Phylogenetic relationships among Puccinellia and allied genera of Poaceae as inferred from chloroplast DNA restriction site variation

A cladistic analysis of chloroplast DNA restriction site variation among accessions of Catabrosa P. Beauv., Phippsia (Trin.) R. Br., Sclerochloa P. Beauv., and Puccinellia Pari, resolved a monophyletic Puccinellia, with Sclerochloa as its sister group, Phippsia the sister of the Puccinellia + Sclerochloa clade, and Catabrosa situated more distantly. These results suggest that the taxonomic fusion of Phippsia and Puccinellia, which has been proposed in light of the existence of natural hybrids between them (currently recognized as the nothogenus × Pucciphippsia Tsvelev), would yield a grouping that would not be monophyletic unless Sclerochloa also was included. The set of restriction site characters that resolve these relationships provides minimal support for species groupings within Puccinellia, and the groupings that are resolved are inconsistent in some cases with species boundaries as determined by morphology and isozymes.     

Phylogenetic relationships inCrossostylis (Rhizophoraceae) inferred from restriction site variation of chloroplast DNA

Phylogenetic relationships among the nine species ofCrossostylis (Rhizophoraceae) were elucidated using cladistic analysis of restriction site variations of chloroplast DNA. As a result, this genus was found to comprise two pronounced monophyletic groups as follows:C. biflora, C. grandiflora, C. multiflora andC. sebertii; andC. cominsii, C. pachyantha, C. parksii, C. richii andC. seemannii. Moreover, the monophyly ofC. biflora, C. grandiflora andC. sebertii in the former group and the monophyly ofC. pachyantha, C. parksii, C. richii andC. seemannii in the latter group were also suggested. The molecular tree corresponded well with that inferred from morphological data and no discrepancy was recognized. Many of the floral morphological characters reflected lineage, but all seed coat characters were homoplasious. Evolutionary trends in some morphological characters were optimized on the cpDNA tree obtained. Species from New Caledonia and Polynesia were monophyletic, as were those from the Solomon Islands, Vanuatu and the Fiji Islands. All species endemic to the Fiji Islands made a cluster, and this suggests that speciation occurred from a single ancestral species on the Islands.     

Phylogenetic systematics of New WorldIpomoea (Convolvulaceae) based on chloroplast DNA restriction site variation

Chloroplast DNA restriction site variation was studied in 31 New World species ofIpomoea, representing a majority of the New World sections and series within the genus. Using 14 endonucleases, a total of 124 phylogenetically informative restriction sites was detected. Dollo parsimony, Wagner parsimony, and bootstrap methods were employed to construct phylogenetic trees and evaluate confidence intervals of monophyletic groups. With a few exceptions, groups circumscribed on the basis of morphological variation are in agreement with groupings based on restriction site variation. Relationships between subgeneric groupings, however, disagree substantially with those proposed in the past. Although conflicting hypotheses for some intersectional relationships are not presently resolvable, cpDNA restriction site analyses propose the following refinements of existing classification schemes.Ipomoea ser.Setosae is divided into distantly related groups, as is sect.Pharbitis. SeriesTyrianthinae, a proposed segregate of sect.Pharbitis, is associated with sect.Calonyction and the Tricolor complex (subg.Quamoclit).Ipomoea sect.Batatas is segregated from other herbaceous groups of the heterogeneous subg.Quamoclit sensu lato and aligned as a derivative ofI. setosa, subg.Eriospermum. To test for homology of key characters weighted in traditional schemes, morphological features were studied with respect to their distribution on lineages defined by restriction site data. Characters such as setose sepals, foliose-pubescent sepals, and erect growth habit, among others, are interpreted as having multiple origins, while 3-locular ovaries, 4-locular ovaries, and long-haired seeds have evolved only once.     

Phylogenetic relationships ofCrepidiastrum (Asteraceae) of the Bonin (Ogasawara) Islands based on chloroplast DNA restriction site variation

RFLPs of cpDNA were investigated for seven species ofCrepidiastrum, of which three are endemic to the Bonin Islands. As an outgroup for rooting the tree,Paraixeris denticulata was also examined. Approximately 350 restriction sites were surveyed using 16 restriction enzymes. A total of 26 restriction site mutations were detected, and seven of them were phylogenetically informative. Wagner parsimony analysis resulted in four most parsimonious trees. In the tree obtained, the Bonin endemics are monophyletic with four mutations and a bootstrap value of 0.98 for the branch. This result agrees with that obtained from a previous electrophoretic analysis (Ito and Ono 1990), and supports the hypothesis that the three Bonin endemics have been evolved from a common ancestor. The Bonin endemics cluster together withC. lanceolatum, suggesting that the endemics andC. lanceolatum share a common ancestor, although the bootstrap probability is not very high (0.78) and thus other possibilities cannot be rejected.     

