Ortet selection remains an integral component of cacao breeding programme to develop improved clones and expand the gene pool of available germplasm. This study assessed the population structure of 168 cacao clones developed recently from selected ortets in on-station and on-farm progeny trials in Ghana using 45 SNP markers. Selection of ortets was primarily based on high bean yield, high yield efficiency, adaptability to marginal growing conditions, and low incidence of black pod and cocoa swollen shoot virus diseases. Additionally, 58 SNPs were employed to verify the parentage of 752 bi-clonal seedlings supplied to farmers for commercial plantations. Pairwise multilocus matching based on 45 SNPs showed that the 168 clones were all distinct. Overall, the clones had moderate genetic diversity (He = 0.349 ± 0.022) and shared ancestry with Marañón, Guiana, Contamana, Iquitos, Amelonado, Trinitario, Nanay and Purús based on Bayesian clustering, principal coordinates, and parentage analyses. Parentage analysis of bi-clonal seedlings assigned parent-offspring trios (>80% confidence level) to 65.2% of the farmers' varieties based on breeder's active clone collection. The results of the parentage analysis suggested the existence of mislabelled clones in the seed gardens, necessitating the need for correct clone identification or rogueing. Taken together, this study presents a new group of cacao genetic resources with potential to broaden the gene pool of cacao in cacao improvement programmes. Further, the study conveys evidence of the need for countries with established seed garden systems to constantly monitor the genetic purity of seedlings produced from the seed gardens.

Response of clones of Canada thistle from North America and leafy spurge from North America and Eurasia to treatment with chlorsulfuron, clopyralid, and glyphosate was determined. Roots of Canada thistle plants from different locations responded differentially to injury from chlorsulfuron and clopyralid but not to glyphosate. Clones of Canada thistle varied significantly in response to all herbicide treatments. Roots of leafy spurge plants from different locations were differentially susceptible to injury from glyphosate. Clones of leafy spurge varied significantly for all responses to each herbicide. The differential effects of chlorsulfuron, glyphosate, and clopyralid on clones of Canada thistle and leafy spurge suggest that genetically-based differences may account for the failure of the herbicides to kill all plants within collection locations or between collection locations. Cross tolerance to the herbicides was not found in leafy spurge or Canada thistle.

The antigenic relationships of 7 stocks and 7 clones of Trypanosoma vivax from East and West Africa were compared by immune lysis. Sera from goats infected with different stocks and clones of T. vivax, collected on days 40 and 80 after infection, were used in the immune lysis test with homologous and heterologous stocks and clones of trypanosomes. Sera from infected cattle were included to compare stocks and clones from Kenya. The parasites that were used as antigen in the immune lysis tests were collected from infected mice when variable antigen type (VAT) homogeneous populations were used, from goats for infection with stocks and clones from Nigeria, The Gambia and Uganda, and from cattle for Kenyan stocks. Reciprocal cross-reactivity between sera and parasites was found between all the stocks and clones from Nigeria and The Gambia with the exception of one clone from Nigeria that was not recognized by antisera to a clone from The Gambia. There was also cross-reactivity between a stock and clone from Uganda and stocks and clones from Nigeria and The Gambia. Sera from goats infected with stocks and clones from Nigeria, The Gambia and Uganda recognized parasite populations that were homogeneous for one VAT (ILDat 1.2) of the rodent infective stock from Nigeria. Some antisera to West African stocks recognized another stable variant from a Ugandan stock adapted to rodents (ILDat 2.1), indicating that these VATs were expressed in the repertoires of the heterologous stocks. There was no cross-reaction between stocks from Nigeria, The Gambia or Uganda with Kenyan stocks. A stock from Galana (Kenya) and Bamburi (Kenya) showed reciprocal cross-reactivity. Two other Kenyan stocks, from Kilifi and Likoni, also showed cross-reactivity by immune lysis but showed no antigenic relationship with the other Kenyan stocks.

