Chloroplast DNA Restriction Site Variation Research Articles

Relationships in Ananas and other related genera using chloroplast DNA restriction site variation.

Chloroplast DNA (cpDNA) diversity was examined using PCR-RFLP to study phylogenetic relationships in Ananas and related genera. One hundred fifteen accessions representing the seven Ananas species and seven other Bromelioideae including the neighboring monospecific genus Pseudananas, two Pitcairnioideae, and one Tillandsioideae were included in the study. Eight primers designed from cpDNA were used for generating fragments. Restriction by 18 endonucleases generated 255 variable fragments. Dissimilarities were calculated from the resulting matrix using the Sokal and Michener index and the neighbor-joining method was used to reconstruct the diversity tree. Phylogenetic reconstruction was attempted using Wagner parsimony. Phenetic and cladistic analyses gave consistent results. They confirm the basal position of Bromelia in the Bromelioideae. Ananas and Pseudananas form a monophyletic group, with three strongly supported sub-groups, two of which are geographically consistent. The majority of Ananas parguazensis accessions constitute a northern group restricted to the Rio Negro and Orinoco basins in Brazil. The tetraploid Pseudananas sagenarius joins the diploid Ananas fritzmuelleri to constitute a southern group. The third and largest group, which includes all remaining species plus some accessions of A. parguazensis and intermediate phenotypes, is the most widespread and its distribution overlaps those of the northern and southern groups. Ananas ananassoides is dominant in this sub-group and highly variable. Its close relationship to all cultivated species supports the hypothesis that this species is the wild ancestor of the domesticated pineapple. The data indicate that gene flow is common within this group and scarcer with both the first and second groups. Comparison of cpDNA data with published genomic DNA data point to the hybrid origin of Ananas bracteatus and support the autopolyploidy of Pseudananas. The Ananas-Pseudananas group structure and distribution are consistent and we propose a scenario based on the refugia hypothesis to explain our data. These results and hypotheses bring some interesting points to consider in the current discussion on Ananas taxonomy.

Evolution of Hedera (the Ivy Genus, Araliaceae): Insights from Chloroplast DNA Data

Hedera L., the ivy genus, comprises approximately 16 taxa distributed throughout Europe, North Africa, Macaronesia, and Asia. Phylogenetic relationships within Hedera were examined using chloroplast DNA restriction site variation and noncoding sequence data. The cpDNA data were compared with the published nuclear ribosomal internal transcribed spacer (ITS) data. Phylogenetic incongruence between the two data sets is evident, with no identical clades shared between the topologies. Three centers of diversification for Hedera are hypothesized: Europe, Western Asia, and the Macaronesian region, with allopolyploidization playing a major part in the evolution of Hedera. The maternal parents of the polyploid species H. hibernica, H. iberica, and H. pastuchovii are identified on the basis of the comparison of the chloroplast DNA phylogeny and the ITS topology. The diploid H. helix is supported as the maternal parent of the tetraploid H. hibernica. The comparison of the cpDNA and the ITS phylogenies also indicates that H. canariensis was the diploid maternal ancestor that hybridized with H. hibernica, resulting in the formation of H. iberica. The maternal parent of the hexaploid H. pastuchovii is perhaps H. nepalensis var. sinensis. Diversification of taxa in each region is relatively recent, as indicated by relatively low levels of sequence divergence.

Chloroplast DNA evidence for the roles of island colonization and extinction in Tolpis (Asteraceae: Lactuceae)

Tolpis consists of ∼13 species native to Africa, Europe, and Macaronesia, with at least one species endemic to each of the four major archipelagos of the Azores, Madeira Islands, Canary Islands, and Cape Verde Islands. All but two of these species develop woody stems by maturity. Chloroplast DNA restriction site variation was analyzed for all species of Tolpis and four outgroups in order to understand the patterns of island colonization and evolution of woodiness in this genus. Parsimony analyses revealed a strongly supported monophyletic Tolpis. Within the genus, the following three well-supported groups were detected: all species from the Canary Islands and Cape Verde Islands, both Azorean species, and both continental species. The Canary Island/Cape Verde clade was sister to the two continental species, and the Azorean clade was sister to this group. The two Madeiran species of Tolpis occupied the basalmost positions within the genus. When biogeography was mapped onto this phylogeny, nine equally parsimonious reconstructions (five steps each) of dispersal history were detected, which fell into two groups: eight reconstructions implied that Tolpis colonized Madeira from the continent, followed by continental extinction and subsequent continental recolonization, while one reconstruction implied that Tolpis colonized Macaronesia four times. Two of the reconstructions involving continental extinction required the least amount of overall dispersal distance. The cpDNA phylogeny also suggests that woodiness arose in the common ancestor of all extant Tolpis, followed by two independent reversals to an herbaceous habit. Assuming that one of the eight reconstructions favoring continental extinction and recolonization is true, our results suggest that Tolpis may represent the first documented example of a woody plant group in Macaronesia that has recolonized the mainland in herbaceous form.

