Similar Haplotypes Research Articles

β-Thalassemia Haplotypes in Romania in the Context of Genetic Mixing in the Mediterranean Area

The purpose of this meta-study was to investigate β-thalassemia (β-thal) mutations and their chromosomal background in order to highlight the origin and spread of thalassemia alleles in the European and Mediterranean areas. Screening of more than 100 new Romanian β-thal alleles was also conducted. The results suggest an ancient introduction of mutations at codon 39 (C > T) (HBB: c.118C > T) and IVS-I-6 (T > C) (HBB: c.92 + 6T > C) in Romania. A comparative study was performed based on restriction fragment length polymorphism (RFLP) haplotypes associated with β-thal mutations in Romania and in Mediterranean countries. Each common β-thal allele from different populations exhibits a high degree of haplotype similarity, a sign of a clear unicentric origin for the IVS-I-110 (G > A) (HBB: c.93-21G > A), IVS-I-6, IVS-II-745 (C > G) (HBB: c.316-106C > G) and codon 39 mutations (the 17a [+ − − − − + +], 13c [ − + + − − − +], 17c [ + − − − − − +] and 14a [− + + − + + + ] ancestral RFLP background, respectively), followed by recurrent recombination events. This study also showed that geographic distances played a major role in shaping the spread of the predominant β-thal alleles, whereas no genetic boundaries were detected between broad groups of populations living in the Middle East, Europe and North Africa. The analyses revealed some discrepancies concerning Morocco and Serbia, which suggest some peculiar genetic flows. Marked variations in βA were observed between Southeast Asia and the Mediterranean, whereas a relative genetic homogeneity was found around the Mediterranean Basin. This homogeneity is undoubtedly the result of the high level of specific historic human migrations that occurred in this area.

Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome

The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343-3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter-gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026-1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.

Extending the Debate on Poor Response to Hepatitis B Virus Vaccination in Children With Celiac Disease: Which Question Remains?

Dear Editor, A poorer response to hepatitis B vaccination, in coeliac subjects, compared to healthy subjects, has been largely debated. Almost all authors postulated that human leukocyte antigen (HLA) genotype DQ2, found in 90 - 95% of coeliac patients, could represent the main cause in determining the impaired antibody response to recombinant HBV vaccine (1), as well as observed also in healthy not responder subjects. However it has been supposed that gluten intake could represent the main factor in influencing a poorer response to vaccine, since in several studies, it has been observed that the percentage of responders in patients compliant with a gluten free diet (GFD) was similar to healthy subjects (2, 3). Since type I diabetes (T1DM) and coeliac disease (CD) have the same genetic background, given by the HLA molecules that have also been identified as haplotypes associated with unresponsiveness to hepatitis B virus (HBV) vaccination (DR3 and DR4 for T1DM, DQ2 and DQ8 for CD), we firstly compared three different groups of patients, corresponding to T1DM, CD and DMT1-CD, that had in common the same HLA haplotypes, to establish the weight of specific haplotypes of HLA and/or gluten that could favor a poorer response to HBV vaccine. In 30 children suffering from both CD and DMT1, vaccinated by the administration of three doses of vaccine (Engerix-B, Glaxo Smith Kline, London, United Kingdome) at the age of 3, 5 and 11 months of life, according to the national vaccination schedule, we discovered 16 (53.3%) non-responders. This percentage was similar to a previous study on 60 coeliac patients (4), although not significantly higher, compared to a previous study on 100 diabetics (5) (Table 1). Table 1. Characteristics of Patients With Type 1 Diabetes Mellitus, Celiac Disease and Associated Type 1 Diabetes Mellitus/Coeliac Disease a As the mean age and the anti-HBs antibodies titers was similar between coeliacs and coeliacs/diabetics, we consider that the presence of T1DM and its HLA haplotype seems to not decrease anti-HBs antibodies production and percentage of responders. The open question is: what is the role of gluten in this matter? Comparing the T1DM/CD and T1DM, in which both groups had a similar HLA haplotype, we found a higher non-significant percentage of non-responders in T1DM/CD than in T1DM (53.3% vs. 38.2%), although the first group even had a significantly lower mean age (P < 0.0001), which usually is associated to a higher titer of anti HBs antibodies (P < 0.02) and a higher percentage of responders, as we also found in our study (Table 1). The question still remains open: what is the role of gluten in this matter? First of all, we observed that the percentage of non-responders is higher in T1DM/CD patients, compared with diabetics (53.3% vs. 38.2%). However, if we compare the first group with coeliacs, the percentage of non-responders is similar (53.3% vs. 50%). As the genetic substrate of HLA haplotypes, in the two diseases, is the same, this comparison indirectly confirms that gluten certainly represents a second variable, which favors a further decrease of efficacy to HBV vaccine, beyond the HLA system. As written in 1890 by in the chapter “The Science of Deduction” of the book “The Sign of Four, eliminate all other factors and the one which remains must be the truth (6).”