Two genetically defined parents of Eimeria tenella, each characterized by a selectable phenotype, were mated to provide ‘recombinant’ oocysts for an analysis of the inheritance of DNA markers into the sporocyst stage of the life-cycle. A total of 23 populations was established from infection with a putative single sporocyst and their inheritance of DNA markers provided compelling evidence that the 2 sporozoites within each sporocyst are genetically identical. Each of the 5 polymorphic DNA markers used segregated independently within the ‘recombinant’ parasites and only 1 of the parental forms was inherited in 22 of the populations aimed to have been established from a single sporocyst.

Subtherapeutic doses of chloroquine have been reported to enhance infectivity of drug-resistant Plasmodium species to their vectors. In this investigation, Plasmodium yoelii nigeriensis N67 strain showed enhanced infectivity to mosquitoes when stimulated by chloroquine. Both sensitive and resistant clones were derived from the N67 strain by dilution, showing that this strain is polymorphic for the resistant trait. A resistant subline was derived by selection under drug pressure from a chloroquine-sensitive clone, but neither the sensitive nor the resistant clones or sublines showed enhancement of infectivity in the presence of chloroquine. This suggests that the enhancement of infectivity shown by the N67 strain is a response to chloroquine stimulation shown only by certain of the genotypes within it, and that this response to chloroquine is not a trait causally connected with the genes coding for chloroquine resistance.

Peach-potato aphids, Myzus persicae (Sulzer), collected in Scotland in the years 1995 and 2002–2004 were characterized using four microsatellite loci and three insecticide resistance mechanisms. From 868 samples, 14 multilocus genotypes were defined (designated clones A–N). Five of these (denoted A, B, H, M and N) carried modified acetylcholinesterase (MACE) resistance, the most recent resistance mechanism to have evolved in M. persicae. The current paper shows that the continued presence of MACE aphids is due to turnover, as clones A and B were replaced in field samples by clones H, M and N in later seasons. Thus, insecticide-resistant populations in Scotland can be attributed to multiple waves of rapid clone colonisations and not to the continued presence of stable resistant clones or mutation or sexual recombination in local populations. The MACE clones carried varying levels of the other insecticide resistance mechanisms, kdr and esterase. The presence of these mechanisms could alter the clones success in the field depending on insecticide spraying (positive selection) and resistance fitness costs (negative selection).

Microsatellite genotyping was used to identify common clones in populations of the Myzus persicae group from various hosts and regions in mainland Greece and southern Italy and to compare their distribution and occurrence on tobacco and other crops. Common clones were defined as genotypes collected at more than one time or in more than one population; and, therefore, unlikely to be participating in the annual sexual phase on peach. Sixteen common genotypes were found, accounting for 49.0% of the 482 clonal lineages examined. Eight of these genotypes were subjected, in the laboratory, to short days and found to continue parthenogenetic reproduction, i.e. they were anholocyclic. Four of the six commonest genotypes were red, and one of these accounted for 29.6% of the samples from tobacco and 29.4% of those from overwintering populations on weeds. All six commonest genotypes were found on weeds and five of them both on tobacco and on other field crops. In mainland Greece, the distribution of common clones corresponded closely with that of anholocyclic lineages reported in a previous study of life cycle variation. Common genotypes were in the minority in the commercial peach-growing areas in the north, except on weeds in winter and in tobacco seedbeds in early spring, but predominated further south, away from peach trees. This contrasts with the situation in southern Italy, reported in a previous paper, where peaches were available for the sexual phase, yet all samples from tobacco were of common genotypes.