Phylogenetic relationships in tribe Lepidieae (Brassicaceae) based on chloroplast DNA restriction site variation

Tribal and subtribal boundaries within the Brassicaceae are often artificially drawn. Most of the currently recognized tribes and subtribes are separated by only a few morphological characters. Furthermore, these characters are variable even within genera, or they conflict with one another in their distribution patterns, resulting in controversial classification systems. Therefore, tribes and subtribes as traditionally delimited may not reflect natural groups. Up to now no cladistic analysis has been performed in tribe Lepidieae. In the current study, we have analyzed restriction site variation of chloroplast DNA among 41 species representing 19 genera to get insights into phylogenetic relationships within the Lepidieae. Phylogenetic lineages derived from our chloroplast data were critically compared with the traditional concepts. Our chloroplast DNA phylogeny most easily supports the classification of genera in the system of Hayek with some modifications.

New Combinations in Tillaea (Crassulaceae)

New Combinations in Tillaea (Crassulaceae)

Phylogenetic Relationships Within Lithophragma (Saxifragaceae): Hybridization, Allopolyploidy, and Ovary Diversification

We explore phylogenetic relationships in Lithophragma through parsimony and maximum like- lihood estimation analyses of internal transcribed spacer sequences of 18S-26S ribosomal DNA. Results based on internal transcribed spacer sequences are compared with those from previous studies based on chloroplast DNA restriction site, morphological, and flavonoid variation. Phylogenetic analysis of internal transcribed spacer sequences produces a highly resolved topology with six main clades. These results suggest that three previously described species of Lithophragma are not monophyletic. Based on this topology and previous findings, two species not recognized in the most recent monograph, L. thompsonii and tetraploid L. bolanderi, are hypothesized to have arisen through hybridization and allopolyploidy, respectively. Flowers of Lithophrag- ma exhibit a diverse array of ovary positions ranging from what has been described as superior to deeply inferior. Analysis of ovary position in light of our phylogenetic results reveals a complex pattern of diversi- fication in Lithophragma. This pattern is explored through character mapping and correlation analyses and is found to be inconsistent with either an active or a passive trend toward greater inferiority. A weak relation- ship between variation in ovary position and the topological position of each taxon suggests homoplastic

Phylogenetic relationships in tribe Lepidieae (Brassicaceae) based on chloroplast DNA restriction site variation

Phylogenetic relationships in tribe Lepidieae (Brassicaceae) based on chloroplast DNA restriction site variation

Molecular Phylogeny of Artemisia Section Tridentatae (Asteraceae) Based on Chloroplast DNA Restriction Site Variation

Chloroplast DNA restriction site variation was used to examine phylogenetic relationships in Artemisia sect. Tridentatae, a complex of eleven species of woody shrubs, which are dominant components of sagebrush communities of western North America. Twenty-seven endonucleases were utilized to identify 82 variable site mutations, 27 of which were phylogenetically informative. The resulting cpDNA phylogeny indicates that sect. Tridentatae is monophyletic, with the exception of A. palmeri and A. bigelovii, two historically anomolous species. A sister-group relationship between A. palmeri and species of subg. Artemisia supports the exclusion of A. palmeri from sect. Tridentatae (subg. Seriphidium), and its inclusion within subg. Artemisia. Artemisia bigelovii, a species with heterogamous capitula, is nested within the Tridentata clade, supporting its inclusion within the section. Introgression and subsequent chloroplast capture of the Tridentatae genome by two unrelated species, A. californica and A. fihlifolia, may explain the unexpected placement of these two species in the Tridentata clade. Low cpDNA sequence divergence provides only limited resolution of phylogenetic relationships within sect. Tridentatae, indicative of a recently differentiated and/or hybridizing polymorphic species complex. In addition, the cpDNA data provide only equivocal evidence for either of two competing hypotheses regarding the origin and phylogenetic relationship of sect. Tridentatae within Artemisia s.l.

