Boesenbergia longiflora (Zingiberaceae) and descriptions of five related new taxa
Yüklə 321,14 Kb. Pdf görüntüsü
|
- Bu səhifədəki naviqasiya:
- Chloroplast trnK intron (including the protein coding matK gene)
- Combined analyses
Fig. 4. One of 37 best, Maximum Likelihood phylograms (-ln=2218.749) for Boesenbergia longiflora and closely related taxa based on analysis of nuclear ribosomal ITS data for all samples and clones. Support values (Bootstrap/Posterior Probability) for critical branches are shown above branches. Bold typeface highlights strongly supported positions of the different
also be cloned to clarify a few polymorphisms. Underlined samples are placed in conflicting positions on the chloroplast phylogeny. Note: lower branches were pruned to fit page and are not to scale. 56
Fig. 5. Single best Maximum Likelihood phylogram (-ln=3953.067) for B. longiflora and closely related taxa based on analysis of chloroplast trnK intron data. Support values (Bootstrap/ Posterior Probability) for critical branches are shown above branches. Numbers in bold typeface indicate strong support. Underlined samples are placed in conflicting positions on the nuclear ribosomal phylogeny. Note: lower branches were pruned to fit page and are not to scale. 57
The identification of at least two disparate ITS copies for B. longiflora requires further discussion. Only one sample of B. longiflora was available for inclusion in this study. This sample, M11P48 was from cultivated plants grown by the first author, but originally collected in Burma (Kress 03-7305, US). Multiple clones representing one
(ITS copy “A”) while the other B. longiflora copy fell sister to the B. kerrii clade (ITS copy “B”) as is shown in Fig. 4. Although a number of tests have been proposed to distinguish between the processes of hybridisation and incomplete lineage sorting (Joly et al. 2009) all have limitations. We were restricted here by the single sample for B. longiflora, but hopefully, more samples will be available for future analyses. The majority of the polymorphic samples were identified as B. kingii based on morphology. Six of the twelve samples required cloning to generate clean ITS sequences. These samples fall into two categories. The first group included samples with multiple ITS sequence types, but those sequences were all quite similar with only a few different bases or slight length variations. Analyses of the ITS data partition placed all of these sequences in the B. kingii sensu lato clade as described above (B. hamiltonii + B. kingii + B. maxwellii ), and with moderate to high support (75% BS, 0.98 PP) but with poor resolution within the clade (Fig. 4). Further, most of the B. kingii samples clustered with moderate support (70% BS, 1.00 PP). Among the ingroup members, B. kingii is the most broadly distributed species and is the most genetically diverse taxon. Chloroplast trnK intron (including the protein coding matK gene) A total of 36 potentially parsimony-informative characters (15 for ingroup only) were used to generate almost 100,000 maximum parsimony trees. However, maximum likelihood analyses resulted in a single best tree (Fig. 5). The likelihood tree had a topology identical to several of the MP trees. As with the results of the ITS analyses, both MP and ML analyses identified two clades within the ingroup, one including samples of B. collinsii + B. kerrii +
and a clade comprising B. hamiltonii and B. kingii (63% BS; 0.83 PP). Three taxa were resolved and supported as monophyletic: B. collinsii (65% BS, 0.94 PP) B. kerrii (63% BS, 0.94 PP) and B. maxwellii (99% BS, 1.00 PP). The relationship of B. maxwellii to B. hamiltonii and B. kingii differed here relative to the ITS results, but only with weak (65% BS; 0.85 PP) support. Sequences for two samples were not available for this data set, B. hamiltonii M3212 and B. maxwellii MP1450. The two samples with names underlined in Fig. 4, B. kingii M11P77 and M11P78, were identical and clearly supported as members of the B. kingii group in the phylogeny produced by analyses of the nuclear ITS dataset. Results of the chloroplast data analyses (Fig. 5) clearly (88% BS, 1.00 PP) placed these two samples in a clade with B. hamiltonii. Combined analyses The combined data set required a number of samples to be excluded. Because the ITS data required cloning for some samples, results of the ITS MP analyses were used to select the clone with the shortest branch for each sample (as suggested by Beilstein et 58
al. 2008) for subsequent use in the combined analyses. This was done only when all clones for a particular sample either formed a monophyletic lineage or clustered within a moderately or well-supported lineage (BS≥75%). In the instance of B. kingii samples
, there was positional conflict between the nuclear and plastid datasets. Those samples were excluded from the combined analysis. As mentioned, there was only a single sample of B. longiflora available for this study. The nuclear data set included two distinctly different copies, A and B. Rather than totally exclude this critical taxon, we selected the nuclear copy B that best matched the chloroplast phylogeny, while recognising we do not know which better represents the evolutionary history of the species. Maximum parsimony analysis produced 468 shortest trees. Maximum likelihood analyses produced three equally likely trees, one of which is shown in Fig. 6. Both MP and ML analyses identified two clades within the in-group most similar to those of the ITS data analyses, a B. kingii clade including samples of B. hamiltonii + B.
0.78 PP. Unlike the ITS data analyses results, the combined data analyses produced highly resolved topologies within this clade. Significantly, B. maxwellii is resolved as monophyletic (83% BS; 1.00 PP). Boesenbergia hamiltonii and B. kingii samples are grouped together with 51% BS and 0.95 PP. Boesenbergia hamiltonii was also resolved as monophyletic, but with weak support (<50% BS, 0.86 PP). The B. longiflora sensu lato clade was strongly supported (95% BS; 1.00 PP) with significant internal structure and support. Boesenbergia collinsii was supported as monophyletic (100% BS; 1.00 PP) as was B. kerrii (93% BS, 1.00 PP). The single sample of B. longiflora was sister to B. kerrii (64% BS, 0.64 PP), but this placement should be viewed with caution. Multiple accessions for each taxon (except B. longiflora) were included to assess genetic variation within and among the newly identified taxa. The amount of sequence variation within each taxonomic clade was generally less than the amount of variation between clades as is shown by the phylograms in Figs. 4 -6. Despite the higher level of sequence diversity within B. kingii, it is supported as monophyletic. The results of both maximum parsimony and maximum likelihood analyses of DNA data presented above consistently identified five mostly strongly supported clades within the B. longiflora complex: B. collinsii, B. hamiltonii, B. kerrii, B. kingii and B. maxwellii. The data also support two sister relationships, one between B. collinsii and B. kerrii, and one between B. hamiltonii and B. kingii. The position of B. longiflora and B. maxwellii are less clear. The relationship of B. longiflora to these taxa is uncertain due to polymorphism in the nuclear (ITS) data set, but it is clearly closely related to them. Boesenbergia maxwellii jumps between the two clades depending upon data set examined. Finally, additional data are needed to test between various hypotheses (incomplete concerted evolution due to genetic drift post polyploidisation, hybridisation, or incomplete lineage sorting) to explain the high level of genetic variation detected in the nrITS of B. kingii. Overall, although there are a number of questions remaining, the molecular data allowed for the delineation of six taxa. 59
Yüklə 321,14 Kb. Dostları ilə paylaş:
|