis of population structure revealed two groups (K = 2) with evidence for six sub-groups. Additionally, the population structure of a subset of 110 lines was determined (K = 3) for testing marker-trait associations (MTAs). Phenotypic traits included the concentrations of protein and nine mineral elements in the seeds. Two MTAs were significant (p < 0.01) for concentrations of Ca and K, and three MTAs were significant for Cu and Ni concentrations. The results indicate that this population is useful for genome-wide association studies on other economic traits given the level of genetic diversity uncovered and the marker-trait associations in seed minerals discovered.

Population genetic structure of the messmate pipefish Corythoichthys haematopterus in the northwest pacific: evidence for a cryptic species

The population genetic structure of the messmate pipefish, Corythoichthys haematopterus, in the northwest Pacific was investigated based on the partial mitochondrial DNA cytochrome b (589 bp) and 16S rRNA (528 bp) region sequences of 108 individuals collected from six sites along the coast of the Japanese archipelago and one site on Mactan Island, the Philippines. A total of 60 and 28 haplotypes were obtained from the cytochrome b and 16S rRNA regions, respectively. Two genetically distinct lineages were detected: lineage A and B, which are separated by mean pairwise genetic distances of 23.3 and 14.1% in the partial cytochrome b and 16S rRNA genes, respectively. Such a huge genetic divergence between lineages, which is comparable to or even higher than the interspecific level, and the difference in their geographical distributions and habitat preferences suggests that they are distinct species, although there is no marked difference in their morphology. Haplotype network and gene and nucleotide diversity statistics indicate that the two lineages have different biogeographic histories: lineage A experienced rapid population expansion after a population bottleneck whereas lineage B has a long evolutionary history in a large stable population. In contrast, the levels of genetic variation among populations are relatively low in both lineages, probably because of frequent gene flow among populations resulting from the dispersal of pelagic larvae by the Kuroshio Current. These results indicate that past climatic events and contemporary oceanographic features have played a major role in establishing the population genetic structure of C. haematopterus.Electronic supplementary materialThe online version of this article (doi:10.1186/2193-1801-2-408) contains supplementary material, which is available to authorized users.

Social Network–Based Recruitment Successfully Reveals HIV-1 Transmission Networks Among High-Risk Individuals in El Salvador

HIV in Central America is concentrated among certain groups such as men who have sex with men (MSM) and female sex workers (FSWs). We compared social recruitment chains and HIV transmission clusters from 699 MSM and 787 FSWs to better understand factors contributing to ongoing HIV transmission in El Salvador. Phylogenies were reconstructed using pol sequences from 119 HIV-positive individuals recruited by respondent-driven sampling (RDS) and compared with RDS chains in 3 cities in El Salvador. Transmission clusters with a mean pairwise genetic distance ≤ 0.015 and Bayesian posterior probabilities =1 were identified. Factors associated with cluster membership were evaluated among MSM. Sequences from 34 (43%) MSM and 4 (10%) FSW grouped in 14 transmission clusters. Clusters were defined by risk group (12 MSM clusters) and geographic residence (only 1 spanned separate cities). In 4 MSM clusters (all n = 2), individuals were also members of the same RDS chain, but only 2 had members directly linked through recruitment. All large clusters (n ≥ 3) spanned >1 RDS chain. Among MSM, factors independently associated with cluster membership included recent infection by BED assay (P = 0.02), sex with stable male partners (P = 0.02), and sex with ≥ 3 male partners in the past year (P = 0.04). We found few HIV transmissions corresponding directly with the social recruitment. However, we identified clustering in nearly one-half of MSM suggesting that RDS recruitment was indirectly but successfully uncovering transmission networks, particularly among recent infections. Interrogating RDS chains with phylogenetic analyses may help refine methods for identifying transmission clusters.

Characterization of Tanzanian elite sweet potato genotypes for sweet potato virus disease (SPVD) resistance and high dry matter content using simple sequence repeat (SSR) markers

A total of 57 sweet potato genotypes with high dry matter content and resistant to sweet potato virus disease (SPVD) were characterized using four simple sequence repeat (SSR) markers. The germplasm included 20 genotypes identified as having high dry matter content and 25 accessions tolerant to SPVD in a study conducted in Tanzania in 2008. The total number of alleles within the 57 genotypes across 4 loci was 395, with an average of 4 alleles per locus. The unweighted pair group method with arithmetic mean (UPGMA) and analysis of molecular variance (AMOVA) using generated SSR data, grouped the 57 genotypes into two major clusters, with mean pair-wise genetic distance of 0.55. No specific grouping was observed in relation to SPVD resistance, dry matter content and geographic location. The four microsatellites markers distinguished the 57 Tanzanian sweet potato genotypes into two major clusters. The relatively high level of genetic diversity indicates broad genetic base for sweet potato breeding in Tanzania. The results obtained demonstrate the efficiency of SSR marker technique for the assessment of genetic relationships and distinguishing between Tanzanian sweet potato genotypes. The findings of this of this study, provide valuable information to breeders to facilitate cost effective germplasm conservation and development of improved sweet potato varieties resistant to SPVD and containing high dry matter. Key words: Simple sequence repeat (SSR), Ipomoea batatas, cluster analysis, genetic diversity.