Chloroplast DNA Evidence on the Origin and Radiation of the Giant Lobelias in Eastern Africa

Chloroplast DNA restriction-site variation was surveyed for all 21 species, five non-autonymic subspecies, and six putative F1 hybrids of tetraploid giant lobelias from eastern Africa (Lobeliaceae, Lobelia subgenus Tupa section Rhynchopetalum; 95 accessions), the Brazilian L. organensis, and all four hexaploid Chilean species of section Tupa. The survey used 14 enzymes and revealed 275 synapomorphic mutations and 85 autapomorphic mutations. Morphological and biogeographical interpretation of the molecular phylogeny suggests that the giant lobelias arrived in eastern Africa on the ancient upland features of Tanzania, possibly the Uluguru Mts., as a colonist with a branched inflorescence from the Asia/Pacific region. One early lineage dispersed to southern Tanzania where it founded a clade of 14 extant species, all with unbranched inflorescences, that shows strong geographic patterns of phylogenetic relationship centered in the Western Rift, Eastern Rift, and Ethiopian mountains. Within the Branched Inflorescence clade, one lineage diversified to form five extant species restricted to the Eastern Arc mountains in Tanzania, and its sister-lineage gave rise to the morphologically and geographically heterogeneous group that includes L. organensis. Phylogenetic relationships show a pattern of movement from ancient upland features to Miocene, Pliocene, Pleistocene, and Recent volcanoes, with early diversification primarily geographic in nature, and recent speciation primarily altitudinal and predominantly upward. Simple interpretation of our evidence indicates putative instances of a relictual species, F1 hybrids, species of ancient hybrid origin, and extant ancestor-descendant (or progenitor-derivative) species pairs

Chloroplast-DNA variation in the genus Lotus (Fabaceae) and further evidence regarding the maternal parentage of Lotus corniculatus L.

To resolve the maternal parentage of the tetraploid Lotus corniculatus, restriction-site variation of chloroplast DNA (cpDNA) was studied in several accessions of that species, in the four putative parental diploid species, L. tenuis, L. alpinus, L. japonicus and L. uliginosus, and in four phylogenetically more distant diploid species, L. hispidus, L. edulis, L. ornithopodoides and Tetragonolobus maritimus var. siliquosus. Evidence of cpDNA maternal inheritance was obtained by using reciprocal controlled crosses between plants of L. corniculatus and natural tetraploid individuals of L. alpinus showing very distinct restriction patterns. Interspecific cpDNA variation in the eight Lotus species and T. siliquosus was analysed by comparing cpDNA fragment patterns produced by five restriction endonucleases and totalling 304 distinct fragments. Genetic differentiation in cpDNA was very high between the L. corniculatus group and L. hispidus on the one hand, and the three other species on the other hand. Sixteen restriction-site mutations and eight length polymorphisms were identified among the five species of the L. corniculatus group and L. hispidus, Lotus uliginosus, L. alpinus and L. japonicus showed at least six DNA changes with regard to the molecule of L. corniculatus. Accordingly, these species should be excluded as maternal progenitors of L. corniculatus. Conversely, the cpDNA of L. tenuis differed from that of L. corniculatus by only two small-length mutations. As also suggested previously from an analysis of several nuclear markers, the results reported here show decisively that L. tenuis may be considered as the most probable maternal ancestor of L. corniculatus.

Chloroplast DNA Evidence for Divergence in Ferocactus and its Relationships to North American Columnar Cacti (Cactaceae: Cactoideae)