The probability that similar haplotypes are identical by descent.

The logic of gene mapping in highly penetrant diseases is to find the minimal overlap of haplotypes that are identical by descent (IBD). If the pedigree is unknown, identity by descent of haplotype overlap cannot be established with certainty. In many cases, it is intuitively clear that similar haplotypes are indeed IBD. The logical and statistical evaluation of haplotype overlap requires that probabilities of IBD are substantial. It is, therefore, important to estimate these probabilities. In this paper, we derive a recursive formula for the probability of IBD. Simulations are used to validate the expected values and to study the variability around the expected value. We demonstrate that for populations 1000 generations of age - without bottlenecks - haplotypes of 1 cM consisting of at least five microsatellite markers have a significant probability to be IBD. Likewise, SNP haplotypes of 1 cM should consist of at least nine identical SNP alleles for a similar probability of IBD. Without considering bottlenecks, haplotypes consisting of as few as three SNPs spanning a region of less than 0.01 cM are likely IBD in populations that are 10000 generations of age.

Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance.

BackgroundAflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus. However, resistance to aflatoxin accumulation in maize is a complex trait with low heritability. Here, two complementary analyses were performed to better understand the mechanisms involved. The first coupled results of a genome-wide association study (GWAS) that accounted for linkage disequilibrium among single nucleotide polymorphisms (SNPs) with gene-set enrichment for a pathway-based approach. The rationale was that the cumulative effects of genes in a pathway would give insight into genetic differences that distinguish resistant from susceptible lines of maize. The second involved finding non-pathway genes close to the most significant SNP-trait associations with the greatest effect on reducing aflatoxin in multiple environments. Unlike conventional GWAS, the latter analysis emphasized multiple aspects of SNP-trait associations rather than just significance and was performed because of the high genotype x environment variability exhibited by this trait.ResultsThe most significant metabolic pathway identified was jasmonic acid (JA) biosynthesis. Specifically, there was at least one allelic variant for each step in the JA biosynthesis pathway that conferred an incremental decrease to the level of aflatoxin observed among the inbred lines in the GWAS panel. Several non-pathway genes were also consistently associated with lowered aflatoxin levels. Those with predicted functions related to defense were: leucine-rich repeat protein kinase, expansin B3, reversion-to-ethylene sensitivity1, adaptor protein complex2, and a multidrug and toxic compound extrusion protein.ConclusionsOur genetic analysis provided strong evidence for several genes that were associated with aflatoxin resistance. Inbred lines that exhibited lower levels of aflatoxin accumulation tended to share similar haplotypes for genes specifically in the pathway of JA biosynthesis, along with several non-pathway genes with putative defense-related functions. Knowledge gained from these two complementary analyses has improved our understanding of population differences in aflatoxin resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1874-9) contains supplementary material, which is available to authorized users.