The genus Astylosternus in the Upper Guinea rainforests, West Africa, with the description of a new species (Amphibia: Anura: Arthroleptidae)

Astylosternus laticephalus sp. nov. Rödel, Hillers, Leaché, Kouamé, Ofori-Boateng, Diaz &amp; Sandberger is described fromeastern Ivory Coast and western and central Ghana, and compared to Astylosternus occidentalis Parker, 1931 from thewestern part of the Upper Guinea forest zone (western Ivory Coast, Liberia, Guinea and Sierra Leone). Based on a com-prehensive sample, including specimens from the entire range, the latter species is re-described. The new species is char-acterized by a body shape typical for frogs of the genus Astylosternus, but has an exceptionally broad head, i.e. broaderthan in A. occidentalis. The basic dorsal pattern of A. laticephalus sp. nov. consists of a brownish to brownish red colour-ation with distinct red dots (red dots are only rarely present in A. occidentalis). The new species has bicoloured eyes withthe lower part of the iris being grey, the upper third of the iris is orange to red (A. occidentalis always has a uniform greyishiris). Males of the new species lack spines on the throat, belly (always present in A. occidentalis males), and a layer ofblack nuptial skin in the pectoral region (present in male A. occidentalis from western Guinea). Astylosternus laticephalussp. nov. differs from A. occidentalis by a mean pairwise genetic distance of 3.2% in the investigated part of the mitochon-drial 16S rRNA gene. Genetic divergence to the morphologically most similar Central African species, A. diadematus,was 11.9%. We briefly discuss the phylogenetic position of West African Astylosternus, hint on the possibility that thegenus might be paraphyletic and discuss the biogeography of West African Astylosternus, in particular with respect to forest cover fluctuations in the past.

The genus Astylosternus in the Upper Guinea rainforests, West Africa, with the description of a new species (Amphibia: Anura: Arthroleptidae)

Astylosternus laticephalus sp. nov. Rodel, Hillers, Leache, Kouame, Ofori-Boateng, Diaz & Sandberger is described fromeastern Ivory Coast and western and central Ghana, and compared to Astylosternus occidentalis Parker, 1931 from thewestern part of the Upper Guinea forest zone (western Ivory Coast, Liberia, Guinea and Sierra Leone). Based on a com-prehensive sample, including specimens from the entire range, the latter species is re-described. The new species is char-acterized by a body shape typical for frogs of the genus Astylosternus, but has an exceptionally broad head, i.e. broaderthan in A. occidentalis. The basic dorsal pattern of A. laticephalus sp. nov. consists of a brownish to brownish red colour-ation with distinct red dots (red dots are only rarely present in A. occidentalis). The new species has bicoloured eyes withthe lower part of the iris being grey, the upper third of the iris is orange to red (A. occidentalis always has a uniform greyishiris). Males of the new species lack spines on the throat, belly (always present in A. occidentalis males), and a layer ofblack nuptial skin in the pectoral region (present in male A. occidentalis from western Guinea). Astylosternus laticephalus sp. nov. differs from A. occidentalis by a mean pairwise genetic distance of 3.2% in the investigated part of the mitochon-drial 16S rRNA gene. Genetic divergence to the morphologically most similar Central African species, A. diadematus, was 11.9%. We briefly discuss the phylogenetic position of West African Astylosternus, hint on the possibility that thegenus might be paraphyletic and discuss the biogeography of West African Astylosternus, in particular with respect to forest cover fluctuations in the past.

Phylogenetic relationship of Turkish Apis mellifera subspecies based on sequencing of mitochondrial cytochrome C oxidase I region

Mitochondrial DNA sequence variation can be used to infer honey bee evolutionary relationships. We examined DNA sequence diversity in the cytochrome C oxidase I (COI or Cox1) gene segment of the mitochondrial genome in 112 samples of Apis mellifera from 15 different populations in Turkey. Six novel haplotypes were found for the COI gene segment. There were eight variable sites in the COI gene, although only three were parsimony-informative sites. The mean pairwise genetic distance was 0.3% for the COI gene segment. Neighbor-joining (NJ) trees of the COI gene segment were constructed with the published sequences of A. mellifera haplotypes that are available in GenBank; the genetic variation was compared among the different honeybee haplotypes. The NJ dendogram based on the COI sequences available in GenBank showed that Eastern European races were clustered together, whereas the Mellifera and Iberian haplotypes were clustered far apart. The haplotypes found in this study were clustered together with A. mellifera ligustica and some of the Greek honey bees (accession Nos. GU056169 and GU056170) found in NCBI GenBank database. This study expands the knowledge about the mitochondrial COI region and presents the first comprehensive sequence analysis of this region in Turkish honeybees.