An analysis of chloroplast DNA restriction site variation was undertaken to investigate the evolutionary divergence of Ferocactus and its possible relationship with North American columnar cacti of tribe Pachycereeae. Our chloroplast DNA study using parsimony-based phylogenetic reconstruction methods provides molecular synapomorphies to define major lineages within Ferocactus and columnar cacti of the tribe Pachycereeae. The issue of monophyly in Ferocactus remains problematic: it appears to be a paraphyletic assemblage derived from an Echinocactus-like ancestor from which three major lineages have evolved. Also, there is a lack of support for the hypothesized basal position of F flavovirens and F robustus, and no evidence was found to favor the phylogenetic relationship of Ferocactus with North American columnar cacti, in particular with Escontria chiotilla. For the columnar cacti, the study supports the monophyly of the tribe Pachycereeae as well as its two subtribes: Stenocereinae and Pachycereinae. In the Stenocereinae, Stenocerelus dumortieri was found to be in a basal position, and forms a phylogenetically distinct lineage from Stenocereus s. str. and other columnar cacti such as Escontria, Polaskia, and Myrtillocactuis. This supports the segregation of S. dumortieri from Stenocereus, and the resurrection of Isolatocereus dumortieri as a distinct genus.

Phylogenetic implications of chloroplast DNA restriction site variation in subtribes Raphaninae and Cakilinae (Brassicaceae, tribe Brassiceae)

Chloroplast DNA restriction site data was used to assess relationships among 41 taxa of the subtribes Raphaninae and Cakilinae (tribe Brassiceae, Brassicaceae). A total of 456 restriction site mutations was observed, with 237 (52%) being phylogenetically informative. Cladistic analysis, based on Wagner parsimony analysis, indicated four major clades: (i) CAKILE, (ii) CRAMBE, (iii) NIGRA lineage, and (iv) RAPA-OLERACEA lineage. The CAKILE clade was divided into two lineages: (i) Cakile, Erucaria (including Reboudia), and Didesmus (previously assigned by Schulz to the Raphaninae) and (ii) Crambella (previously assigned by Schulz to the Raphaninae). The Raphaninae as currently circumscribed is polyphyletic in origin. The cpDNA data supported separate subtribal status for Crambe (Raphaninae) and indicated two major lineages corresponding to sect. Dendrocrambe and the combined sections Crambe and Leptocrambe. Enarthrocarpus arcuatus, Enarthrocarpus lyratus, Morisia monanthos, Raphanus raphanistrum, Raphanus sativus, and Rapistrum perenne were included in the RAPA-OLERACEA lineage of subtribe Brassicinae. Ceratocnemum rapistroides, Cordylocarpus muricatus, Guiraoa arvensis, Hemicrambe fruticulosa, Kremeriella cordylocarpus, Muricaria prostrata, Otocarpus virgatus, Raffenaldia primuloides, and Rapistrum rugosum were included in the NIGRA lineage of subtribe Brassicinae. Key words: Brassicinae, Raphaninae, Cakilinae, chloroplast DNA restriction site variation, molecular systematics.

Reexamination of series relationships of South American wild potatoes (Solanaceae: Solanum sect. Petota): evidence from chloroplast DNA restriction site variation

Chloroplast DNA (cpDNA) restriction enzyme site analysis was used to test hypotheses of series and superseries affiliations of 76 taxa, representing 11 of the 13 South American series (material unavailable for two series) of wild potatoes (Solanum sect. Petota) recognized in the latest classification by Hawkes. The cladistic results, combined with those from earlier cpDNA studies of 30 taxa of the Mexican and Central American species (representing eight series; ser. Conicibaccata and ser. Tuberosa have representatives in Mexico and in South America), support four main clades for 17 of the 19 series examined in sect. Petota: (1) the Mexican and Central American diploid species, exclusive of S. bulbocastanum, S. cardiophyllum, and S. verrucosum, (2) S. bulbocastanum and S. cardiophyllum (ser. Bulbocastana, ser. Pinnatisecta), (3) South American diploid species constituting all of ser. Piurana, but also members of ser. Conicibaccata, ser. Megistacroloba, ser. Tuberosa, and ser. Yungasensia, (4) all Mexican and Central American polyploid species (ser. Longipedicellata, ser. Demissa), S. verrucosum (diploid Mexican species in ser. Tuberosa), and South American diploid and polyploid members of ser. Acaulia, ser. Circaeifolia, ser. Commersoniana, ser. Conicibaccata, ser. Cuneoalata, ser. Lignicaulia, ser. Maglia, ser. Megistacroloba, ser. Tuberosa, and ser. Yungasensia. Each of these clades contains morphologically and reproductively very diverse species, and there are no evident morphological features that unite members within a clade to therefore distinguish them. These results strongly suggest a need for a reevaluation of the series and superseries classifications of sect. Petota.