Myzus persicae (Sulzer) collected in Scotland were characterized for four microsatellite loci, intergenic spacer fingerprints and the resistance mechanisms modified acetylcholinesterase (MACE), overproduced carboxylesterase and knockdown resistance (kdr). Microsatellite polymorphisms were used to define a limited number of clones that were either fully susceptible to insecticides or possessed characteristic combinations of resistance mechanisms. Within these clones, intergenic spacer fingerprints could either be very consistent or variable, with the latter indicating ongoing evolution within lineages, most likely derived from the same zygote. Two clones (termed A and B) possessed all three resistance mechanisms and predominated at sites treated with insecticides. Their appearance on seed potatoes and oilseed rape in Scotland in 2001 coincided with extensive insecticide use and severe control failures. Clones C, I and J, with no or fewer resistance mechanisms, were found in samples from 1995 and were dominant at untreated sites in 2001. A comparison of Scottish collections with those from other UK and non-UK sites provides insight into the likely origins, distribution and dynamics of M. persicae clones in a region where asexual (anholocyclic) reproduction predominates, but is vulnerable to migration by novel genotypes from areas of Europe where sexual (holocyclic) reproduction occurs.

The relative contributions of host plant, herbivore species and clone to variation in the interaction between cereal aphids and wheat were investigated using five clones each of three species, Rhopalosiphum padi (Linnaeus), Sitobion avenae (Fabricius) and Schizaphis graminum (Rondani), on seedlings of two cultivars of Triticum aestivum L. and one cultivar of Triticum durum Desf. More individuals and biomass of R. padi than of the other two species were produced on seedlings. The three wheat cultivars lost similar amounts of biomass as a result of infestation by aphids, with the amount lost depending on aphid species: S. avenae caused the lowest loss in biomass. Variation in aphid biomass production was due mostly to differences among aphid species (70%), less to the interaction between wheat type and aphid species (7%), and least to aphid clone (1%). The specific impact of the aphids on the plants ranged from 1.7 to 3.7 mg of plant biomass lost per mg of aphid biomass gained, being lowest for R. padi and highest for S. graminum. Variation in plant biomass lost to herbivory was due mostly to unknown sources of error (95%), probably phenotypic differences among individual seedlings, with 3% due to aphid species and none attributable to aphid clone. For these aphid–plant interactions, differences among aphid clones within species contributed little to variation in aphid and plant productivity; therefore, a small sample of clones was adequate for quantifying the interactions. Furthermore, one clone of each species maintained in the laboratory for about 200 parthenogenetic generations was indistinguishable from clones collected recently from the field.

The variability within schistosome populations was explored using mixed populations of cercariae from multimiracidial snail infections and individual clones of Schistosoma mansoni cercariae obtained from monomiracidial snail infections. We investigated the heterogeneity between different clones of S. mansoni with respect to infectivity and metabolism. One difference between clones of cercariae was found in the recovery of adult worms from Balb/C mice. Recovery of adult worms was greater after infections with a mixed population than with a clonal population. To investigate some biochemical features of individuals in clones or mixed populations, the uptake of [35S]methionine into individual parasites and their membrane proteins was measured. Isoelectric focusing of a soluble membrane fraction: the frozen–thawed supernatant extracted from individual clones, showed the presence of proteins of isoelectric point between 7.2 and 8.2 in all clones. These proteins were less labelled with [35S]methionine in the clones than in the mixed population. It was concluded that basic proteins are synthesized by all clones and in the mixed population but at different rates. Differences in the rate of incorporation of [35S]methionine into the surface membranes of schistosomula and adult worms derived from individual clones are reported. In addition, a direct correlation between the percentage of recovery of adult worms from mice infected with individual clones of S. mansoni and the rate of incorporation of [35S]methionine into schistosomula of these particular clones was observed. It is suggested that the high rate of metabolism shown by an individual clone may account for the enhanced survival of the cercariae derived from that clone during penetration of the skin and migration through the vertebrate host. In order to examine individuals in a population of schistosomula, from a clone or mixed population, the lysosome-specific fluorescent probe LysoTracker DND-99 was used to label the parasites and quantitative fluorescent measurements were made on individual parasites. There were significant differences between clones and a mixed population. Furthermore, the variation between individuals from a mixed population was greater than from that in any clone, just as was found in the infectivity studies. Freshly transformed schistosomula of individual clones labelled with the LysoTracker DND-99 showed less variations in the quantitative uptake of the dye within a single clone when compared to the mixed population. We conclude that for any biochemical and biological parameter, a population of cercariae consists of individuals showing a wide range of values, with a much greater range in a mixed population. This variability is likely to have great relevance for infectivity of the final host and the efficacy of drugs and the immune system.