Loss and Gain of Natural Killer Cell Receptor Function in an African Hunter-Gatherer Population.

Modulating natural killer cell functions in human immunity and reproduction are diverse interactions between the killer cell immunoglobulin-like receptors (KIR) of Natural Killer (NK) cells and HLA class I ligands on the surface of tissue cells. Dominant interactions are between KIR2DL1 and the C2 epitope of HLA-C and between KIR2DL2/3 and the C1 epitope of HLA-C. KhoeSan hunter-gatherers of Southern Africa represent the earliest population divergence known and are the most genetically diverse indigenous people, qualities reflected in their KIR and HLA genes. Of the ten KhoeSan KIR2DL1 alleles, KIR2DL1*022 and KIR2DL1*026 likely originated in the KhoeSan, and later were transmitted at low frequency to the neighboring Zulus through gene flow. These alleles arose by point mutation from other KhoeSan KIR2DL1 alleles that are more widespread globally. Mutation of KIR2DL1*001 gave rise to KIR2DL1*022, causing loss of C2 recognition and gain of C1 recognition. This makes KIR2DL1*022 a more avid and specific C1 receptor than any KIR2DL2/3 allotype. Mutation of KIR2DL1*012 gave rise to KIR2DL1*026, causing premature termination of translation at the end of the transmembrane domain. This makes KIR2DL1*026 a membrane-associated receptor that lacks both a cytoplasmic tail and signaling function. At higher frequencies than their parental allotypes, the combined effect of the KhoeSan-specific KIR2DL1*022 and KIR2DL1*026 is to reduce the frequency of strong inhibitory C2 receptors and increase the frequency of strong inhibitory C1 receptors. Because interaction of KIR2DL1 with C2 is associated with risk of pregnancy disorder, these functional changes are potentially advantageous. Whereas all other KhoeSan KIR2DL1 alleles are present on a wide diversity of centromeric KIR haplotypes, KIR2DL1*026 is present on a single KIR haplotype and KIR2DL1*022 is present on two very similar haplotypes. The high linkage disequilibrium across their haplotypes is consistent with a recent emergence for these KIR2DL1 alleles that have distinctive functions.

DNA barcode assessment of Mediterranean mayflies (Ephemeroptera), benchmark data for a regional reference library for rapid biomonitoring of freshwaters

Accurate identification of aquatic species is fundamental to freshwater research. In this paper, we targeted Ephemeroptera, a key taxonomic insect group for biomonitoring of water bodies and present an overview on the efficacy of the DNA barcoding approach to document species identity in the Mediterranean region. We sequenced the mitochondrial cytochrome c oxidase (COI) in 39 nominal species. Sample discrimination and species identification were investigated by evaluating haplotype identity and similarity, intra-/interspecific genetic distances, optimal identification of barcoding gap thresholds, estimates of species monophyly and comparative species matches on available reference libraries. The resolving power of the obtained data was discussed in the light of statistical tools such as Spider R-package and Poisson Tree Processes. High levels of species identification were achieved with all the used methodologies, and the occurrence of cryptic species was suggested. We conclude that DNA barcoding is a powerful tool for taxonomic research in Mediterranean mayflies, with great promise to ameliorate biodiversity inventories of freshwater ecosystems and to provide the necessary accuracy for water quality assessment programs. Our results further indicated we need to upgrade the current regional mayfly diversity knowledge. The development of a Mediterranean reference library could integrate this new information system.

Genotype and Haplotype Analyses of TP53 Gene in Breast Cancer Patients: Association with Risk and Clinical Outcomes.

