30 GENERAL INTRODUCTION AND DISCUSSION
1.5. CYTOGENETICS IN ARACEAE AND THE AREAE 31
Literature
Ronquist, F. and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models.
Bioinformatics 19:1572-1574.
Thorne, J.L., Kishino, H., 2002. Divergence time estimation and rate evolution with multilocus data sets. Syste-matic Biology 51:689-702.
Stamatakis, A., 2006. RAxML-VI-HPC: Maximum Likelihood-based Phylogenetic Analyses with Thousands of Taxa and Mixed Models. Bioinformatics 22(21):2688-2690.
Phylogenetic Analyses
- Matrix (3321 bp, 335 bp parsimony informative) from 2 chloroplast genes: trnK and rpGene - Best maximum likelihood tree search with RAxML (Stamatakis, 2006) Maximum likelihoodbootstrap analysis with RAxML (GTRCAT model, 1334 replicates)
Posterior probabilitiescalculation with MrBayes (GTR+I+Γ, 1,000,000 generations, sampled every 100th, temp=0.3, burnin=4750, 99 % credible set contains 10362 trees, Ronquist & Huelsenbecek, 2003)
- Dating analysis implemented in multidivtime (Bayesian dating method of Thorne & Kishino, 2002)
Fig. 1: Maximum likelihood phylogram of 89 Areae and 14 outgroup taxa with diploid chromosome numbers plotted next to species names. Support values at branches are maximum likelihood bootstrap percentages and posterior probabilities (ML/PP>85 %). The karyogram is ofTyphonium tubispathum, this is the third record of2n= 10in Araceae.Orange:
taxa with chromosome numbers based onx= 13;Red:taxa with chromosome numbers based onx= 14;Purple:hypothesized chromosome reduction events;Blue:hypothesized polyploidization events;Yellowcircles: age in million years (SD in all cases<8 Ma).
Biarum bovei Biarum straussii Eminium heterophyllum JZZ 4Eminium heterophyllumBiarum dispar SBL 564Biarum tenuifoliumBiarum carduchorumBiarum pyramiiBiarum ditschianumBiarum ditschianum MJBiarum davisii ssp. davisiiBiarum davisiiBiarum kotschyi Arum cyrenaicum Arum sp.nov. I 21 05 M.N.
Arum purpureospathumArum maculatumArum balansanum Arum nigrumArum creticumArum pictumArum hygrophilumArum italicumArum pictum 273 Arum italicum WL Arum sp.nov. 24219 Arum sp.nov. 26940Arum korolkowiiArum dioscoridisArum concinnatumArum dioscoridis 15038Arum rupicola
Arum orientaleTheriophonum infaustumTyphonium giganteumDracunculus canariensisTyphonium venosumTyphonium tentaculatumDracunculus vulgarisTyphonium hirsutumEminium sp.n.JJMZ 67Eminium spiculatumHelicodiceros muscivorusTyphonium brevipesTyphonium diversifoliumTyphonium horsfieldiiTyphonium larseniiTyphonium goaligongenseKUNTyphonium goaligongense Theriophonum dalzelii
Typhonium wilbertii Typhonium angustilobum Typhonium eliosurum
Typhonium browniiAlocasia gageanaAlocasia cucullataSteudnera discolorColocasia giganteaRemusatia viviparaArisaema speciosumPinellia ternataTyphonium saraburiense?Typhonium huenseTyphonium variansTyphonium sp.n. H.AR.543Typhonium bachmaenseTyphonium trilobatumTyphonium digitatumTyphonium adnatumTyphonium circinnatumTyphonium gallowayiTyphonium lineareTyphonium gracileTyphonium roxburghiiTyphonium orbifoliumTyphonium reflexumTyphonium tubispathumTyphonium albidinervumTyphonium blumeiTyphonium sp.n. H.AR.555Typhonium violifolium1Typhonium violifolium2Typhonium baoshanenseKUNTyphonium jingpingenseTyphonium jingpingenseKUNTyphonium flagelliformeAriopsis peltataTyphonium cordifoliumTyphonium pedunculatumTyphonium filiforme1Typhonium sp.n. H.AR.532Typhonium echinulatumTyphonium filiforme2Typhonium glaucumTyphonium griseumTyphonium subglobosum Protarum sechellarumArisarum vulgare
Peltandra virginica Typhonodorum lindleyanum Caladium bicolor
Xanthosoma sagittifolium
ML PP
96 2474 22/2626
26 56 56 56 2828
2828 8484
28 2884 28
28 2828 56
52 2626 26 5216 16
> 110
160 16
26/52 18/36,40
10/12?
8?