Patterns of freshwater biodiversity in Europe: lessons from the spring snail genus Bythinella

Aim We analyse patterns of biodiversity in the spring snail genus Bythinella, a group of highly isolated and stenotopic freshwater species. We aim to test: (1) whether there are European areas of increased diversity (i.e. ‘hotspots’), (2) whether the potential hotspots inferred show qualitative differences in biodiversity characteristics such as endemicity, distinctiveness of taxa, age of lineages or degree of fragmentation, and (3) whether these hotspots match the Pleistocene refugia of Bythinella spp. Location Europe, Asia Minor. Methods The analyses are based on genetic data from 717 Bythinella specimens sampled at 194 sites. We used haplotypes as operational units in all analyses. To test hypothesis 1, mean pairwise genetic distances between Bythinella populations within each 1° × 1° geographical grid cell sampled in Europe were calculated. Within individual mountain ranges, grid cells with high diversity were grouped with neighbouring ones and hotspots were identified based on pre-defined criteria. Then, to test hypothesis 2, different biodiversity indices of these regions were calculated and compared. Finally, to test hypothesis 3, the spatial distribution of the identified hotspots was compared with the known Pleistocene refugia of Bythinella spp. Results Five areas showed increased levels of genetic diversity: the Massif Central/Pyrenees, the western and eastern Alps, and the western and eastern Carpathians. These regions showed qualitative differences in biodiversity, with the eastern Carpathians holding the highest number of (endemic) haplotypes, the oldest and most distinct lineages and the highest degree of fragmentation. Only three of the five detected hotspots matched previously identified Pleistocene refugia for Bythinella spp. Main conclusions The genetic diversity of Bythinella spp. is not randomly distributed throughout Europe. Some of the hotspots we identify coincide with those found in other freshwater taxa; others have not previously been reported. Thus, spring organisms may reflect a unique evolutionary history that is distinct from lentic and lotic taxa. Our findings may be useful for conservation purposes even though the species-level taxonomy of the genus is still under discussion.

Disease-associated XMRV sequences are consistent with laboratory contamination

BackgroundXenotropic murine leukaemia viruses (MLV-X) are endogenous gammaretroviruses that infect cells from many species, including humans. Xenotropic murine leukaemia virus-related virus (XMRV) is a retrovirus that has been the subject of intense debate since its detection in samples from humans with prostate cancer (PC) and chronic fatigue syndrome (CFS). Controversy has arisen from the failure of some studies to detect XMRV in PC or CFS patients and from inconsistent detection of XMRV in healthy controls.ResultsHere we demonstrate that Taqman PCR primers previously described as XMRV-specific can amplify common murine endogenous viral sequences from mouse suggesting that mouse DNA can contaminate patient samples and confound specific XMRV detection. To consider the provenance of XMRV we sequenced XMRV from the cell line 22Rv1, which is infected with an MLV-X that is indistinguishable from patient derived XMRV. Bayesian phylogenies clearly show that XMRV sequences reportedly derived from unlinked patients form a monophyletic clade with interspersed 22Rv1 clones (posterior probability >0.99). The cell line-derived sequences are ancestral to the patient-derived sequences (posterior probability >0.99). Furthermore, pol sequences apparently amplified from PC patient material (VP29 and VP184) are recombinants of XMRV and Moloney MLV (MoMLV) a virus with an envelope that lacks tropism for human cells. Considering the diversity of XMRV we show that the mean pairwise genetic distance among env and pol 22Rv1-derived sequences exceeds that of patient-associated sequences (Wilcoxon rank sum test: p = 0.005 and p < 0.001 for pol and env, respectively). Thus XMRV sequences acquire diversity in a cell line but not in patient samples. These observations are difficult to reconcile with the hypothesis that published XMRV sequences are related by a process of infectious transmission.ConclusionsWe provide several independent lines of evidence that XMRV detected by sensitive PCR methods in patient samples is the likely result of PCR contamination with mouse DNA and that the described clones of XMRV arose from the tumour cell line 22Rv1, which was probably infected with XMRV during xenografting in mice. We propose that XMRV might not be a genuine human pathogen.

Characterization of Ugandan Sweetpotato Germplasm Using Fluorescent Labeled Simple Sequence Repeat Markers

The genetic relationships among 192 superior, high–yielding, and disease-resistant sweetpotato [Ipomoea batatas (L.) Lam] accessions from the Ugandan germplasm collection were analyzed using 10 fluorescent labeled simple sequence repeat (SSR) markers. Relatedness among the genotypes was estimated using the Nei and Li genetic distance coefficient, cluster analysis and principle component analysis methods of NTSYS-pc software. The polymorphic information content of the SSR markers used in this study ranged from 0.23 to 0.76 for loci IB-S07 and IB-R12, respectively, with a mean value of 0.62. The number of polymorphic alleles detected per locus ranged from two to six with a mean of four, a confirmation of the effectiveness of microsatellite detection on an automated ABI 3730 sequencer. The mean pairwise genetic distance among the 192 genotypes was 0.57, an indication of moderately high genetic diversity. Cluster analysis divided the accessions into four major groups with no relationship to the district of origin. Two sets of duplicates were identified through SSR genotyping in this study. Up to 190 distinct accessions for use as potential parental genotypes in hybridization schemes for cultivar development in the region were identified.