The article entitled “Molecular Phylogeny and Systematics of the Lilium

carniolicum group (Liliaceae) based on nuclear ITS sequences” was written by I.

Resetnik, Z. Liber, Z. Satovic, P. Cigic, and T. Nikolic in the journal “Plant
Systematics and Evolution”, volume number 265, pages 45-58, and was published on
March 2007.
The use of nuclear ribosomal DNA in the study was somewhat less convincing in
proving phylogenetic relationships between plants as the best material being studied
for plant phylogeny was the gene sequences in different regions of the chloroplast.
Although unusual, the introduction laid evidence to support the compatibility of
nrDNA for the said study. In the case of Lilium carniolicum group, their nrDNA
carries more informative data compared to the chloroplast. According to the study, the
information in the gathered yielded no apparent resolution among the group. The
evidence was not considered strong because other groups within the genera has been
able to be analyzed with the chloroplast gene-based study.

The plants collected were from their natural population which is a convincing
evidence that the samples possess the organelles or structures which they must
naturally possess rather than getting samples from the cultivated plants as those plants
are grown under the controlled condition of the researcher. The number of samples
collected in the study differ from each species. The findings indicate that species with
smaller number of accessions collected was based on the conservation memorandum
which also justifies the limited samples from other taxa. The choosing of outgroup
was done correctly as it was chosen through differences in floral characteristics and
correctly placed in the root of the tree.
As for the DNA extraction, the usage of the same brand of DNA analyzer and
PCR purification kit has somewhat increased the confidence of the results gathered.
Using the same brand indicates a continuous analysis of their genome as these
products are designed to be compatible and complementary with one another.
However, a sample of a certain species showed ambiguity. It was helpful that the
researchers examined the second and third part of the species’ nrDNA which was also
relevant to the ITS of the other samples. Having a backup plan is crucial in doing a
chemical analysis because once ambiguous data is obtained and kept, it will surely
affect the results and the species might be placed on the wrong group.

The sequence data gathered regarding the ITS1 and ITS2 regions of the plants’
germplasm were initially aligned using the Clustal X (Thompson et al. 1997), a
computer program used for Bioinformatics - multiple sequence alignment, with the
program’s default parameters to avoid technical errors and personalized information
that may lead to inaccuracy. The multiple sequence alignment from the samples were
compared to the previously published Liliumsequences (Nishikawa et al. 2001,
Nishikawa et al. 1999). The accurate discussion of the process in this study indicates
that the model or tree created was valid. The appearance of polytomy in the tree
lessens the integrity of the tree constructed. The researchers might lack sufficient data
or have done inappropriate analysis of characters. Also, the length of number of base
pairs in the study was short and insufficient considering each chromosome contains
over 100 million base pairs (T. Annunziato 2008). It is important in every study to
prepare sufficient or extra data in case of the appearance of ambiguous data.
The discussion regarding the phylogeny construction consist of both the weight of
the evidences from the ITS sequence. It emphasized the value of multiple iterations to
keep the integrity of the phylogeny. The researchers also used different morphological
characteristics which was able to support the tree created. Another good point in the
discussion includes chemotaxonomy or the usage of chemical compounds as
identification; anthocyanin production was present in all the species under the
group.the limited sampling for the section Liriotypus did not allow to draw any firm
conclusions with regard to their evolution. Clearly, more extensive sampling will be
necessary to clarify relationships within both the section and genus. In addition, the
discussion of the shortcomings and errors in the study was helpful for the readers and
future researchers. The discussion was clear and contributed to the existing
knowledge regarding the study.