Phylogenetic relationships in Betula (Betulaceae) based on AFLP markers

The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade

Phylogenetic Signal in AFLP Data Sets

AFLP markers provide a potential source of phylogenetic information for molecular systematic studies. However, there are properties of restriction fragment data that limit phylogenetic interpretation of AFLPs. These are (a) possible nonindependence of fragments, (b) problems of homology assignment of fragments, (c) asymmetry in the probability of losing and gaining fragments, and (d) problems in distinguishing heterozygote from homozygote bands. In the present study, AFLP data sets of Lactuca s.l. were examined for the presence of phylogenetic signal. An indication of this signal was provided by carrying out tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA). A measure of the support for internal branches in the optimal parsimony tree (MPT) was made using bootstrap, jackknife, and decay analysis. Finally, the extent of congruence in MPTs for AFLP and internal transcribed spacer (ITS)-1 data sets for the same taxa was made using the partition homogeneity test (PHT) and the Templeton test. These analytical studies suggested the presence of phylogenetic signal in the AFLP data sets, although some incongruence was found between AFLP and ITS MPTs. An extensive literature survey undertaken indicated that authors report a general congruence of AFLP and ITS tree topologies across a wide range of taxonomic groups, suggesting that the present results and conclusions have a general bearing. In these earlier studies and those for Lactuca s.l., AFLP markers have been found to be informative at somewhat lower taxonomic levels than ITS sequences. Tentative estimates are suggested for the levels of ITS sequence divergence over which AFLP profiles are likely to be phylogenetically informative. [Amplified Fragment Length Polymorphism (AFLP) markers; congruence; Dollo parsimony; g1 statistic; internal transcribed spacer (ITS) sequences; Lactuca; partition homogeneity test (PHT); phylogenetic signal.

Zooming in on the lettuce genome: species relationships in Lactuca s.l., inferred from chromosomal and molecular characters

Lactuca sativa (cultivated lettuce) is the world's most important leafy salad vegetable. Apart from L. sativa , the genus Lactuca contains ca. 75 wild species, potentially useful to improve, for example, taste, texture, and disease resistance of cultivated lettuce. The wild species L. serriola (Prickly Lettuce), L. saligna (Least Lettuce), and L. virosa (Great Lettuce) are commonly used for lettuce improvement. In preliminary experiments, we established that there is a close connection between evolutionary distances of wild species relative to cultivated lettuce, and their position in the lettuce gene pool (i.e., the possibility to hybridize them with cultivated lettuce). In the present thesis, we established evolutionary relationships among L. sativa and 22 wild species in order to predict this position. We determined that L. sativa , L. serriola , L. dregeana , and L. altaica are closely related, and can be regarded as conspecific. L. aculeata is closely related to them, but is a distinct species. L. serriola , L. dregeana , L. altaica, and L. aculeata occupy the primary gene pool of cultivated lettuce. They can be easily hybridized with cultivated lettuce, and thus are readily accessible gene sources for lettuce improvement. L. saligna and L. virosa are less closely related to L. sativa , and occupy the secondary gene pool (i.e. hybridization with L. sativa is possible, but difficult). All primary and secondary gene-pool species can be classified in Lactuca sect. Lactuca subsect. Lactuca . We found that all tertiary gene-pool species (hybridization with L. sativa only possible with radical techniques) can be classified in the remaining sections of the genus Lactuca (sections Phaenixopus , Mulgedium, and Lactucopsis ). These sections are the most promising sources of wild species for future improvement of cultivated lettuce. In the experiments, the tertiary gene-pool species were represented by L. viminea , L. tatarica , L. sibirica , and L. quercina . Surprisingly, the species classified in Lactuca sect. Lactuca subsect. Cyanicae are not evolutionary close to cultivated lettuce. They are not part of the lettuce gene pool, and should be excluded from Lactuca . To determine the evolutionary relationships among L. sativa and its wild relatives, we examined the genomes of the species at various levels, which provided additional information on genome evolution. We established, that in general the genome sizes in the group increased during evolution, while the ratio of AT/GC nucleotides decreased. Genome complexity for species with 2C DNA amounts below 8.5 pg was similar, but species with 2C DNA amounts exceeding 8.5 pg had more complex and less similar genomes. The species from the primary gene pool share a common ancestor, but the genomes of L. sativa / L. serriola , L. saligna , and L. virosa , evolved in different directions. The present thesis demonstrates that with the proper combination of techniques, a plant systematic study can provide both practically applicable results and fundamental evolutionary insights, thus bridging the gap between fundamental and applied research

Fragment Length Distributions and Collision Probabilities for AFLP Markers

AFLP is a DNA fingerprinting technique frequently used in plant and animal sciences. A drawback of the technique is the occurrence of multiple DNA fragments of the same length in a single AFLP lane, which we name a collision. In this article we quantify the problem. The well-known birthday problem plays a role. Calculation of collision probabilities requires a fragment length distribution (fld). We discuss three ways to estimate the fld: based on theoretical considerations, on in-silico determination using DNA sequence data from Arabidopsis thaliana, or on direct estimation from AFLP data. In the latter case we use a generalized linear model with monotone smoothing of the fragment length probabilities. Collision probabilities are calculated from two perspectives, assuming known fragment counts and assuming known band counts. We compare results for a number of fld's, ranging from uniform to highly skewed. The conclusion is that collisions occur often, with higher probabilities for higher numbers of bands, for more skewed distributions, and, to a lesser extent, for smaller scoring ranges. For a typical plant genome an AFLP with 19 bands is likely to contain the first collision. Practical implications of collisions are discussed. AFLP examples from lettuce and chicory are used for illustration

Snellere vermeerderingsmethode. Stengel Hippeastrum produceert vele bollen.

Wanneer dunne bloemstengelschijfjes van Hippeastrum op de juiste voedingsmedia in vitro geisoleerd worden, zijn deze in staat om adventieve bolletjes te vormen. Essentieel hierbij is, dat het juiste stadium van de bloemstengel gekozen wordt en dat er aanvankelijk althans in donker wordt gekweekt. De ontstane bolletjes kunnen later in het licht volledige plantjes vormen. De bolletjes van deze plantjes kunnen weer opgedeeld worden, waardoor verdere vegetatieve vermeerdering mogelijk i