Variations in the TP53 gene have been suggested to play a role in many cancers, including breast. We previously observed an association between TP53 haplotypes based on four polymorphisms (rs17878362, rs1042522, rs12947788, and rs17884306) and the risk of colorectal and pancreatic cancer. Based on these results, in the present study, we have investigated the same polymorphisms and their haplotypes in 705 breast cancer cases and 611 healthy controls in relation to the disease risk, histopathological features of the tumor and clinical outcomes. In comparison to the most common haplotype A1-G-C-G, all the other identified haplotypes were globally associated with a significantly decreased breast cancer risk (P = 0.006). In particular, the A2-G-C-G haplotype was associated with a marked decreased risk of breast cancer when compared with the common haplotype (P = 0.0001). Moreover, rs1042522 in patients carrying the GC genotype and receiving only the anthracycline-based chemotherapy was associated with both overall and disease-free survival (recessive model for overall survival HR = 0.30 95% CI 0.11–0.80, P = 0.02 and for disease-free survival HR = 0.42 95% CI 0.21–0.84, P = 0.01). Present results suggest common genetic features in the susceptibility to breast and gastrointestinal cancers in respect to TP53 variations. In fact, similar haplotype distributions were observed for breast, colorectal, and pancreatic patients in associations with cancer risk. Rs1042522 polymorphism (even after applying the Dunn-Bonferroni correction for multiple testing) appears to be an independent prognostic marker in breast cancer patients.

Multi‐hierarchical macroecology at species and genetic levels to discern neutral and non‐neutral processes

AbstractAimLarge‐scale DNA barcoding allows the simultaneous assessment of variation in community composition at species level and below. We here propose that the patterns emerging across multiple hierarchical levels can be used to discern the effects of neutral and non‐neutral macroecological processes, which otherwise have proven difficult to separate.LocationIberian Peninsula.MethodsWe performed cox1 barcoding on 20 complete assemblages of leaf beetles for 4533 individuals of 203 species. The neutrality of cox1 sequence evolution was tested using Tajima's test. Haplotypes (n = 2020) were grouped into nested n‐step networks of up to five intraspecific hierarchical levels. We then assessed whether the spatial variation in assemblage composition at all hierarchical levels from haplotype to species was self‐similar (fractal) and predictable from level to level.ResultsTajima's test on a subset of widely sampled species (n = 136) was consistent with neutral evolution in 83% of the species, but only 3% of cases exhibited balancing selection. Multiple hierarchical levels representing haplotype genealogies of various ages showed a similar rate of distance decay of assemblage similarity. In addition, we found strong log‐log correlations between hierarchical level (lineage age) and number of lineages, lineage range size and assemblage similarity. Similarity at the species level was strongly correlated to similarity at the haplotype level for the whole assemblage (r2 = 0.75) or for within‐species haplotype similarity (mean r2 = 0.17, SE = 0.03).Main conclusionsThese findings suggest great regularities in the pattern of assemblage variation at all lineage ages that are best explained by the enduring action of stochastic (neutral) processes of mutation and dispersal. The multi‐hierarchical analysis therefore bridges predictions of the neutral theory of molecular evolution and the neutral theory of biodiversity. Neutral processes thus emerge as a unifying principle of ecology and evolution, which has deep implications in biodiversity assessment and conservation.

Mitochondrial DNA revealed the extent of genetic diversity and invasion origin of populations from two separate invaded areas of a newly invasive pest, Cydia pomonella (L.) (Lepidoptera: Tortricidae) in China.

Cydia pomonella is a serious invasive insect pest in China, and has caused severe damage to the production of apple and pear in its invaded areas. This species is distributing in the northwest and northeast of China, but no occurrence of it has been recorded in the large areas (about 3000-5000 km away) between the invaded northwestern and northeastern regions despite continuous monitoring. As yet the genetic diversity and invasion origin of the C. pomonella populations in Northwestern and Northeastern China is obscure. In this study, we investigate the genetic diversity of 14 populations of C. pomonella sampled throughout the main distribution regions in Northwestern (Xinjiang and Gansu Provinces) and Northeastern (Heilongjiang Province) China and compared them with nine populations from Europe and other continents using the mitochondrial COI, COII and Cytb genes. Both the populations from Northeastern and Northwestern China shared some haplotypes with populations from other countries. Haplotypes of the three mitochondrial genes had a different distribution in Northeastern and Northwestern China. The northeastern populations had more private haplotypes than the northwestern populations. A large number of the individuals from northwestern populations shared a few haplotypes of each of the three genes. The haplotype numbers and haplotype diversities of the northeastern populations were similar to those of field populations in other countries, but were higher than those of the northwestern populations. Populations from the Northwestern China showed similar haplotype number and haplotype diversity. We conclude that the population genetic background of C. pomonella populations in Northeastern and Northwestern China varies due to different invasion sources and that this should be considered before the application of new pest control tactics.