10 101010 28 282856782828/56 28/84 5628 112112
30 26
Areae
Basic Chromosome
Numbers Ploidy LevelsMechanisms
100
100
87
100
100
88
87 88100
100 100
89 100 94
100 100
100 98 100 89
100 98
100 100 97 100 10096 100 99 100
100
100
100
100
100
100
89
100
100
98 100 10096 99 100 98 100100
100 97
100 100 87
9892100 100
100 94
100
100 1009999 100 100 100 100
100 100
100 100 100
89
999895100 100
100 99
100 96
100 98 100 99 100
62
59 47
Species name ! Diploid chromosome number
0.01
Typhoniumcorecore Areae
MEDITERRANEANSE ASIA
Sauromatum (S ASIA) Theriophonum(INDIA)
unplaced
AUSTRALIANTyphonium
Arum, Dracunculus, Eminium, HelicodicerosBiarum
x = 12 x = 14 x = 13 x = 8 x = 5, 8 x = 9
x = 13 x = 13
x = 11 x = 5
2x 2x, 8x 2x 2x, 4x, 6x 2x, 4x 2x 20x, 22x, 32x 2x, 8x 2x, 4x 2x, 4x
Polyploidization Aneuploidization
Polyploidization (auto!,allo!) at least 6 x independently in core Areae (<!)
Only in three different ploidy levels
Polyploidization Reduction
Reduction with following multiple rounds of autopolyploidization?
Fragmentation of genome?
Polyploidization Aneuploidization Reduction
(fusion, translocation?)
Arum
? Discussion
The most common basic chromosome numbers in the Areae arex= 13andx= 14. The frequency of polyploids points to numerous hybridization or autopolyploidization events. An-euploidization and subsequent polyploidization events (or vi-ce versa), or other complex chromosome rearrangements, seem to have played an important role only in the evolution of Bia-rumand the coreTyphonium. In all Areae,2n= 10is so far only found in the ca. 47 Ma old coreTyphonium, which is embedded among taxa with higher chromosome numbers.
This reduction of chromosome number and the negative cor-relation between chromosome number and size (Fig. 2) point to chromosome fusion and translocation events.
Fig. 2: Minimal and maximal chromosome sizes from chro-mosome counts of 19 Areae, plotted over their chromoso-me number. Chromosochromoso-me sizes increase with decreasing chromosome number.
20 40 60 80
2468101214
Diploid chromosome numbers / 2n
Chromosome size / µm
maximum size minimum size
Introduction
The Areae clade (Fig. 1) includes about 150 species in the ge-neraArum, Biarum, Dracunculus, Eminium, Helicodiceros, TheriophonumandTyphonium. They range from Australia over South East Asia to the Mediterranean region and ha-ve been introduced to (sub-) tropical Africa. Chromosome numbers are available for 40% of the species and range from 2n= 160to2n= 10, the lowest chromosome number found in Araceae. We collected data from the literature and analy-zed them on a new chloroplast phylogeny that includes 89 Areae from all seven genera. We also estimated the ages of the clades.
Ludwig-Maximilians-Universität München
Natalie Cusimano & Susanne S. Renner Munich University (LMU), Germany, cusimano@lrz.uni-muenchen.de
Polyploidy, aneuploidy, and chromosome number
evolution of Arum and its allies (Areae, Araceae)
32 GENERAL INTRODUCTION AND DISCUSSION
Table 1.3: Unpublished chromosome counts ofTyphonium andSauromatum species.
Species Chromosome No. 2n=
Typhonium saraburiense? 18
tubispathum 10
pedunculatum 8, 10*
sp. nov.(H.AR.555) 10, 12*
filiforme 12 (+1B*)
orbifolium/violifolium? 22
varians 10
Sauromatum horsfieldii 26
hirsutum 26
are also species with x = 12 and x = 11, and one species, B. dispar, with 2n = 74 (n = x = 37), indicating more complex changes than just multiplications of the entire genome. In Sauromatum (x = 13), as well as in Arum (x = 14), all chromosome number changes represent polyploidization events, leading up to a hexaploid level (Arum italicum with 2n = 84). Theriophonum finally has a constant number of 2n= 16. Apparently, speciation in these genera is associated with polyploidy and/or dysploidy (e.g., switches fromx= 14 tox= 13 or perhaps vice versa), both of which may have occurred repeatedly.
While some Australian Typhonium species have 2n = 160 (Briggs in Evans, 1962), one of the highest numbers reported for the family, others have 2n = 10, the lowest chromosome number known in Araceae (Wang et al., 2002: Typhonium jingpingense; Zhi-Ling et al., 2007: Typhonium baoshanense). My own counts for additional Typhonium s.str. species (Table 1.3, Fig. 1.7) have revealed further cases of 2n = 10 and other low numbers (2n = 8, 12, needing confirmation).
