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8. MOLECULAR PHYLOGENY OF THE GENUS LOLIUM
been generated for many taxonomic groups, they have not produced a clear-cut picture and
reconstructed phylogenetic trees have often been controversial.
The first classification based on molecular data was published by “Angiosperm Phylogeny
Group” in 1998 with aim to compile published phylogenetic trees into a hierarchical system
at and above the level of family (Savolainen and Chase 2003). Ironically, notwithstanding
this fact, molecular analyses are often treated as additional data, with lower “taxonomic”
value in comparison with morphology, especially at the species level. This philosophical
pillar still holds in the majority of taxonomic systems of plants, in which the morphological
distinctiveness is the only accepted condition for registering a new species. For instance,
reproductively isolated, cryptic species of Aneura pinquis will not be registered as long as
morphological differences are found, even though their DNA fingerprints are completely different
(Bączkiewicz et al. 2007). Likewise, since early 1980s sibling species of Conocephalum
conicum (L.) have been recognized by means of isoenzymes and more recently DNA
markers (Szweykowski et al. 1981; Sawicki et al. 2005). Nevertheless, they were elevated to
the rank of taxonomic species with names C. conicum and C. salebrosum after distinct morphological
traits had been identified (Szweykowski et al. 2005). At the opposite extreme, not
everyone accepts objections to species status of morphologically different taxa, yet similar at
the DNA level and not isolated reproductively. Even though, morphological differences are
more related with varieties, ecotypes or environments. A nice empirical example of this sort
involves classification of species within the genus Lolium. Apart from questionable status of
multiflorum and perenne subspecies (Chapter 2-7), taxonomic position of the others is also
subjected to a contentious debate over much of the twentieth century. How are the Loliums
grouped depends both on morphological traits considered the most important and statistical
or analytical methods employed. Traditionally, the species of the genus are recognised on
the basis of such traits as plant height, leaf and spike morphology and many others (Chapter
1). Unfortunately, the majority of these characters are quantitative with the overlapping range
of variation (Loos 1993a; Bennett 1997). It is not surprising because they are controlled by
a huge number of QTLs distributed over the whole genome. Species have a mixture of positive
and negative alleles at each QTL and none of them is fixed in a given taxa (Chapter 7).
Although L. temulentum and L. persicum can be delimitated on the basis of floret number
per a spikelet (Polok 2005) also this trait has a little value for taxonomy. At least six major
QTLs are responsible for floret number and QTLs acting to increase the number of florets
are equally distributed at least in multiflorum and perenne (Chapter 7). Serious difficulties are
encountered as well when grain morphology is used for species classification. The seeds
of out-pollinated taxa, L. perenne (ssp. multiflorum and ssp. perenne), L. rigidum and selfpollinated
L. loliaceum are much the same.
A basic point for phylogenetic considerations is that evolution is a genetic process. Over
time genome sequences are changing through different mutations (point, chromosomal, insertional
etc.), that are further undergoing selection and eventually fixation. The extent of
these changes reflects the evolutionary distinctiveness of populations, species and higher
taxa. In addition, the changes are clocklike i.e., although the clock ticks at various speed
across nucleotide positions within a codon, among different genes, among different classes
of DNA within a genome and finally, among different genomes, the clock can be calibrated
providing biogeographical, tectonic or any other past event is known (Savolainen and Chase