Ted H. M. Mes

Genetic structure of a population sample of apomictic dandelions

In Northern Europe, dandelion populations consist solely of triploid or higher polyploid apomicts. Without a regular sexual cycle or lateral gene transmission, a clonal structure is expected for Taraxacum apomicts, although this was not found by compatibility analysis. In this study, we investigate whether this observation could be suported by performing independent tests based on data from hypervariable microsatellite markers as well as more conservative data based on allozymes and matrilinear cpDNA markers. In addition, population genetic methods were used to test departure from panmictic expectations, which is expected for clonal populations. Results indicated that many data sets, again, did not agree with expectations from clonal evolution because only small groups of genotypes exhibit no marker incompatibility. Population genetic analysis revealed that virtually all genotypes, but not individuals, agreed with random segregation and genotypic equilibria. Exceptions were genotypes with rare allozyme alleles or nearly identical microsatellite genotypes. Consequently, a population sample of apomictic dandelions essentially harbours genotypes that resulted from segregation and/or recombination and only a few genotypes that may have differentiated by somatic mutations.

The evolution of growth‐forms in the Macaronesian genus Aeonium (Crassulaceae) inferred from chloroplast DNA RFLPs and morphology

Phylogenetic relationships among species of Aeonium were studied using morphological characters and chloroplast DNA RFLPs. Cladistic analysis of weighted morphological data indicates that the small, herbaceous and least woody species are basal in the genus. Chloroplast DNA data gave similar results, supporting the separation of the herbaceous or small, woody species from the large, hapaxanth rosettes, rosette trees, and branched subshrubs with yellow, white or red flowers as well as the only (herbaceous) species with axillary inflorescences. The relationships among the species descending from a polytomy that comprises all species of the genus as well as a polytomy which comprises 18 of the 26 species studied, are only very incompletely resolved, except for two monophyletic clades that contain the branched subshrubs with yellow flowers (A. sect. Aeonium) and the branched subshrubs and rosette trees with white or red flowers (A. sect. Leuconium), respectively. Cladistic analysis of the combined morphological and chloroplast DNA data improved resolution considerably. Four monophyletic clades are distinguished, each of which, except for three species, comprises only one of the five main growth‐form types. Although Aeonium is generally regarded as an outstanding example of adaptive radiation, this mode of speciation seems to have been of minor significance in the evolution of the genus, because each growth‐form apparently evolved only once. Instead, island speciation in the absence of major ecological shifts, is probably more important in the evolution of the genus.

Technical variability and required sample size of helminth egg isolation procedures

Measurements of parasite load are often very variable. This implies that little confidence can be attached to single measurements of parasite numbers and egg concentrations, and that many measurements are required for the detection of differences between groups of hosts or parasites. For studies that aim to detect these differences, it is important to increase the precision (closeness of repeated measures to each other) of parasite numbers, because it determines the number of samples that is needed to find significant differences among groups. In this study, sample sizes required to detect group differences were estimated using nematode egg counts of faecal samples of dairy cattle. They were found to be much lower for a centrifugation technique than for the widely used McMaster technique in replicate samples, in spite of a generally similar mean FEC. For example, the sample size required to detect FEC differences between groups of 10, 50, and 250 eggs per gram (EPG) were 46, 25, and 27 for the McMaster technique and 8, 5, and 12 for the SSF method, respectively. Interestingly, sample sizes required for faeces with a relatively high egg concentration (approximately 1000 EPG) were also considerably lower than for the McMaster technique in spite of a higher mean EPG of the latter method. This implies that technical variation can be reduced considerably by simple methods of egg isolation. Given that the range of egg concentration is similar for a number of nematodes of livestock and human helminths, a reduction of technical error will aid studies with many group comparisons such as vaccination strategies against parasites with typically low FECs and studies of the genetics of host resistance. It may also lead to improved guidelines for measures related to public health.

Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle.

BackgroundParasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance.Results and ConclusionTo quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the ~10% most and least infected daughters within each family (selective genotyping). Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position.

Detection of genetically divergent clone mates in apomictic dandelions.

This study aims to identify genetically diverged clone mates in apomictic dandelions. Clone mates are defined as individuals that may have diverged as a result of mutation accumulation and that have undergone only clonal reproduction since their most recent common ancestor. Based on distinctive morphology and an aberrant and rare chloroplast haplotype, northwest European individuals of Taraxacum section Naevosa are well suited for the detection of clonal lineages in which mutation has occurred. In the case of strictly clonal reproduction, nuclear genetic variability was expected to be hierarchically organized. Nucleotide polymorphisms in internal transcribed spacer (ITS) sequences, however, were incompatible with a clonal structure of the Norwegian individuals, probably due to persistent ancestral polymorphisms that pre‐date the origin of the Naevosa clone. This interpretation is supported by the presence of ITS variants in section Naevosa that were also found in distantly related dandelions. In contrast to the ITS sequence data, amplified fragment length polymorphisms (AFLPs), isozymes and microsatellites strongly supported the contention of prolonged clonal reproduction and mutation accumulation in Norwegian Naevosa. Because these markers are generally considered to be more variable and more rapidly evolving than ITS sequences, mutations in these markers probably evolved after the origin of the clone. Within the Norwegian clone, a surprising number of markers distinguished the clone mates. As a consequence, incorporation of mutation in the detection of clone mates is anticipated to have a big impact on estimates of size, geographical range and age of clones as well as on experimental designs of studies of clonal plants.