Overall, Typhonium s.str. exhibits base chromosome numbers of x = 4∗, 5, 6∗, 8, 9, 11, and 13.
Genome Size
Genome size is an important cytological parameter, also referred to as C-value, where C stands for constant, as genome sizes have been found to be constant
∗chromosome numbers in need of further confirmation
1.5. CYTOGENETICS IN ARACEAE AND THE AREAE 33
Table 1.4: Genome sizes of Areae species from Plant DNA C-values database; Chr.No. = Chromosome number; Est. Meth. = Estimation methods: Fe = Feulgen microdensitometry, FC:
PI = flow cytometry using propidium iodide.
Species Chr.No. 2n= Est. Meth. 1C (pg) Reference
Biarum tenuifolium 22, 26 FC:PI 3,10 Zonneveld et al., 2005 Dracunculus canariensis 28 FC:PI 3,89 Zonneveld et al., 2005
Dracunculus vulgaris 28 Fe 6,83 Bennett, 1972
Arum maculatum 56 Fe 10,93 Bennett and Smith, 1976
Typhonium flagelliforme 16 Fe 5,17 Ghosh et al., 2001
Typhonium trilobatum 40 Fe 6,59 Ghosh et al., 2001
within species but highly variable between species. C-values in angiosperms span a huge range: from 0.10 pg in Fragaria viridis (Antonius and Ahokas, 1996), 0.16 pg in Arabidopsis thaliana (Bennett et al., 2003), and 63 Mbp in Genlisea margaretae (Greilhuber et al., 2006) to 127.4 pg inFritillaria assyriaca (1pg DNA
= 0,965x109 base pairs; Bennett and Smith, 1976), which represents a 1200-fold difference. Genome size does not directly correlate with organismal complexity (C-value paradox). The differences in genome size are mostly due to changes in the proportion of non-coding and repetitive DNA (both via downsizing and uploading).
Physiological and ecological parameters, such as habitat, temperature, humidity, sexual system, pollination, or latitudinal range, may correlate with genome size at the intra- and interspecific level, but there is no widely accepted hypothesis explaining the observed striking differences. Large genomes may impose ecological and evolutionary constraints, for example, because cell division takes longer, and this might explain why genera with large genomes are underrepresented in extreme habitats (Knight et al., 2005; Leitch et al., 2007).
The Plant C-values Database of Royal Botanical Gardens Kew (http://data.
kew.org/cvalues/homepage.html; Bennett and Leitch, 2005) includes 73 records for Araceae representing 30% of the family’s genera and some 2% of its species.
There are six reports for Areae (Table 1.4). The data do not suggest a correlation of genome size and chromosome number.
34 GENERAL INTRODUCTION AND DISCUSSION
A
D B
C
E F
H
10 µm
10 µm
G
10 µm 5 µm
5 µm 10 µm
5 µm 5 µm
Figure 1.7: Chromosome spreads of A, B: Typhonium tubispathum 2n = 10; C: Typhonium orbifolium / violifolium 2n= 22;D:Typhonium filiforme 2n= 12;E:Typhonium saraburiense 2n= 18;F:Typhonium varians 2n= 10;G: Sauromatum horsfieldii 2n= 26;H:Sauromatum hirsutum 2n= 26.
1.5. CYTOGENETICS IN ARACEAE AND THE AREAE 35
References
Antonius, K. and H. Ahokas. 1996. Flow cytometric determination of polyploidy level in spontaneous clones of strawberries. Hereditas 124:285.
Bedalov, M. and P. K¨upfer. 2006. Studies on the genusArum (Araceae). Aroideana 29:108–131.
Bennett, M. and I. Leitch. 2005. Nuclear DNA amounts in angiosperms: Progress, problems and prospects. Ann. Bot. 95:45–90.
Bennett, M., I. Leitch, H. Price, and J. Johnston. 2003. Comparisons with Caenorhabditis (similar to 100 Mb) and Drosophila (similar to 175 Mb) us-ing flow cytometry show genome size in Arabidopsis to be similar to 157 Mb and thus similar to 25 % larger than theArabidopsis genome initiative estimate of similar to 125 Mb. Ann. Bot. 91:547–557.
Bennett, M. and J. B. Smith. 1976. Nuclear DNA amounts in angiosperms. Philos.
Trans. R. Soc. Lond. B Biol. Sci. 274:227–274.
