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Systematics |
2Universität Osnabrück, Spezielle Botanik, Barbarastrasse 11, 49076 Osnabrück, Germany; 3Institute for Systematic Botany, University Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland; 4Universität Osnabrück, Botanischer Garten, Albrechtstrasse 29, 49076 Osnabrück, Germany; 5Plant Biology, University of California, Davis, California 95616 USA
Received for publication May 6, 2003. Accepted for publication September 18, 2003.
| ABSTRACT |
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Key Words: biogeography Brassicaceae hybridization Lepidium long-distance dispersal molecular phylogenetics polyploidy
| INTRODUCTION |
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In the present study we clarify the evolutionary history of Lepidium s.s. in Australia/New Zealand by comparing noncoding cpDNA and ITS sequences from 18 Australian/New Zealand species along with 38 species from the other continents. This represents the whole spectrum of variation in Lepidium s.s. Here we show that Australian/New Zealand Lepidium s.s. species are a polyploid group that descended from Californian ancestors hybridizing in Australia with Lepidium species originating from South Africa.
| MATERIALS AND METHODS |
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Molecular methods
Methods for DNA extraction, PCR, and direct sequencing of ITS and noncoding cpDNA (trnT/trnL spacer, trnL intron, trnL/trnF spacer) are given elsewhere (Bowman et al., 1999
; Mummenhoff et al., 2001
). To study the parental ITS units in presumed hybridogenous Australian Lepidium, the PCR products of selected Australian/New Zealand polyploids (L. fasciculatum, L. pseudohyssopifolium, L. pseudotasmanicum, L. muelleriferdinandi, L. oleraceum, L. banksii) were cloned and 28 clones were sequenced. The PCR products of the entire ITS region were purified with the QIAquick purification kit (Qiagen, Hilden, Germany) and directly ligated into plasmid vector pGEM T-Easy (Promega, Madison, Wisconsin, USA) and transformed into competent cells (E. coli strain DH
). Cells were plated on "Luria Broth Base" plates containing ampecillin. White colonies were selected with IPTG (Isopropyl-ß-D-thiogalactopyranoside) and ß-galactosidase and they were grown in the same medium. Plasmid preparation was performed using QIAprep Spin Miniprep kit (Qiagen). The same primers as for the PCR amplification were used for sequencing. Compilation of the information obtained from direct sequencing and from clone sequencing reveals one nucleotide polymorphism in L. oleraceum and L. fasciculatum, respectively, two polymorphic sites in L. pseudohyssopifolium, and three in L. muelleriferdinandi. Thus, we treated these nucleotide sites as polymorphic character states in the ITS data set used for subsequent phylogenetic analyses.
The DNA sequences were aligned by hand. Regions of ambiguous alignment were eliminated. Insertions/deletions (indels) were treated as missing data in the ITS matrix. In our recent cpDNA analysis (Mummenhoff et al., 2001
) we demonstrated that indels
3 base pairs (bp) provided reliable phylogenetic information. Therefore, indels in the cpDNA data were coded as missing in the core data matrix but six indels
3 bp were recoded as additional binary characters. Alignments are available upon request.
Phylogenetic analysis
Parsimony analysis of ITS and cpDNA assumed unordered and unweighted character states (i.e., Fitch parsimony) and used the heuristic search strategy in PAUP (version 4.0b10; Swofford, 2000
) with tree bisection-reconnection (TBR) branch swapping, and 100 random taxon additions. Up to 10 000 trees were kept from each random addition sequence replicate.
Bootstrap support values were obtained from 100 replicates by using an heuristic search and simple addition. The inclusion of hybrids in cladistic analyses may effect tree topology (McDade, 1992
), e.g., as a consequence of recombination between divergent parental ITS types (Baldwin and Sanderson, 1998
). All Australian species of presumed hybrid origin were included in the final data set because the exclusion of these species in initial analyses had no effect on topology of the remaining species.
