Boesenbergia longiflora (Zingiberaceae) and descriptions of five related new taxa

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Fig. 3. One of many shortest 

maximum parsimony phylograms (simplified) for Boesenbergia 

and other representatives of Zingiberaceae based on plastid trnK data analysis, rooted using 

Siphonochilus J.M.Woods & Franks as suggested by Kress et al. (2002). The position of the 

genus Boesenbergia, the 

B. longiflora clade and the taxa sampled for this study are indicated.  

 indicate branches with MP Bootstrap values ≥50%.


Boesenbergia longiflora and related taxa

tree topologies were consistent between data partitions. In cases where tree topology 

differed, branch support for the conflicting topology was reviewed. If branch support 

was weak (<65% BS, <0.95 PP) the data for those taxa were analysed in combination. 

As stated above, the ITS data for one taxon included two very different copies. In 

another instance, there was strong positional conflict among the nuclear and plastid 

phylogenies for one sample. Disparate copies were included in all individual data 

set analyses, but only one copy was included in combined data analyses.  The ITS 

copy retained for combined analyses was selected to best match to the chloroplast 


Maximum parsimony and maximum likelihood (ML) analyses were conducted 

in PAUP* (version 4.0b10, Swofford 2002). Heuristic search methods were conducted 

in each case with 1000 random addition replicates for MP and 10 random addition 

replicates for ML, each with tree bisection and regrafting (TBR) branch swapping.  

Maximum Parsimony analyses were conducted under Fitch parsimony criteria (Fitch 

1971). Maximum likelihood analyses were conducted using model parameters selected 

by jModelTest (version 0.1.1 available at; Posada 2008, Guindon 

& Gascuel 2003) under both the Akaike Information Criterion (AIC; Akaike 1974) and 

the Bayesian Information Criterion (BIC; Schwarz 1978). All Maximum Likelihood 

trees were saved. Both AIC criterion and BIC criterion models were analysed for all 

data partitions, but only the trees from the AIC analyses will be discussed as both 

methods produced nearly identical trees.

Branch support was estimated using parsimony bootstrap (BS) in PAUP* and 

posterior probabilities (PP) in MrBayes v3.2.1 (Ronquist & Huelsenbeck 2003). 

MrBayes analyses were conducted through the CIPRES portal (Cyberinfrastructure 

for Phylogenetic Research; Miller et al. 2010) and used partitioned data whenever 

appropriate (partitions = 5

ʹtrnK IGS + 3ʹtrnK IGS, matK, ITS) and were run in triplicate 

to ensure convergence. Bootstrap values were based on 1,000 pseudoreplicates, each 

with 100 random addition replicates, TBR branch swapping, saving a maximum of 

10 trees per random addition replicate and hold=4 trees. The number of generations 

necessary to estimate posterior probabilities varied depending upon the dataset and the 

time required to reach stasis (average standard deviation of the splits frequency <0.01).

Results and discussion

A number of exploratory analyses were conducted to evaluate the consistency of the 

phylogenetic hypotheses generated by the different data partitions. As stated above, 

some of the data generated from the nuclear ribosomal partition were noisy, indicating 

the presence of divergent ITS copies within a sample. Although it is not common

multiple copies of ITS have been detected in a number of genera and species of 

Zingiberaceae including Alpinia (Liu et al. 2009), and Cornukaempferia (L. Prince 

pers. obs.), and multiple ITS copies per individual is prevalent in Curcuma


et al. 2012) and Kaempferia (L. Prince, pers. obs.). The presence of multiple, strikingly 

different copies can be explained by a number of different evolutionary histories, a 


Gard. Bull. Singapore 65(1) 2013

few of which are presented here. The ITS region is present in hundreds (or thousands) 

of copies, often on multiple, different chromosomes. Processes affecting the utility 

of ITS for phylogenetic reconstruction were reviewed by Álvarez & Wendel (2003) 

including a discussion of the processes described below.

One explanation for the detection of multiple different copies in one organism 

is that the multiple copies were present in the ancestor and those copies are being 

maintained through time. Another explanation is recent genetic drift of some copies 

due to relaxed evolutionary constraints. Given the importance of this region for the 

functionality of the organism, it would not be likely unless there has been duplication 

(perhaps due to polyploidisation). Chromosome counts have not been made for the 

sample of 

B. longiflora (Kress 03-7305, US) included here, so perhaps this is a plausible 

explanation. Yet another possibility is recent gene flow between closely related taxa. 

If hybridisation happened in the recent past, there is a possibility that the two different 

copies have not yet had the time to undergo concerted evolution. If this process is 

incomplete, each parental copy will be recovered and, in a phylogenetic analysis, the 

different copies would each cluster with one of the (putative) parents. Alternatively, 

chimeric ITS sequences might be detected.

No matter the source of multiple, different copies of ITS present within any given 

organism, there is ample indication that most organisms undergo concerted evolution 

of the ITS region, a process by which the different copies are homogenised across the 

genome resulting in a single (or at least dominant) copy per organism. The length of 

time for complete homogenisation of the ITS of any given organism is unknown and 

likely highly variable. Although there has been a great deal of speculation regarding 

concerted evolution and homogenisation in purported hybrid taxa of flowering plants, 

our best understanding of the actual time required is gleaned from experiments with 

artificial  hybrids  (e.g.,  Armeria: Fuertes Aguilar et al. 1999, Feliner et al. 2001; 


: Mráz et al. 2011) and in recently derived polyploidy taxa (e.g., Spartina

Ainouche et al. 2004; Helictotrichon: Winterfeld et al. 2009; Oryza: Ying et al. 2010).

Nuclear ribosomal ITS data

The aligned data matrix included 86 potentially parsimony-informative characters (43 

for ingroup only). As indicated above, several samples required cloning to obtain clean 

ITS sequences. Two other samples, indicated by an asterisk in Fig. 4, should be cloned 

to clarify a few polymorphisms. Maximum parsimony analysis produced over 100,000 

shortest trees and could not be run to completion. One of the 37 shortest ML trees is 

shown in Fig. 4.

The ML phylogram presented in Fig. 4 identifies a moderately supported clade 

that includes all samples of B. kerrii and B. collinsii plus one of the 

B.  longiflora 

clones (88% BS; 1.00 PP). Both B. kerrii and B. collinsii are resolved as monophyletic 

with moderate to strong support. The other ingroup clade is moderately to strongly 

supported (75% BS; 0.98 PP), and includes all samples of B. kingiiBhamiltonii

B. maxwellii and two clones of 

B. longiflora. Resolution within the clade is poor and 

internal branches are generally poorly supported although most of the B. kingii samples 

and clones cluster together with 70% BS and 1.00 PP.


Boesenbergia longiflora and related taxa

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