3.3 Phylogenetic analyses
Three unlinked low-copy nuclear gene (Acc 1, DMC 1, andGBSSI ) and three chloroplast region (trn L-F, mat K,
and rbc L) sequences were separately amplified and sequenced for
all the accessions of R. yenchiana . They were then analyzed with
published St - and Y -type sequences from twelve species
of Roegneria and those from 33 diploid taxa representing 19 basic
genomes in Triticeae. Consequently, six homoeologous sequences
representing two distinct types (St - and Y -type) of
each nuclear gene and three sequences of each chloroplast region were
detected from all the accession of R. yenchiana . Four datasets,
including Acc1 data, DMC1 data, GBSSI data, and
combined chloroplast (trn L-F + mat K + rbc L) data,
were used to conduct separately alignments and phylogenetic analyses.
The features of Acc1 data, DMC1 data, GBSSI data,
and combined chloroplast data were summarized in Table S3. The alignedAcc1 sequences yielded a total of 1400 characters of which 411
variable characters and 201 were informative. ML analysis of theAcc1 data yielded a single phylogenetic tree (-Lnlikelihood =
5890.5424). ML and Bayesian analyses of the Acc1 data recovered
the same topology. The tree illustrated in Figure 3 was the ML tree of
bootstrap support (BS) above and posterior probabilities (PP) below
branches. The Acc1 sequences of R. yenchiana were
represented in two clades, corresponding to the two genomic types
(St and Y ). The St -type Acc1 sequences
of R. yenchiana were in one monophyletic group and then formed a
paraphyletic grade with those St-type sequences from otherRoegneria and Pseudoroegneria . The Y -typeAcc1 sequences of R. yenchiana and the sequence ofRoegneria ciliaris formed a paraphyletic grade. Of 959
total characters of the DMC1 data, 343 characters were variable
and 158 characters were informative. ML and Bayesian analyses of theDMC1 data recovered the same topology. The ML tree (-Lnlikelihood
= 4907.2580) inferred from the DMC1 data showed that theSt -type and Y - type sequences from the new species
were split into two well supported clades (Figure S1). TheSt -type DMC1 sequences of R. yenchiana were
scattered in different group and clustered with those from different
species of Roegneria . The Y -type DMC1 sequences
of R. yenchiana formed one monophyletic group and grouped with
the sequence of Roegneria brevipes . In the GBSSI sequence
data matrix, of the 1104 total characters, 472 were variable and 277
were parsimony informative. ML and Bayesian analyses of the GBSSIdata recovered the same topology. In ML tree (-Lnlikelihood = 8424.8144)
inferred from the GBSSI data, the St -type GBSSIsequences of R. yenchiana formed one monophyletic group, and then
clustered with one group including Roegneria gmelinii andRoegneria pendulinus(Figure S2). TheY -type GBSSI sequences of R. yenchiana were in
one monophyletic group and formed a paraphyletic grade with thoseY -type sequences from several species of Roegneria(R. semicostatus , R. anthosachnoides , and R.
ciliaris ). The combined trn L-F, mat K, and rbc L
data yielded a total of 3089 characters of which 306 were variable
characters and 132 were informative. ML and Bayesian analyses of the
combined chloroplast data recovered the same topology. In ML tree
(-Lnlikelihood = 7088.8370) inferred from the combined chloroplast data,
all the accessions of R. yenchiana formed one monophyletic group,
and this group was clustered with the species from Roegneria andPseudoroegneria (Figure S3).