Genetic variation within and between vegetative compatibility groups (VCGs) of Amylostereum areolatum (Fr.) Boid. and Amylostereum chailletii (Pers.: Fr.) Boid. isolates was investigated. DNA fingerprints were made using the M13 core sequence as a primer. A total of 53 isolates of A. areolatum and 57 isolates of A. chailletii from Lithuania, Sweden, Denmark and Great Britain were studied. In all cases isolates belonging to the same VCG showed identical DNA banding patterns, suggesting that VCGs correspond to clones. In A. areolatum the vast majority of the isolates (spread by Sirex juvencus L.) were assigned to dispersive clones, that have wide geographical distribution (i.e. the same genotypes were detected in Lithuania, Sweden and Denmark), with low genetic variation between the different clones. By contrast, A. chailletii population structure was consistent with the spread of airborne basidiospores produced by outcrossing. Only a small fraction of A. chailletii isolates studied, could be assigned to dispersal clones with a local distribution, spread by Urocerus gigas L. Overall, M13 fingerprinting detected low genetic differentiation in both species in the samples we studied.

Well watered (WW) or drought-stressed (DS) saplings of ozone-sensitive and ozone-tolerant (less sensitive) birch (Betula pendula Roth) clones were exposed for 43 d to 0 nl l−1 or 100 nl l−1 ozone. Relative growth rates of leaves, stem, and roots, leaf discolouration, stomatal conductance and induction of genes encoding stress-related proteins PR-10, PAL and a LEA-group protein BP8 were determined. In general, both ozone and drought stress, singly and in combination, increased transcript levels of PR-10 in both clones. This was related to lower induction of PAL (except in older leaves of the tolerant clone), and increased proportions of visibly injured and yellowed leaves in ozone-exposed plants. The clones differed in their stomatal conductance and growth responses. In the less sensitive clone 2, ozone did not affect growth rates, but high stomatal conductance was observed in WW ozone-exposed plants. The more sensitive clone 5 showed, on the contrary, reduced growth rates and low stomatal conductance in WW ozone plants. Interestingly, clone 2 was sensitive to drought stress alone, whereas clone 5 was highly sensitive to ozone and drought stress experienced together. The results show that appearance of visible injuries (necrotic flecks) and enhanced yellowing of leaves coincided with the induction of genes for stress proteins PR-10 and PAL. The short-term growth responses, however, seemed to be separate processes. Additionally, stomatal conductance was related to leaf injuries and growth rates in a complicated manner, emphasizing the complex nature of ozone sensitivity/tolerance mechanisms in birch.

A benznidazole-resistant population of Trypanosoma cruzi, Y strain, was selected after 25 successive passages (8 months) in mice treated with a single high drug dose. Initially, the resistant parasites produced a low parasitaemia level and low mortality rate in infected mice. Thereafter, the parasitaemia level and mortality rate increased to the same value obtained for mice infected with the wild-type strain. Long-term treatment with benznidazole (100 mg/kg/day) cured 71–80% of mice infected with the wild-type strain. No cure was observed in mice infected with the selected resistant parasite population. Treatment with 500 mg/kg of benznidazole at peak parasitaemia cleared all blood parasites from mice infected with wild-type parasites. No effect on parasitaemia level was observed in mice infected with the selected parasites. Benznidazole-resistant parasites showed cross-resistance to different drugs. Contrary to wild type, all clones analysed from the resistant T. cruzi population were resistant to benznidazole. Without drug pressure the resistance phenotype of clones was far more stable than that presented by the resistant population. This work demonstrates, for the first time, the in vivo selection of a population and clones of T. cruzi resistant to benznidazole, and makes available an experimental model for the study of mechanisms of drug resistance in T. cruzi.