360
13.2.3.2 Phylogenetic Relationships of Cedrela Species from the Yungas
The aligned ITS dataset consisted of a matrix of 131 sequences. Direct sequencing
produced ITS sequences of C. angustifolia (13 samples), C. balansae (43), and
C. saltensis (12), while sequencing of bacterially cloned amplicons yielded 60
clones from 9 samples of C. balansae and 4 samples of C. saltensis (Table 13.1).
Three additional sequences from GenBank were used as reference sequences of
C. saltensis, C. balansae, and C. angustifolia. Phylogenetic analysis based on this
matrix returned a tree that grouped the sequences into two main clades. The first
clade (90% bootstrap support) grouped sequences of C. angustifolia, while
sequences of C. balansae and C. saltensis occupied the second clade (95% bootstrap support). Within this second clade, there were two sub-clades. The first one
grouped most of the sequences of C. balansae obtained through direct sequencing
and through bacterial cloning from samples that belong to either C. balansae or
C. saltensis (91% bootstrap support). The second sub-clade (100% bootstrap support) included most of the sequences from direct sequencing from samples of
C. saltensis, some sequences from samples of C. balansae and sequences from
samples classified as either C. balansae or C. saltensis that had been obtained
through bacterial cloning. In agreement with the results of the AFLP analyses, both
sub-clades contained sequences of both C. balansae and C. saltensis (Zelener
et al. 2016).
Network analysis further assessed the genealogical relationships among the
sequences, which were mostly congruent with the phylogenetic analysis (data
shown in Zelener et al. 2016). Four ribotypes were found among the 128 sequences.
One ribotype was present exclusively in C. angustifolia; a second ribotype was a
singleton, which appeared in a sample of C. balansae (CbAcBA11); a third ribotype
was present in sequences from samples of C. balansae; and a fourth one was present
in C. saltensis.
In order to compare results achieved by a Bayesian method from AFLP markers
and those from ITS analyses, we constructed a second map to display the latitudinal
distribution of the ITS ribotypes that were identified in each of the 15 populations
(Table 13.1; Fig. 13.4c). Each circle in this map represents the ribotype of a sample.
Interestingly, ribotypes 3 and 4 appeared in bacterially cloned sequences obtained
from both a sample of Pintascayo population of C. balansae and a sample of San
Andrés population of C. saltensis (data shown in Zelener et al. 2016). In addition,
some samples of C. balansae – from Pintascayo population – and C. saltensis, from
San Andrés population, retained ITS paralogs that had originated in either C. balansae or C. saltensis, as expected in recent hybrids (Nieto Feliner and Rosselló 2007;
Coleman 2009).
N. Zelener et al.
13.2.3.2 Phylogenetic Relationships of Cedrela Species from the Yungas
The aligned ITS dataset consisted of a matrix of 131 sequences. Direct sequencing
produced ITS sequences of C. angustifolia (13 samples), C. balansae (43), and
C. saltensis (12), while sequencing of bacterially cloned amplicons yielded 60
clones from 9 samples of C. balansae and 4 samples of C. saltensis (Table 13.1).
Three additional sequences from GenBank were used as reference sequences of
C. saltensis, C. balansae, and C. angustifolia. Phylogenetic analysis based on this
matrix returned a tree that grouped the sequences into two main clades. The first
clade (90% bootstrap support) grouped sequences of C. angustifolia, while
sequences of C. balansae and C. saltensis occupied the second clade (95% bootstrap support). Within this second clade, there were two sub-clades. The first one
grouped most of the sequences of C. balansae obtained through direct sequencing
and through bacterial cloning from samples that belong to either C. balansae or
C. saltensis (91% bootstrap support). The second sub-clade (100% bootstrap support) included most of the sequences from direct sequencing from samples of
C. saltensis, some sequences from samples of C. balansae and sequences from
samples classified as either C. balansae or C. saltensis that had been obtained
through bacterial cloning. In agreement with the results of the AFLP analyses, both
sub-clades contained sequences of both C. balansae and C. saltensis (Zelener
et al. 2016).
Network analysis further assessed the genealogical relationships among the
sequences, which were mostly congruent with the phylogenetic analysis (data
shown in Zelener et al. 2016). Four ribotypes were found among the 128 sequences.
One ribotype was present exclusively in C. angustifolia; a second ribotype was a
singleton, which appeared in a sample of C. balansae (CbAcBA11); a third ribotype
was present in sequences from samples of C. balansae; and a fourth one was present
in C. saltensis.
In order to compare results achieved by a Bayesian method from AFLP markers
and those from ITS analyses, we constructed a second map to display the latitudinal
distribution of the ITS ribotypes that were identified in each of the 15 populations
(Table 13.1; Fig. 13.4c). Each circle in this map represents the ribotype of a sample.
Interestingly, ribotypes 3 and 4 appeared in bacterially cloned sequences obtained
from both a sample of Pintascayo population of C. balansae and a sample of San
Andrés population of C. saltensis (data shown in Zelener et al. 2016). In addition,
some samples of C. balansae – from Pintascayo population – and C. saltensis, from
San Andrés population, retained ITS paralogs that had originated in either C. balansae or C. saltensis, as expected in recent hybrids (Nieto Feliner and Rosselló 2007;
Coleman 2009).
N. Zelener et al.