Highly discriminatory capacity of the PowerPlex® Y23 System for the study of isolated populations

In order to evaluate the forensic utility of the new PowerPlex® Y23 System, two Northern Spanish populations, the autochthonous Basque Country (N=105) and Cantabria (N=98), were typed. Two of the new markers incorporated in the panel, the rapid mutating loci DYS576 and DYS570, were among the most discriminative markers in both population datasets. In terms of the analysis of 23 Y-STRs, the two populations showed high haplotype diversities, with values slightly superior in the population of Cantabria (1±0.0015) than in the Basque Country (0.9987±0.0016). The comparison of the discrimination capacity obtained with the analysis of 23 Y-STRs and other available markers sets of 12 Y-STRs (PowerPlex® Y System) or 17 Y-STRs (YFiler™), clearly demonstrated an improvement in the population of the Basque Country. Nevertheless, in Cantabria this augment was only seen when the number of markers was increased from 12 to 23, since the study of 17 Y-STRs was enough to differentiate all haplotypes. Therefore, this study shows that the improvement in forensic parameters by increasing the number of Y-STR markers analyzed is much more pronounced in the case of isolated populations such as the autochthonous population of the Basque Country, as it facilitates the differentiation among similar haplotypes. Moreover, by the use of the PowerPlex® Y23 identification of population specific haplotypes increased in both populations. Ultimately, the analysis of 23 Y-STRs differentiated among the two geographically close populations of Basque Country and Cantabria. Indeed it showed significant differences between the Basque Country population and all European populations included, meanwhile Cantabria did exhibit significant proximity with the Iberian and the majority of European populations considered.

Assessing the effects of multiple markers in genetic association studies.

Assessing the effects of multiple markers in genetic association studies.

Genomic adaptation of admixed dairy cattle in East Africa

Dairy cattle in East Africa imported from the U.S. and Europe have been adapted to new environments. In small local farms, cattle have generally been maintained by crossbreeding that could increase survivability under a severe environment. Eventually, genomic ancestry of a specific breed will be nearly fixed in genomic regions of local breeds or crossbreds when it is advantageous for survival or production in harsh environments. To examine this situation, 25 Friesians and 162 local cattle produced by crossbreeding of dairy breeds in Kenya were sampled and genotyped using 50K SNPs. Using principal component analysis (PCA), the admixed local cattle were found to consist of several imported breeds, including Guernsey, Norwegian Red, and Holstein. To infer the influence of parental breeds on genomic regions, local ancestry mapping was performed based on the similarity of haplotypes. As a consequence, it appears that no genomic region has been under the complete influence of a specific parental breed. Nonetheless, the ancestry of Holstein-Friesians was substantial in most genomic regions (>80%). Furthermore, we examined the frequency of the most common haplotypes from parental breeds that have changed substantially in Kenyan crossbreds during admixture. The frequency of these haplotypes from parental breeds, which were likely to be selected in temperate regions, has deviated considerably from expected frequency in 11 genomic regions. Additionally, extended haplotype homozygosity (EHH) based methods were applied to identify the regions responding to recent selection in crossbreds, called candidate regions, resulting in seven regions that appeared to be affected by Holstein-Friesians. However, some signatures of selection were less dependent on Holsteins-Friesians, suggesting evidence of adaptation in East Africa. The analysis of local ancestry is a useful approach to understand the detailed genomic structure and may reveal regions of the genome required for specialized adaptation when combined with methods for searching for the recent changes of haplotype frequency in an admixed population.