A Synopsis of Arabidopsis (Brassicaceae)

New combinations in Arabidopsis are proposed. Species previously placed in Cardaminopsis are here transferred to Arabidopsis and taxa previously recognized in Arabidopsis, other than A. thaliana and A. suecica, are excluded from the Distributions and a key to the nine species and five subspecies are presented. Based on analyses of rDNA sequences, the genus Arabidopsis as understood prior to this study is not only highly paraphyletic but also includes taxa that are distant in the Brassicaceae (unpublished results). This situation is particularly alarming given the central place that A. thaliana (L.) Heynhold plays in a myriad of current studies of genome evolution, developmental genetics, morphological evolution and development, etc. (Meyerowitz & Pruitt, 1985; Endress, 1992; Maluszynska & Heslop-Harrison, 1993; Crone & Lord, 1994; Larkin et al., 1994; Price et al., 1994; Teutonico & Osborn, 1994; Zhang & Lechowica, 1994; Tsukaya, 1995). Without a well-documented phylogenetic reconstruction of the genus and a congruent taxonomy, studies that make assumptions about its relations are likely to be inconclusive and to arrive at irrelevant conclusions. A number of recent studies (e.g., Maluszynska & Heslop-Harrison, 1993; Kamm et al., 1995; Tsukaya et al., 1997) have assumed close relationships between A. thaliana and species currently included in the genus that molecular data do not support (Price et al., 1994; O'Kane et al., 1995). The genus has been variously placed close to several other genera (Arabis, Braya, Cardaminopsis, Cymatocarpus, Drabopsis, Halimolobos, Hylandra, Microsisymbrium, Nasturtiopsis, and Neotorularia) based on morphological similarity (Hedge, 1968; Jafri, 1973; Al-Shehbaz, 1988; Ball, 1993). Rather than showing a close relationship among these genera, our work indicates that the circumscription of some of these genera and Arabidopsis is needed to better represent phylogenetic relationships. Recently, for instance, A. erysimoides has been moved to Erysimum (Al-Shehbaz, 1994), A. parvula (Schrenk) O. E. Schulz has been transferred to Thellungiella (Al-Shehbaz & O'Kane, 1995), and both A. gamosepala Hedge and A. tuemurnica Kuan & An have been placed in Neotorularia (Al-Shehbaz & O'Kane, 1997). The nomenclatural changes proposed here aim to align the taxonomy of Arabidopsis with the results of recent analyses of rDNA sequences (O'Kane et al., 1997) and on-going phylogenetic analyses. The changes given here were anticipated by both Hylander (1957) and Ball (1993). Hylander (1957: 602-603) stated that should Cardaminopsis and Arabidopsis be combined, Cardaminopsis must be dropped into the latter genus [Arabidopsis], the limits of which would thereby be considerably widened-or, perhaps more correctly, drawn in quite another way than e.g. by Schulz. Ball (1993: 322) echoed this by stating, It seems probable that Cardaminopsis should be combined with Arabidopsis, and some species of Arabidopsis may have to be removed from the enlarged genus. Furthermore, Jones (1964) suggested that Arabis cebennensis and A. pedemontana might better be placed in the genus Cardaminopsis (here Arabidopsis). These earlier morphological predictions are now strongly supported by two independent molecular studies: Price et al. (1994) using chloroplast DNA restriction site variation and rbcL gene sequences, and O'Kane et al. (1997 and unpublished) using nuclear rDNA sequences. Essentially, the nomenclatural changes proposed herein deal with the transfer of species from Cardaminopsis to Arabidopsis. Except for the nine species and five subspecies treated in this paper, all of the remaining 49 binomials variously assigned to Arabidopsis are excluded from the Work is in progress to assign those to other genera. Arabidopsis (DC.) Heynhold, in Holl & Heynhold, F1. Sachsen 1: 538. 1842; nom. cons. TYPE: Arabidopsis thaliana (L.) Heynhold. Cardaminopsis (C. A. Meyer) Hayek, F1. Steiermark 1: 477. 1908. Syn. nov. Basionym: Arabis sect. CardaNovoN 7: 323-327. 1997. This content downloaded from 207.46.13.128 on Tue, 06 Sep 2016 06:08:56 UTC All use subject to http://about.jstor.org/terms

Implications for the Phylogeny, Classification, and Biogeography of Solanum from cpDNA Restriction Site Variation