Sequence divergence and relative rate test
Pairwise distance divergences were calculated in PAUP under Kimura's two parameter model (K2P) by using the pairwise-deletion option for gaps and ambiguous data. Rate heterogeneity among lineages in the cpDNA and ITS trees was examined by using a tree-wide likelihood ratio (LR) test (Modeltest 3.04; Posada and Crandall, 1998
). This test compares the log likelihoods (determined in 4.0b10) of constrained and unconstrained hypotheses (constrained, DNA substitution rates are equal among lineages; unconstrained, rates are allowed to vary among lineages) under the most adequate substitution model that best fits the data (Huelsenbeck and Rannala, 1997
).
| RESULTS |
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The ITS regions were sequenced for 56 species and 34 clones of selected Australian Lepidium species. The alignment generated a matrix of 456 characters, of which 87 are potentially informative in parsimony analysis. The K2P pairwise sequence divergence among the Lepidium s.s. taxa ranged between 0 and 7.9% and within Australian/New Zealand taxa between 0 and 1.5%.
ITS sequence polymorphism in Australian/New Zealand Lepidium and presumed progenitors
Eighteen Australian Lepidium s.s. taxa were analyzed by direct sequencing. Known polyploids (L. fasciculatum, L. pseudohyssopifolium, L. pseudotasmanicum, L. muelleriferdinandi, L. oleraceum, L. banksii; ploidy level see Fig. 1) were also analyzed by cloning amplified ITS sequences. Three species (L. aschersonii, L. muelleriferdinandii, L. pseudohyssopifolium) show additivity at one nucleotide position that is variable between the Californian (clade C) and South African (clade A) species group (Fig. 1, sites 108, 297, 432). This indicates that the Australian/New Zealand species may have originated by hybridization. With respect to those sites that are variable between the California and South Africa species group (Fig. 1) the Australian species of clade C and A show exactly those character states of the Californian (clade C) or South African (clade A) species, respectively. However, at site 109 most Australian/New Zealand taxa including those of clade C (related to Californian species) are characterized by the nucleotide found in the South African species (clade A).
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= 0.01 level.
We used fossil data (Mai, 1995
) of Rorippa (Brassicaceae) to calibrate mutation rates in Lepidium. Rorippa was found sister to Cardamine in recent phylogenetic analyses (Franzke et al., 1998
; Mitchell and Heenan, 2000
). Assuming a correct dating for the Rorippa fossil, a minimum of K2P sequence divergences of 1.8% (trnT/L spacer, trnL intron) and 4.4% (ITS), respectively, observed between Rorippa and Cardamine taxa analyzed (Franzke et al., 1998
), might then correspond to 2.55 x 106 (million) years ago (Myra), as a rough estimate for divergence time between Rorippa and Cardamine. Thus, 1% sequence divergence corresponds to 0.61.1 x 106 (million) years (Myr) for the ITS regions and 1.32.8 Myr for the cpDNA. Our calibrated ITS rates are in the same order of magnitude as recently published ITS rates, e.g., Gossypium: ca. 1% = 1 Myr (Wendel et al., 1995b
), Gentianalla 1% = 0.61.1 Myr (von Hagen and Kadereit, 2001
), Soldanella 1% = 0.61.3 Myr (Zhang et al., 2001
), Robinsonia 1% = 0.6 Myr (Sang et al., 1995b
), and are thus reasonable.
Sequence divergence among the Australian/New Zealand species ranged from 0 to 1.2% (0.5% mean) for the trnT/L spacer and trnL intron. The ITS divergence ranged from 0.2 to 3.4% (1.2% mean) and from 0 to 1.1% (0.5% mean) among the Australian/New Zealand species of lineage A and C (Fig. 2), respectively. By using the ITS substitution rate calibrated with Cardamine/Rorippa (see above), we roughly estimated an age of 0.71.3 Myr and 0.30.55 Myr for the Australian/New Zealand species of lineage C and A, respectively. As we had to reject a tree-wide constant rate of ITS, the deviating divergence values of these two lineages might result from rate heterogeneity and reticulation between basal lineages. Although noncoding cpDNA evolution (even within the Australia/New Zealand clade) was not clocklike, the estimated age for the Australian/New Zealand lineage ranges from 0.6 to 1.4 Myr. Our time estimates based on ITS and cpDNA data are in the same order of magnitude indicating a Quaternary origin of Australian/New Zealand Lepidium species.