Mouse kidney transplantation: models of allograft rejection.

Rejection of the transplanted kidney in humans is still a major cause of morbidity and mortality. The mouse model of renal transplantation closely replicates both the technical and pathological processes that occur in human renal transplantation. Although mouse models of allogeneic rejection in organs other than the kidney exist, and are more technically feasible, there is evidence that different organs elicit disparate rejection modes and dynamics, for instance the time course of rejection in cardiac and renal allograft differs significantly in certain strain combinations. This model is an attractive tool for many reasons despite its technical challenges. As inbred mouse strain haplotypes are well characterized it is possible to choose donor and recipient combinations to model acute allograft rejection by transplanting across MHC class I and II loci. Conversely by transplanting between strains with similar haplotypes a chronic process can be elicited were the allograft kidney develops interstitial fibrosis and tubular atrophy. We have modified the surgical technique to reduce operating time and improve ease of surgery, however a learning curve still needs to be overcome in order to faithfully replicate the model. This study will provide key points in the surgical procedure and aid the process of establishing this technique.

G.P.318: Natural history of motor function in patients with Fukuyama congenital muscular dystrophy

Fukuyama congenital muscular dystrophy (FCMD), among the most common autosomal recessive disorders in the Japanese population, is characterized by congenital muscular dystrophy and brain malformations. It is essentially limited to Japan, and three-quarters of Japanese patients have a similar haplotype due to the ancestral founder mutation, a 3-kb retrotransposal insertion in the <i>fukutin</i> gene. Patient phenotypes can be classified as mild, typical, and severe depending on peak motor function. The typical form patients can sit without support or slide on the buttocks and account for 75% of FCMD cases. The patients who can crawl or walk are classified as having mild form and those lacking head control as having severe form. The rate of heterozygosity for the ancestral founder mutation was reported to be significantly higher in severe cases. Since the natural history of FCMD was reported long ago, we aimed to reevaluate the natural history of our FCMD patients. We retrospectively studied the medical records in 73 genetically diagnosed FCMD patients followed at our University from 1995. Forty-four patients were homozygous for the ancestral founder mutation and 24 had a compound heterozygous mutation. In the homozygous group, 28 patients were classified as typical form and 8 as mild form. In the heterozygous group, 13 patients had typical form and 8 had severe form. Head control and sitting without support were achieved, on average, at 7.6months (m) and 14.6m of age, respectively, in the homozygous group, but at 16.5m and 39.1m in the heterozygous group. Head control and sitting on average for each phenotype were: (i) 4.5m/9m in the walking, (ii)7.4m/17.7m in the sliding on the buttocks (iii) 10.5m/21.3m in sitting without support, and (iv) 21.7m/- in the severe groups only with head control. Motor function deterioration started at 7.6years, on average. Detailed assessment of motor development patterns for each FCMD phenotype may facilitate conducting clinical trials.

Genome-wide analysis reveals artificial selection on coat colour and reproductive traits in Chinese domestic pigs.