A phylogenetic analysis of Solanum based on chloroplast DNA restriction site variation confirms previous findings that Lycopersicon and Cyphomandra are derived from within Solanum. Three out of four Solanum subgenera with more than one representative in this analysis (Minon, Potatoe, Solanum) are found to be polyphyletic, suggesting that the subgeneric classification of the genus needs revision. Subgenus Leptostemonum is monophyletic within the context of our sampling. Three primary clades can be distinguished within Solanum. Clade I includes representatives of sections Archaesolanum, Dulcamara, Holophylla, Jasminosola- num, and Solanum. Clade II includes members of subgenus Potatoe (sections Basarthrum, Lycopersicon, and Petota). Clade III includes all representatives sampled from subg. Leptostemonum, sects. Allophyllum, Brevan- therum, Gemninata, Pseduocapsicum, and Cyphomandropsis, and species formerly assigned to Cyphomandra. Solanum as a whole and each of the three primary clades apppear to be New World in origin. Within Leptostemonum, African and Australian members are derived from New World ancestors.

Polyphyly of the Tuberous Lomatiums (Apiaceae): cpDNA Evidence for Morphological Convergence

Overlapping patterns of morphological variation in Lomatium have obscured interspecific relationships and thwarted attempts at infrageneric classification. However, the tuberous lomatiums, a group of 13 species mostly from the Inland Pacific Northwest of the U.S.A. and allied primarily by their thickened roots, have long been considered an informal assemblage in Lomatium, although they have received formal taxonomic recognition at the infrageneric level only once. Variation in root morphology is coupled with interspecific differences in leaf and fruit morphology, flower color, and involucel structure. To test the monophyly of the tuberous group and to examine patterns of relationship and morphological divergence among these species, a phylogenetic analysis was conducted using chloroplast DNA (cpDNA) restriction site variation. Samples of all taxa of tuberous lomatiums except the narrowly endemic L. stebbinsii were analyzed. Also included were samples of 18 other species of Lomatium, representing all but one of the morphological groups in the genus, and the related genus, Angelica. Phylogenetic trees of Lomatium were well resolved but generally weakly supported. The tuberous group is apparently polyphyletic, comprising members of at least four distinct lineages: 1) L. watsonii, associated with the L. columbianum group from the Pacific Northwest; 2) L. ambiguum, an apparent relative of several nontuberous species from California; 3) L. hendersonii, one branch of a speciose trichotomy and apparently only distantly related to other tuberous species, and 4) the remaining nine tuberous species sampled. Thus, within Lomatium, tuberous roots may have evolved in parallel several times. Developmental studies are needed to determine the mode of root thickening and the organogenesis of these storage structures.

Chloroplast DNA restriction site variation and RAPD‐analyses in Cochlearia (Brassicaceae): Biosystematics and speciation

Chloroplast DNA (cpDNA) restriction site variation (RFLP), has been analysed in the genus Cochlearia L. sections Cochlearia O.E. Schulz and Glaucocochlearia O.E. Schulz. Members of section Glaucocochlearia are clearly separated from those of section Cochlearia by 28 site mutations, thus supporting taxonomic arrangements into the two sections mentioned. RAPD studies provide further strong evidence for closer relationships among tax a within each section than between sections. CpDNA sequence divergence values in section Cochlearia are extremely low. Although 91 accessions representing 11 species have been analysed by 25 restriction enzymes, only four restriction site mutations were detected characterising six different cp genome types. Low levels of chloroplast DNA divergence would suggest that taxa of section Cochlearia are closely related and most likely have diversified recently. Polyploid Cochlearia offcinalis (2n=24), C. anglica (2n=48) and C. danica (2n=42) displayed infraspecific variation for cp genomes, which could be partly explained by multiple origin and by reticulate evolution. RAPD analyses (22 primers, 140 informative characters, ten taxa from 17 accessions) do not only strongly support these arguments but also helped to clarify speciation processes and biogeographic aspects in more detail. It is argued that South West Europe was the primary center of origin of the polyploids, second centers may be the British Isles, Iceland and locally restricted parts of Middle Europe.