| DISCUSSION |
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Two nuclear genomes in Australian/New Zealand Lepidium
Judged from the cpDNA phylogeny all Australian/New Zealand species harbor a cpDNA type most closely related to that of Californian species, and they are grouped into clade B in 60% of maximally parsimonious trees (Fig. 2). The cpDNA mean sequence divergence values of 0.48% between species from California and Australia/New Zealand compared to the 0.92% sequence divergence observed between Australian/New Zealand species of clade B and South American species, i.e., L. bonariense, L. meyenii, and L. quitense, also supports this close relationship between Californian and Australian/New Zealand species. However, the ITS data provides strong evidence that some Australian/New Zealand Lepidium species contain the nuclear genome of the Californian species (clade C), while others have the nuclear genome of the South African lineage (clade A). The predominance of a distinct ITS type within each Australian lineage (clade C and A), respectively, may be explained by rapid bidirectional concerted evolution following ancient hybridization between species from California and South Africa. The cpDNA data indicates that species of a Californian lineage represented by, e.g., L. dictyotum was the most probable maternal parent of the Australian /New Zealand species, both groups sharing a similar cp-genome. The ITS data confirms this Californian lineage to be among the parental taxa but also indicates that South African species (e.g., L. africanum, etc.) were also involved. The hybridogenous genomic constitution of Australian/New Zealand Lepidium species can also be observed directly in ITS sequences. Nucleotide additivity at three nucleotide sites (Fig. 1) in the ITS regions Australian/New Zealand Lepidium s.s. species indicates that reticulate evolution has occurred as has been demonstrated in Paeonia (Sang et al., 1995a
) and that parental taxa of both continents were involved. The Australian/New Zealand species of clade C and A show with one exception exactly those character states of the Californian or South African species, respectively (Fig. 1). Thus, concerted evolution via gene conversion or unequal crossing-over is apparently operating. The observation of (nearly) homogenous ITS sequences (Fig. 1) indicates (nearly) complete uni- or bidirectional homogenization or transition stages in the homogenization process of the ITS region in the alloploids, respectively (Wendel et al., 1995a
; Campbell et al., 1997
).
Based on PI intron sequences Lee et al. (2002)
demonstrated that many polyploid taxa harbored two or more phylogenetically distinct sequences, confirming a hybrid nature of Australian/New Zealand taxa. The PI intron types of presumed parental taxa of Australian/New Zealand Lepidium (i.e., L. nitidum, L. dictyotum) were also detected in three of nine Australian/New Zealand species, representing clade A and C taxa of the ITS phylogeny (Fig. 2). The remaining six Australian/New Zealand species covered by the PI study were not characterized by a Californian specific (i.e., L. nitidum, L. dictyotum) PI intron type. Furthermore, a South African origin of the nuclear genome of some Australian/New Zealand species demonstrated in the current ITS study was not found in the PI intron analysis (Lee et al., 2002
), but, in the PI study only one South African taxon was analyzed. These discrepancies might be explained by rapid genomic change and gene loss in the polyploids (Soltis and Soltis, 1995
; Song et al., 1995
). For instance, restricted fragment length polymorphism (RFLP) analysis with PI in those Australian species with only a single PI sequence type (e.g., L. hyssopifolium, L. oleraceum) found two loci in both species, meaning one of the homeologues of PI (that putatively being related to the African lineage) was not detected by PCR due to either rapid mutation in the process of pseudogenization of sequences of two homeologous loci via concerted evolution or recombination or gene loss (Wendel, 2000
; Kashkush et al., 2002
). Other discrepancies of species relationships between the cpDNA/ITS and PI intron studies might also be explained by hybridization followed by these mechanisms of rapid genome change, although lineage sorting of PI intron in some Lepidium species cannot be ruled out as another possible cause. In the long run, in order to elucidate the entire reticulate history of Lepidium species, we will need to sequence further single copy nuclear genes.