Pigs from Asia and Europe were independently domesticated from c. 9000 years ago. During this period, strong artificial selection has led to dramatic phenotypic changes in domestic pigs. However, the genetic basis underlying these morphological and behavioural adaptations is relatively unknown, particularly for indigenous Chinese pigs. Here, we performed a genome-wide analysis to screen 196 regions with selective sweep signals in Tongcheng pigs, which are a typical indigenous Chinese breed. Genes located in these regions have been found to be involved in lipid metabolism, melanocyte differentiation, neural development and other biological processes, which coincide with the evolutionary phenotypic changes in this breed. A synonymous substitution, c.669T>C, in ESR1, which colocalizes with a major quantitative trait locus for litter size, shows extreme differences in allele frequency between Tongcheng pigs and wild boars. Notably, the variant C allele in this locus exhibits high allele frequency in most Chinese populations, suggesting a consequence of positive selection. Five genes (PRM1, PRM2, TNP2, GPR149 and JMJD1C) related to reproductive traits were found to have high haplotype similarity in Chinese breeds. Two selected genes, MITF and EDNRB, are implied to shape the two-end black colour trait in Tongcheng pig. Subsequent SNP microarray studies of five Chinese white-spotted breeds displayed a concordant signature at both loci, suggesting that these two genes are responsible for colour variations in Chinese breeds. Utilizing massively parallel sequencing, we characterized the candidate sites that adapt to artificial and environmental selections during the Chinese pig domestication. This study provides fundamental proof for further research on the evolutionary adaptation of Chinese pigs.

Genetic variation amongst biotypes of Dactylopius tomentosus

The tomentose cochineal scale insect, Dactylopius tomentosus (Lamarck) (Hemiptera: Dactylopiidae), is an important biological control agent against invasive species of Cylindropuntia (Caryophyllales: Cactaceae). Recent studies have demonstrated that this scale is composed of host-affiliated biotypes with differential host specificity and fitness on particular host species. We investigated genetic variation and phylogenetic relationships among D. tomentosus biotypes and provenances to examine the possibility that genetic diversity may be related to their host-use pattern, and whether their phylogenetic relationships would give insights into taxonomic relatedness of their host plants. Nucleotide sequence comparison was accomplished using sequences of the mitochondrial cytochrome c oxidase I (COI) gene. Sequences of individuals from the same host plant within a region were identical and characterized by a unique haplotype. Individuals belonging to the same biotype but from different regions had similar haplotypes. However, haplotypes were not shared between different biotypes. Phylogenetic analysis grouped the monophyletic D. tomentosus into 3 well-resolved clades of biotypes. The phylogenetic relationships and clustering of biotypes corresponded with known taxonomic relatedness of their hosts. Two biotypes, Fulgida and Mamillata, tested positive for Wolbachia (α-Proteobacteria), a common endosymbiont of insects. The Wolbachia sequences were serendipitously detected by using insect-specific COI DNA barcoding primers and are most similar to Wolbachia Supergroup F strains. This study is the first molecular characterization of cochineal biotypes that, together with Wolbachia sequences, contribute to the better identification of the biotypes of cochineal insects and to the biological control of cacti using host-specific biotypes of the scale.

Admixture of two phylogeographic lineages of the Eurasian beaver in Poland

The Eurasian beaver (Castor fiber) represents an uncommon example of an endangered species in which the restoration programs proved a spectacular success and led to enormous spatial and demographic expansion. Documented reintroduction of beavers in Poland has been conducted using animals of the eastern European origin, most likely derived from the eastern mtDNA lineage. However demographic and spatial expansion of beavers from Germany, which represent the western lineage, may have led to admixture of these two genetically distinct entities in Poland. We detected significant genetic differentiation between the populations from W and NE Poland both in mitochondrial DNA control region and microsatellites, but also substantial admixture including apparent first-generation migrants between regions. Our results indicate that beavers from the western mtDNA lineage have contributed considerably to the Polish population, particularly in W Poland. As there have been no adequately documented translocations of beavers from the western European populations to Poland, the observed situation appears to result from natural migration or range expansion from the west. In contrast to previous findings we detected a substantial diversity in mtDNA control region, which indicates that either the variation in relict populations has been underestimated, or that additional relict beaver populations survived at the end of the 19th century in Poland and Germany as indicated by considerable similarity of ancient and extant mtDNA haplotypes. The implications of our findings for beaver conservation and management are discussed.