Principal features of the cpDNA evolution in Taraxacum (Asteraceae, Lactuceae): a conflict with taxonomy

Abstract.Phylogenetic relationships based on the chloroplast genome of Taraxacum were studied. Representative samples of 44 sections or species groups and a number of isolated species were analyzed. On the basis of the sequence variation in psbA–trnH and in trnL–trnF, mutations associated with RFLPs were monitored. Five RFLPs without homoplasy were recognized and used to reconstruct four main cpDNA groups (haplotypes); Group I is ancestral and, contrary to the information in the primary sequences, the RFLPs were not distinct from those of the outgroup species of Agoseris and Prenanthes. This group corresponds to dandelions believed to be ancestral on the basis of morphological data and previous studies of the chloroplast genome. A comparison of parsimony analysis of morphological and chloroplast data showed an overall lack of congruence. The conflict can most probably be accounted for as a consequence of reticulation.

Hairpins involving both inverted and direct repeats are associated with homoplasious indels in non-coding chloroplast DNA of Taraxacum (Lactuceae: Asteraceae).

Sequence variation in 2.2 kb of non-coding regions of the chloroplast genome of eight dandelions (Taraxacum: Lactuceae) from Asia and Europe is interpreted in the light of the phylogenetic signal of base substitutions vs. indels (insertions-deletions). The four non-coding regions displayed a total of approximately 30 structural mutations of which 9 are potentially phylogenetically informative. Insertions, deletions, and an inversion were found that involved consecutive stretches of up to 172 bases. When compared to phylogenetic relationships of the chloroplast genomes based on nucleotide substitutions only, many homoplasious indels (33%) were detected that differed considerably in length and did not comprise simple sequence repeats typically associated with replication slippage. Though many indels in the intergenic spacers were associated with direct repeats, frequently, the variable stretches participated in inverted repeat stabilized hairpins. In each intergenic spacer or intron examined, nucleotide stretches ranging from 30 to 60 bp were able to fold into stabilized secondary structures. When these indels were homoplasious, they always ranked among the most stabilized hairpins in the non-coding regions. The association of higher order structures that involve both classes of repeats and parallel structural mutations in hot spot regions of the chloroplast genome can be used to differentiate among mutations that differ in phylogenetic reliability.

Demographic expansion of parasitic nematodes of livestock based on mitochondrial DNA regions that conflict with the infinite‐sites model

Mitochondrial ND4 sequences of populations of four species of parasitic nematodes of livestock were subjected to demographic analyses. Deviation from selective neutrality was detectable using the frequency spectrum of segregating sites and highly negative neutrality statistics. However, the mitochondrial data sets do not comply with the infinite‐sites model that underlies these tests, and as a consequence, it was not established whether these features are solely a result of population expansion, or whether aspects of the molecular evolution of these mitochondrial regions are also involved. Coalescent analyses based on Fus Fs neutrality test, which incorporated estimates of rate heterogeneity, the transition–transversion ratio and nucleotide bias, as well as analyses that are fairly robust to deviations from the infinite‐sites model supported population expansion. Also analyses that do not depend on the infinite‐sites model suggested historical population expansion of these nematodes. The very similar time since expansion, the absence of signatures of positive selection in ND4 and the logical association with human demography imply that selective sweeps of mitochondrial variants are less probable, and that expansion is the most likely scenario for the parasitic nematodes of livestock. The methods used to characterize the expansion have different assumptions and emphasize different aspects of expansions. The resulting restrictions on the interpretation of expansions are outlined.

THE EVOLUTION OF REPRODUCTIVE ISOLATION IN THE ECTOMYCORRHIZAL HEBELOMA CRUSTULINIFORME AGGREGATE (BASIDIOMYCETES) IN NORTHWESTERN EUROPE: A PHYLOGENETIC APPROACH

Abstract. To reconstruct the evolution of reproductive isolation in the ectomycorrhizal Hebeloma crustuliniforme aggregate (Basidiomycetes), phylogenetic relationships were determined between strains that belong to a clade consisting of nine intercompatibility groups (ICGs, biological species). Four of these nine ICGs are partially compatible and belong to the H. crustuliniforme aggregate. Different levels of partial compatibility have been found between these four ICGs. Between ICGs 3 and 4, 15% of the combinations were compatible. One strain was compatible with all isolates of both ICGs 3 and 4 and also with one isolate of ICG 2. Both a nuclear phylogeny, based on ribosomal IGS sequence data, and a mitochondrial phylogeny, based on a group‐I intron located in the large subunit ribosomal RNA gene (LrRNA), were reconstructed. The level of incompatibility was compared with the phylogenetic history of individuals belonging to this clade.

Sedum surculosum andS. jaccardianum (Crassulaceae) share a unique 70 bp deletion in the chloroplast DNA trnL (UAA)-trnF (GAA) intergenic spacer

TrnL (UAA)-trnF (GAA) chloroplast DNA spacer sequences of three species ofMonanthes, Sedum surculosum (=Monanthes atlanticum) andS. jaccardianum were compared.S. surculosum, the systematic position of which has been disputed ever since its discovery, shares a phylogenetically highly significant 70 bp deletion withS. jaccardianum. In addition to this large deletion the two Moroccan species ofS. ser.Monanthoidea differ in three more indels as well as in four nucleotide substitutions from the species ofMonanthes. These data render strong support for the monophyly ofS. ser.Monanthoidea andMonanthes. Spacer length in seven species and one subspecies ofMonanthes is relatively uniform.