Bicontinental hybrid origin of Australian/New Zealand Lepidium s.s
We suggest that Australian Lepidium species are hybrids derived from a cross between colonizing species of the Californian and South African lineages C and A, respectively. Uniform/similar cpDNA and ITS sequences within the lineages containing Australian/New Zealand Lepidium taxa indicate that this ancient hybridization scenario predated the rapid speciation within these lineages. These speciation events probably also include later hybridization events as evidenced from grouping of species in the cpDNA tree (i.e., L. naufragorum, L. banksii, L. flexicaule, L. oleraceum) that are distributed among the two different clades A and C in the ITS tree (Fig. 2). The question of whether polyploid Australian/New Zealand Lepidium are homoploid or alloploid hybrids cannot be answered from our data. The very few South African and Californian species from which chromosome numbers are known are L. africanum (2n = 2x = 16) and L. dictyotum, L. latipes, L. nitidum, (all 2n = 4x = 32), respectively. We generally used herbarium specimens in the current study and thus the ploidy level of Californian and South African Lepidium could not be analyzed. Until this point is clarified, one may suggest that the parental species were perhaps polyploid as polyploidy may have facilitated the establishment of the colonizing taxa from California and South Africa prior to hybridization. This is an attractive hypothesis because polyploidy may confer various characteristics appropriate to colonizing organisms including self-compatibility and buffering the effects of selfing (i.e., inbreeding depression), better vigor, and broader ecological tolerance (Barrier et al., 1999
; Miller and Venables, 2000
). Indeed, based on PI intron sequences, L. nitidum is suggested to be an allopolyploid (Lee et al., 2002
).
The most attractive hypothesis is that the ancient hybridization event occurred in Australia. This implies one dispersal from South Africa and California, respectively. Dispersal from California to South Africa and subsequent hybridization with an endemic taxon (or vice versa) followed by transoceanic migration of the hybrid to Australia may not be excluded. But this scenario is less parsimonious because it requires independent introductions by long-distance dispersals of the different ITS types found in recent Australian/New Zealand taxa.
The origin of Lepidium and of the Brassicaceae as a whole presumably occurred in an area encompassing the Mediterranean and the Irano-Turanian territory, a region extremely diverse ecologically, altitudinally, and geologically (Thellung, 1906
; Mummenhoff et al., 2001
). Fossil data, easy dispersible mucilaginous seeds, widespread autogamy and polyploidy, and low levels of cpDNA divergence between species from different continents or islands suggest a rapid radiation of Lepidium by long-distance dispersal in the Pliocene/Pleistocene (Mummenhoff et al., 2001
). As a consequence of climatic changes in this geological epoch, arid/semiarid regions were established, providing favorable conditions for the radiation of Lepidium worldwide. South Africa was reached by the "arid corridor," a belt of dry country that stretched from the Horn of Africa to Namibia (Hedge, 1976
; Jürgens, 1997
), and immigration of Lepidium into North and subsequently South America in Quaternary times is compatible with our estimates of divergence times, based on cpDNA sequence data (Mummenhoff et al., 2001
).
There are several genera centred in southern Africa with a few species in Australia, e.g., Bulbine (Asphodeliaceae), Wurmbea (Colchicaceae), Caesia (Hemerocallidaceae), Spiloxene (Hypoxidaceae), and Dietes (Iridaceae). In a phylogenetic analysis of Pelargonium (Geraniaceae) the close relationship between the South African and Australian species is caused by long-distance dispersal to Australia, probably as recent as the late Pliocene (Bakker et al., 1998
). In the other cases mentioned above the possibility of recent dispersal across the Indian Ocean has not been confirmed, but it seems unlikely that the distributions date to the Jurassic, which is when the continents were last physically connected via Antarctica.