Chloroquine efficacy studies confirm drug susceptibility of Plasmodium vivax in Chennai, India

BackgroundAssessing the Plasmodium vivax burden in India is complicated by the potential threat of an emerging chloroquine (CQ) resistant parasite population from neighbouring countries in Southeast Asia. Chennai, the capital of Tamil Nadu and an urban setting for P. vivax in southern India, was selected as a sentinel site for investigating CQ efficacy and sensitivity in vivax malaria.MethodsCQ efficacy was evaluated with a 28-day in vivo therapeutic study, while CQ sensitivity was measured with an in vitro drug susceptibility assay. In both studies, isolates also underwent molecular genotyping to investigate correlations between parasite diversity and drug susceptibility to CQ. Molecular genotyping included sequencing a 604 base pair (bp) fragment of the P. vivax multidrug resistant gene-1 (Pvmdr1) for single nucleotide polymorphisms (SNPs) and also the amplification of eight microsatellite (MS) loci located across the genome on eight different chromosomes.ResultsIn the 28-day in vivo study (N=125), all subjects were aparasitaemic by Day 14. Passive case surveillance continuing beyond Day 28 in 22 subjects exposed 17 recurrent infections, which ranged from 44 to 148 days post-enrollment. Pvmdr1 sequencing of these recurrent infections revealed that 93.3% had identical mutant haplotypes (958M/Y976/1076L) to their baseline Day 0 infection. MS genotyping further revealed that nine infection pairs were related with ≥75% haplotype similarity (same allele at six or more loci). To test the impact of this mutation on CQ efficacy, an in vitro drug assay (N=68) was performed. No correlation between IC50 values and the percentage of ring-stage parasites prior to culture was observed (rsadj: -0.00063, p = 0.3307) and the distribution of alleles among the Pvmdr1 SNPs and MS haplotypes showed no significant associations with IC50 values.ConclusionsPlasmodium vivax was found to be susceptible to CQ drug treatment in both the in vivo therapeutic drug study and the in vitro drug assay. Though the mutant 1076L of Pvmdr1 was found in a majority of isolates tested, this single mutation did not associate with CQ resistance. MS haplotypes revealed strong heterogeneity in this population, indicating a low probability of reinfection with highly related haplotypes.

Molecular phylogenetics of Amorpha (Fabaceae): An evaluation of monophyly, species relationships, and polyploid origins

Amorpha L. (false indigos and lead plants) is a North American legume genus of 16 species of shrubs, which is most diverse in the southeastern United States and distinctive due to the reduction of the corolla to a single petal. Most species have limited distributions, but the tetraploid A. fruticosa species complex is widely distributed and its range overlaps those of all of the other species. Morphological variation in the genus is characterized by gradation of characters among species and it has been the subject of repeated taxonomic study due to the difficulty in delimiting species, especially among A. fruticosa and allies. This study presents the first phylogenetic and network analyses for evaluation of relationships amongst Amorpha species based on three non-coding plastome regions (trnD-trnT, trnH-psbA, petN-psbM) and two low-copy nuclear genes (CNGC5, minD). Plastid DNA analyses supported a monophyletic Amorpha with Parryella filifolia and Errazurizia rotundata as successive sister lineages; however, nuclear gene analyses supported the nesting of these two species and thus a paraphyletic Amorpha. Relationships among species of Amorpha were best resolved in the plastid DNA phylogeny and in most cases were concordant with expectations based on morphology. Relationships based on the nuclear gene phylogenies were less clear due to lack of informative variation (CNGC5) or conflict in the data set (minD). The origins of A. fruticosa were unclear, but the plastid phylogeny revealed that this species shares the same or similar plastid haplotype as other species in a geographic region. Putative recombination of diploid species’ alleles was evident in the minD-like network. Phenotypic plasticity in combination with gene flow into this species from different diploids, or even tetraploids, across its range may account for the incredible morphological diversity of the A. fruticosa species complex. Putative progenitors for two other suspected allotetraploid species, A. confusa and A. crenulata, were identified as A. fruticosa and A. herbacea.