The phylogenetic position of East AsianSedumspecies (Crassulaceae) based on chloroplast DNA trnL (UAA)-trnF (GAA) intergenic spacer sequence variation

SUMMARY Phylogenetic relationships of 27 Crassulaceae species, including a broad sample of 19 Sedum species, were inferred from sequence variation of the chloroplast trnL (UAA)–trnF (GAA) intergenic spacer to assess the position of alkaloid containing Asian Sedum species. The overall topology of the phylogeny fully agrees with results based on chloroplast DNA restriction-site variation. The five alkaloidal, Asian Sedum species are included in the Acre lineage. These results support Steven's and co-workers (1995) hypothesis on the distribution of alkaloids in the Crassulaceae which states that the occurrence of alkaloids is restricted to the species of the Acre lineage. Although monophyly of the Acre lineage is strongly supported, relationships within this clade are only partially resolved, probably as a result of incomplete systematic sampling.

RECONSTRUCTION OF THE EVOLUTION OF REPRODUCTIVE CHARACTERS IN PONTEDERIACEAE USING PHYLOGENETIC EVIDENCE FROM CHLOROPLAST DNA RESTRICTION-SITE VARIATION.

We reconstructed the phylogenetic history of Pontederiaceae using chloroplast DNA restriction-site variation from approximately two-thirds of the species in this family of aquatic monocotyledons. The molecular phylogeny was used to evaluate hypotheses concerning the evolution of reproductive characters associated with the breeding system. The family has four main genera, two of which (Eichhornia and Pontederia) have tristylous, predominantly outcrossing species, while two (Monochoria and Heteranthera) have enantiostylous taxa. Self-incompatibility is restricted to some but not all tristylous species. In Eichhornia and Pontederia, predominantly selfing species with small monomorphic flowers (homostyly) have been hypothesized to result from the multiple breakdown of tristyly. Restriction-site variation provided a well supported phylogeny of ingroup taxa, enabling the mapping of reproductive characters onto trees. Two contrasting optimization schemes were assessed, differing in the relative weights assigned to shifts in character states. The reconstructed sequence of floral character-state change was used to assess competing hypotheses concerning the origin and breakdown of tristyly, and the relationships between tristylous and enantiostylous syndromes. Our results indicate that the class of optimization scheme used was the most critical factor in reconstructing character evolution. Despite some topological uncertainties and difficulty in reconstructing the primitive floral form in the family, several broad conclusions were possible when an unordered, unequally-weighted optimization scheme was used: (1) tristyly originated either once or twice, while the occurrence of enantiostyly in Monochoria and Heteranthera was always found to have independent origins; (2) tristyly has repeatedly broken down leading to selfing, homostylous taxa; and (3) self-incompatibility probably arose after the origin of floral trimorphism, a sequence of events that conflicts with some evolutionary models.

Phylogenetic relationships of Thlaspi s.l. (subtribe Thlaspidinae, Lepidieae) and allied genera based on chloroplast DNA restriction-site variation

Chloroplast DNA restriction-site variation was analyzed in 30 accessions representing 20 species from the major lineages in Thlaspi s.l. (previously described as genera by Meyer 1973, 1979) and allied genera from the subtribe Thlaspidinae (Peltaria, Teesdalia, Cochlearia, Ionopsidium, Aethionema). A total of 161 variable restriction sites were detected. Phylogenetic analyses indicated a division of Thlaspi s.l. into three groups consistent with Meyer's genera Thlaspi s. str., Microthlaspi and Noccaea/Raparia. The genus Thlaspi s.l. as currently described proved to be paraphyletic because one of its major lineages, i.e. Thlaspi s. str., appeared to be more closely related to other genera (Peltaria, Teesdalia) than to the remaining lineages of Thlaspi s.l., i.e. Noccaea/Raparia and Microthlaspi. Sequence divergence values (100 x p) between the Thlaspi s.l. lineages were similar to values between these groups and related genera (Teesdalia, Peltaria), respectively. Chloroplast DNA variation was also used to assess subtribal classification of the genera studied. The cpDNA data were inconsistent with the controversial taxonomic classifications based on morphology. The molecular data would suggest that (1) the subtribe Thlaspidinae, as traditionally described, is not monophyletic; (2) the Thlaspidinae should be reduced to a group consisting of Thlaspi s. str., Peltaria, Teesdalia, Microthlaspi, Noccaea/Raparia, and that Aethionema should be excluded from the Thlaspidinae; and (3) Cochlearia and Ionopsidium represent the subtribe Cochleariinae.