Our data provide evidence that Australian/New Zealand Lepidium are polyploid descendants of two different continental ancestors, one probably immigrating from California and the other from South Africa. Long-distance dispersal of colonizing species from California and South Africa to Australia/New Zealand seems unlikely given that these areas are currently separated by more than 10 000 km, respectively. Carlquist (1983)
however, demonstrated intercontinental dispersal (California to Chile) of mucilaginous Lepidium seeds adhering to birds (Mummenhoff et al., 1992
; Norton et al., 1997
) and sea bird migration pathways between coastal California and Australia/New Zealand and between South Africa and Australia/New Zealand (Lincoln et al., 1998
) are fully compatible with the proposed colonization scenario.
Time of origin
Calibration of our molecular trees by using Rorippa fossil data yield ages of approximately 0.71.3 Myr and 0.30.55 Myr for the Australian/New Zealand species of clade C and A, respectively. These age differences might slightly modify our hypothesis that the hybridization of more or less concurrently arriving Californian and South African ancestors predates the radiation of Australian/New Zealand species. Different estimates of time of origin of Australian/New Zealand representatives of clades A and C, respectively, might indicate that the diversification of Californian ancestors in Australia predates a chloroplast transfer into a later arriving South African colonizing species. The evidence against this scenario is the additive sequences in L. aschersonii and L. muelleriferdinandi (Fig. 1). Of course, another possibility is that the A-clade nucleotides in these two species were acquired later by secondary hybridization between clades A and C in Australia and are not relicts of an original hybridization. This would be more consistent with the dating analyses. However, this discrepancy in time estimations may simply be explained by the observed rate heterogeneity between these two lineages and across the whole ITS tree. The low levels of cpDNA and ITS sequence divergence and unresolved topologies within Australian/New Zealand species (due to low numbers of nucleotide substitutions) suggest a rapid and recent radiation of Lepidium after the hybridization event. This coincides with dramatic climatic fluctuations of the Quaternary when a cooling climate and the formation of a more mountainous landscape in New Zealand and a drying trend in Australia may have created novel habitats and thus highly invasible terrain (Markgraf et al., 1995
; McGlone et al., 2001
). This could have provided the necessary ecological space into which Lepidium could have radiated.
Distribution of Australian/New Zealand clade A and C species coincides with rainfall distribution
One of the most important determinants of vegetation types in Australia is the total amount of rainfall (Groves, 1999
). The two Australian/New Zealand lineages reflecting the different continental origins occupy more or less different habitats in Australia and New Zealand, and this reflects the habitats of these clades in their continents of origin. Californian Lepidium of clade C are annual plants of saline areas and are found in open habitats near streams, vernal pools, and margins of salt marshes (Hitchcock, 1936
; Rollins, 1993
), and this also generally applies to the Australian members of the clade. Most Australian species of group C and one New Zealand species (with three subspecies) are typically distributed in arid/semiarid areas of Australia and dry inland regions of New Zealand, respectively. Beadle (1981)
suggested that the dry inland taxa (including Lepidium) were derived from saline and subsaline habitats along the Australian coast. In littoral habits salinity and soil type may impose physiological conditions similar to those of arid areas. One could speculate that seabirds migrating from coastal saline marshes in California might have transported seeds to equivalent habitats in Australia. This leads to the hypothesis that coastal species in Australia or New Zealand are reported to be salt tolerant (e.g., L. aschersonii, Hewson, 1981
; Norton et al., 1997
) and such species might be among the first descendants of the colonizing scenario.
