P. Kuperus

Segregation Models for Disomic, Tetrasomic and Intermediate Inheritance in Tetraploids: A General Procedure Applied to Rorippa (Yellow Cress) Microsatellite Data

Tetraploid inheritance has two extremes: disomic in allotetraploids and tetrasomic in autotetraploids. The possibility of mixed, or intermediate, inheritance models has generally been neglected. These could well apply to newly formed hybrids or to diploidizing (auto)tetraploids. We present a simple likelihood-based approach that is able to incorporate disomic, tetrasomic, and intermediate inheritance models and estimates the double-reduction rate. Our model shows that inheritance of microsatellite markers in natural tetraploids of Rorippa amphibia and R. sylvestris is tetrasomic, confirming their autotetraploid origin. However, in F1 hybrids inheritance was intermediate to disomic and tetrasomic inheritance. Apparently, in meiosis, chromosomes paired preferentially with the homolog from the same parental species, but not strictly so. Detected double-reduction rates were low. We tested the general applicability of our model, using published segregation data. In two cases, an intermediate inheritance model gave a better fit to the data than the tetrasomic model advocated by the authors. The existence of inheritance intermediate to disomic and tetrasomic has important implications for linkage mapping and population genetics and hence breeding programs of tetraploids. Methods that have been developed for either disomic or tetrasomic tetraploids may not be generally applicable, particularly in systems where hybridization is common.

Molecular evidence for an extinct parent of the tetraploid species Microseris acuminata and M. campestris (Asteraceae, Lactuceae)

To determine the origin of the tetraploid annuals Microseris campestris and M. acuminata, chloroplast RFLP, RAPD and ITS sequence variability among nine populations of the two polyploids and 14 populations of the diploid annuals M. elegans and M. douglasii have been surveyed. Previously described variable chloroplast restriction sites infer M. douglasii as the possible maternal parent of both tetraploid species. However, the chloroplast genome typical for M. douglasii has now also been found in some plants of M. elegans. RAPD analysis revealed 172 polymorphic DNA markers that defined all four species as genetically distinct groups, but demonstrated closer associations between M. douglasii and M. acuminata, and between M. elegans and M. campestris. Sequencing of the ITS‐1 and ITS‐2 region yielded 73 phylogenetically informative sites. Thirty base‐pair mutations separated the annual Microseris species from the outgroup, Uropappus lindleyi. The putative interspecific allotetraploid M. campestris contained only one type ITS sequence that, on the basis of eight synapomorphic substitutions was derived from M. elegans. The single ITS of M. acuminata shares six common sites with M. douglasii. Surprisingly, six sites were synapomorphic for the two tetraploids, M. campestris and M. acuminata, suggesting recombination within the ITS of both species with that of a common, now extinct, parental taxon, possibly the donor of the M. douglasii type chloroplasts found in both tetraploids. These results confirm the interpretation of M. campestris as derived from M. douglasii (extinct population) and M. elegans, and resolve the unknown origin of M. acuminata as an intraspecific hybrid between two very distinct populations of M. douglasii, one of them the same extinct M. douglasii form that contributes to M. campestris.

Genetic diversity in diploid vs. tetraploid Rorippa amphibia (Brassicaceae)

The frequency of polyploidy increases with latitude in the Northern Hemisphere, especially in deglaciated, recently colonized areas. The cause or causes of this pattern are largely unknown, but a greater genetic diversity of individual polyploid plants due to a doubled genome and/or a hybrid origin is seen as a likely factor underlying selective advantages related to life in extreme climates and/or colonization ability. A history of colonization in itself, as well as a recent origin, and possibly a limited number of polyploidization events would all predict less genetic diversity in polyploids than in diploids. The null hypothesis of higher gene diversity in polyploids has to date hardly been quantified and is here tested in self‐incompatible Rorippa amphibia (Brassicaceae). The species occurs in diploid and tetraploid forms and displays clear geographical polyploidy in Europe. On the basis of eight microsatellite loci it can be concluded that the level of gene diversity is higher in tetraploids than in diploids, to an extent that is expected under neutral evolution when taking into account the larger effective population size in the doubled cytotype. There is thus no evidence for reduced genetic diversity in the tetraploids. The evidence presented here may mean that the tetraploids’ origin is not recent, has not been affected by bottlenecks and/or that tetraploids were formed multiple times while an effect of introgression may also play a role.

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.

Incipient adaptive radiation of New Zealand and Australian Microseris (Asteraceae): an amplified fragment length polymorphism (AFLP) study

The disjunct allotetraploid lineage of the North American genus Microseris in New Zealand and Australia originated from one or a few diaspores after a single introduction via long‐distance dispersal. The plants have evolved into four morphologically distinct ecotypes: ‘fine‐pappus’, ‘coastal’, ‘murnong’, and ‘alpine’, from which the first two are grouped as Microseris scapigera, mainly from New Zealand and Tasmania, and the latter two as M. lanceolata, endemic to the Australian mainland. Three chloroplast (cp) DNA types were distinguished in each of the species, but their distribution, especially in M. lanceolata, showed discrepancies with ecotype differentiation. Here, we analyse the genetic structure of the nuclear (n) DNA among two plants of each of 55 New Zealand, Tasmanian, and Australian Microseris populations for amplified fragment length polymorphisms (AFLPs). The nuclear genetic structure is compared to geographical, ecotype, and cpDNA distribution, in order to resolve and illustrate the early process of adaptive radiation. The strongest signal in the AFLP pattern was related to geographical separation, especially between New Zealand and Australian accessions, and suggested an initial range expansion after establishment. The ecotypic differentiation was less‐well reflected in the AFLP pattern, and evidence was found for the occurrence of hybridization among plants at the same geographical region, or after dispersal, irrespective of the cpDNA‐ and ecotypes. This indicated that the ecotype characteristics were maintained or re‐established by selection. It also showed that genetic differentiation is not an irreversible and progressive process in the early stage of adaptive radiation. Our results illustrate the precarious balance between geographical isolation and selection as factors that favour differentiation, and hybridization as factor that reduces differentiation.

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.