Bogner, J. and G. Petersen. 2007. The chromsome numbers of the aroid genera.
Aroideana 30:82–90.
Greilhuber, J., T. Borsch, K. Mueller, A. Worberg, S. Porembski, and W. Barthlott. 2006. Smallest angiosperm genomes found in Lentibulariaceae, with chromosomes of bacterial size. Plant Biol. 8:770–777.
Knight, C., N. Molinari, and D. Petrov. 2005. The large genome constraint hy-pothesis: Evolution, ecology and phenotype. Ann. Bot. 95:177–190.
Larsen, K. 1969. Cytology of vascular plants: III. A study of Aroids. Dan. Bot.
Ark. 27:39–49.
Leitch, I. J., J. M. Beaulieu, K. Cheung, L. Hanson, M. A. Lysak, and M. F. Fay.
2007. Punctuated genome size evolution in Liliaceae. J. Evol. Biol. 20:2296–
2308.
Marchant, C. J. 1973. Chromosome Variation in Araceae IV: From Acoreae to Lasieae. Kew Bull. 28:199–210.
Petersen, G. 1989. Cytology and systematics of Araceae. Nord. J. Bot. 9:119–166.
Petersen, G. 1993. Chromosome numbers of the genera of Araceae. Aroideana 6:37–46.
Sheffer, R. and T. Croat. 1983. Chromosome-numbers in the genus Anthurium .2.
Am. J. Bot. 70:858–871.
36 GENERAL INTRODUCTION AND DISCUSSION Sheffer, R. and H. Kamemoto. 1976. Chromosome-numbers in the genus
An-thurium. Am. J. Bot. 63:74–81.
Soltis, D. E. and P. S. Soltis. 1999. Isozyme evidence for ancient polyploidy in primitive angiosperms. Syst. Bot. 15:328–337.
Wang, Z., H. Li, and F. Bian. 2002. Typhonium jinpingense, a new species from Yunnan, China, with the lowest diploid chromosome number in Araceae. Novon 12:286–289.
Zhi-Ling, D., C. Shao-Tian, J. Yun-Heng, and L. Heng. 2007.Typhonium baosha-nense Z. L. Dao & H. Li, a new species of Araceae from western Yunnan, China.
Acta Phytotaxon. Sin. 45:234–238.
Chapter 2
Reevaluation of the cox1 group I intron in Araceae and Angiosperms indicates a history dominated by loss rather than horizontal transfer
Cusimano, N., Zhang, L.-B. and S. S. Renner. 2008.
Molecular Biology and Evolution 25(2): 265-276.
37
38 CHAPTER 2. THE COX1 INTRON IN FLOWERING PLANTS
2.1 Abstract
The origin and modes of transmission of introns remain matters of much debate.
Previous studies of the group I intron in the angiosperm cox1 gene inferred fre-quent angiosperm-to-angiosperm horizontal transmission of the intron from appar-ent incongruence between intron phylogenies and angiosperm phylogenies, patchy distribution of the intron among angiosperms, and differences between cox1 ex-onic coconversion tracts (the first 22 nucleotides downstream of where the intron inserted). We analyzed thecox1 gene in 179 angiosperms, 110 of them containing the intron (intron+) and 69 lacking it (intron−). Our taxon sampling in Araceae is especially dense to test hypotheses about vertical and horizontal intron transmis-sion put forward by Cho and Palmer (1999, Multiple acquisitions via horizontal transfer of a group I intron in the mitochondrial coxl gene during evolution of the Araceae family. Mol. Biol. Evol. 16:1155-1165). Maximum likelihood trees of Araceaecox1 introns, and also of all angiosperm cox1 introns, are largely congru-ent with known phylogenetic relationships in these taxa. The exceptions can be explained by low signal in the intron and long-branch attraction among a few taxa with high mitochondrial substitution rates. Analysis of the 179 coconversion tracts reveals 20 types of tracts (11 of them only found in single species, all involving silent substitutions). The distribution of these tracts on the angiosperm phylogeny shows a common ancestral type, characterizing most intron+and some intron− an-giosperms, and several derivative tract types arising from gradual back mutation of the coconverted nucleotides. Molecular clock dating of small intron+ and intron− sister clades suggests that coconversion tracts have persisted for 70 million years in Araceae, whosecox1 sequences evolve comparatively slowly. Sequence similar-ity among the 110 introns ranges from 91% to identical, while putative homologs from fungi are highly different, but sampling in fungi is still sparse. Together, these results suggest that the cox1 intron entered angiosperms once, has since largely or entirely been transmitted vertically, and has been lost numerous times, with coconversion tract footprints providing unreliable signal of former intron presence.