The annual life form typically found in Australian species of group C is generally far more abundant in the arid areas than in any other Australian climate, and the annual habit appears to be a preadaptation to the erratic rainfall (Beadle, 1981
). African clade A species occur in a wide range of habitats from subalpine areas in Lesotho to semi-desert habitats on the central plateau to winter-rainfall areas in the Cape Floristic Region. As all the South African species fall together in one unresolved group in the cpDNA tree and along with Australian/New Zealand species in the ITS phylogeny, we cannot establish which South African species is sister to the Australian/New Zealand clade. New Zealand species are coastal whereas Australian species are distributed along the mesic margins of southeast Australia. These areas receive more rain than the inland with a substantial portion of the rain in winter, similar to southern South Africa. Southeast Australia and New Zealand have a diverse invasive flora derived from South Africa (Hewson, 1981
; Marchant et al., 1987
; Carr, 1993
). Australian/New Zealand members of group A are typically perennial herbs (Hewson, 1981
) as are the South African species (Marais, 1970
; Jonsell, 1975
). African and Australian members of Group A are difficult to distinguish morphologically, and L. africanum has been repeatedly confused with L. hyssopifolium and L. pseudohyssopifolium (Ryves, 1977
; Hewson, 1981
). Lepidium africanum, a highly successful weed in Australia, is found in the same area as Australian members of clade A. African species (L. africanum, L. divaricatum), along with Australian relatives of clade A, are naturalized in New Zealand (Webb et al., 1988
), and South African species (L. africanum, L. divaricatum, L. capense, L. schinzii) are even adventive in the British Islands. Thus, South African Lepidium appeared to be successful colonizers both in the present and in the past, and apparently they transmitted these capabilities to their Australian descendants.
Origin of New Zealand Lepidium s.s
There is insufficient resolution on our molecular trees to disentangle the migration patterns and directions across the Tasmanian Sea. Some species are common between New Zealand and Australia (e.g., L. hyssopifolium, L. pseudohyssopifolium, L. pseudotasmanicum, L. flexicaule, L. desvauxii). Lepidium desvauxii is native to southeast Australia, Tasmania, and probably New Zealand; L. flexicaule is native to New Zealand and Tasmania, whereas Australian L. pseudotasmanicum and L. pseudohyssopifolium are naturalized in New Zealand (Hewson, 1981
; Webb et al., 1988
). This indicates recent and possibly frequent dispersal across the Tasmanian Sea, probably by coastal and wetland birds (McGlone et al., 2001
).
There is extensive documentation of dispersal between New Zealand and Australia, and possibly in both directions, for a wide range of both monocots and dicots, e.g., Rytidosperma (Linder and Walsh, 1995
), Hebe (Garnock-Jones, 1993
), and alpine plants in general (Raven, 1973
). Recently it was suggested that the New Zealand flora has been predominantly formed by long-distance dispersal from or via Australia during the Late Miocene to the Pleistocene period followed by speciation into characteristic New Zealand types (Pole, 1994
; McGlone et al., 2001
; Winkworth et al., 2002
) and that this applies particularly to the herbaceous species such as Lepidium (Mitchell and Heenan, 2000
). Then the presence of New Zealand endemic taxa within ITS clades A and C, respectively, and among two subclades within clade B (cpDNA tree) would suggest that there have been at least two dispersals and colonizations to New Zealand.
Do they look like hybrids?
To seek morphological confirmation of the hybrid origin of all Australian/New Zealand Lepidium s.s. species from Californian and South African parental taxa, we analyzed those characters that differ between those taxa representing descendents of the parental lineages in hybrid polyploid Australian/New Zealand Lepidium species. Two characters showed additivity of character states. Fruit valves of South African (clade A) taxa are veinless whereas fruits of the Californian (clade C) taxa are characterized by veins. The Australian/New Zealand species show either of these contrasting character states: L. pseudopapillosum fruit is veined, whereas all other Australian/New Zealand taxa have veinless fruits. A second morphological fruit character distinguishing the parental lineages (stylus present or absent) is even more equally distributed among Australian/New Zealand taxa. Fruits of South African Lepidium taxa are characterized by the presence of a stylus whereas fruits of the Californian taxa have a sessile stigma. Ten and five species of the Australian/New Zealand taxa are characterized by either one character state, respectively, and three Australian taxa (L. fasciculatum, L. desvauxii, L. pseudohyssopifolium) are polymorphic for this character. This pattern does not follow the distribution of Australian/New Zealand species in the ITS tree. Such additivity of character states in the presumed hybrid taxa might therefore reflect morphologically the hybrid origin of the Australian/New Zealand Lepidium s.s. species.
| FOOTNOTES |
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6 Mummenhoff{at}biologie.uni-Osnabrueck.DE ![]()
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