Biology Reference
In-Depth Information
9
Molecular Phylogeny of Palms
9.1 Introduction
We have thus far covered the use of genomics in individual palm species or genus.
We devote this chapter exclusively to the use of DNA sequence variations in rear-
ranging to clarify the taxonomic relationship of palms. A taxon (plural—taxa) is
any group of organisms that is given a formal taxonomic name. A taxon is called
monophyletic if it includes a group of organisms descending from a single ancestor
or a common ancestor. If some of the members of the taxa do not share a common
ancestor, then it is known as paraphyletic. A polyphyletic taxon is one whose mem-
bers do not all have a common ancestor. Arecaceae, the palm family, is recognized
as a monophyletic group among plants. The Arecaceae family is located within the
commelinid clade of the monocotyledons group of plants. Arecoideae, Calamoideae,
Ceroxyloideae, Coryphoideae, and Nypoideae are the five subfamilies of the palm
family. Presently, the relationship among the 183 genera and 2364 species
[1,2]
of
these five subfamilies is not completely resolved. A growing knowledge on the sub-
ject has made inroads toward achieving the objective. In estimating the phylogenetic
structure of a taxon, the strength of DNA markers is measured by the number of par-
simony informative (PI) sites or characters.
9.2 Random Primers and DNA Barcodes [2-5]
RAPD and ISTR genetic markers
[3]
identified and differentiated 66 genotypes in 50
palm genera. However, these markers are not suitable for genetic relationship analy-
sis above the genus level
[3]
. A three-locus DNA barcode was used to identify with
98% accuracy 296 species of woody trees, shrubs, and palms of a forest plot
[4]
. The
DNA barcode for phylogenetic applications in palms has recently been explored
[5]
.
9.3 Markers for Palms from Other Monocot Plants [7-9]
About 96 nuclear “conserved intron-scanning primers” (CISP) were evaluated among
the members of subfamilies of palms. Seven of them were useful in comparing sub-
families, and four of the loci have potential in comparing the related genera
[6]
.
Nuclear CISPs were designed by the alignment of ESTs of onion and banana with
BACs (bacterial artificial chromosome) of rice. Ninety-six of them gave a successful
amplification rate of 32.3% in the DNA of members of the palm family
[7]
. Scarcelli
et al.
[8]
developed about 100 new primers amplifying the selected regions in plastid