Phylogenetic analysis of Helianthus (Asteraceae) based on chloroplast DNA restriction site data

 Chloroplast DNA (cpDNA) restriction site data were used to analyze phylogenetic relationships within Helianthus. Data from new samples were consistent with previous results and showed the genus to be a well-defined (11 site changes) lineage within subtribe Helianthinae. The affinities of 2 species, Viguiera similis and V. phenax (V. ludens) that have sometimes been included in Helianthus were shown to lie outside the genus. The two species of Phoebanthus, however, formed a phylogenetic ingroup to the perennial Helianthus. Within the genus, cpDNA data indicated that there are four distinct phylogenetic lineages. Two of the lineages each contained a single, annual species (H. agrestis and H. porteri, respectively). The remaining annual species collectively formed a third lineage (sect. Helianthus). The fourth lineage contained all of the perennial species, including those of Phoebanthus. Within the perennial lineage, there was little variation in restriction site characters. The 3 species of series Pumili formed a paraphyletic group at the base of the perennial lineage, and the 3 species of series Ciliares formed a group that was supported by a single restriction site character. Received: 2 September 1996 / Accepted: 25 October 1996     

Phylogenetic relationships in Ephedra (Ephedraceae) inferred from chloroplast and nuclear DNA sequences

Sequences of the nuclear ribosomal DNA internal transcribed spacer region 1 and the chloroplast-encoded genes maturase K and ribulose-1,5 biphosphate carboxylase large subunit were obtained from species of Ephedra (Ephedraceae) representing the geographic range and morphological diversity of the genus. Phylogenetic analyses of the DNA data indicate that relationships within the genus are better predicted by geographic region of origin than by ovulate cone characters. The sampled species with dry, winged (versus fleshy) ovulate cone bracts or single-seeded cones do not form monophyletic groups and therefore the previous classification systems of Ephedra based on these aspects of bract morphology appear to be largely unnatural. Three groups were identified among the Old World species studied, one comprising European and Mediterranean species and two including only Asian species. The sequence data suggest a possible early divergence of a New World clade of Ephedra from among the Old World groups. The South American species form a distinct clade apparently related to one of two groups of North American species, which accords with a frequent floristic pattern of close relationships between species groups in western South America and southwestern North America.     

Phylogeny ofTyphonium (Araceae) inferred from restriction fragment analysis of chloroplast DNA

The interrelationship of the ten species of the genusTyphonium and related genera in subtribe Arinae of the Araceae was inferred by chloroplast DNA restriction fragment analysis. A total of 42 site mutations were observed and 26 site mutations were shared by two or more species. A majority rule consensus tree was made by performing 100 bootstrap replicates using Wagner Parsimony. Two groups ofTyphonium were recognized significantly as monophyletic groups, i.e. 1)Typhonium larsenii andT. kunmingense, and 2)T. trilobatum, T. blumei andT. flagelliforme.     

Phylogenetic origin of Beckmannia （Poaceae） inferred from molecular evidence

The phylogenetic origin of Beckmannia remains unknown. The genus has been placed within the Chlorideae, Aveneae （Agrostideae）, Poeae, or treated as an isolate lineage, Beckmanniinae. In the present study, we used nuclear internal transcribed spacer （ITS） and chloroplast trnL-F sequences to examine the phylogenetic relationship between Beckmannia and those genera that have assumed to be related. On the basis of the results of our studies, the following conclusions could be drawn： （i） Beckmannia and Alopecurus are sister groups with high support; and （ii） Beckmannia and Alopecurus are nested in the Poeae clade with high support. The results of our analysis suggest that Beckmannia should be placed in Poeae.     

Phylogenetics and character evolution in the grass family (Poaceae): Simultaneous analysis of morphological and Chloroplast DNA restriction site character sets

A phylogenetic analysis of the grass family (Poaceae) was conducted using two character sets, one representing variation in 364 mapped and cladistically informative restriction sites from all regions of the chloroplast genome, the other representing variation in 42 informative “structural characters.” The structural character set includes morphological, anatomical, chromosomal, and biochemical features, plus structural features of the chloroplast genome. The taxon sample comprises 75 exemplar taxa, including 72 representatives of Poaceae and one representative of each of three related families (Flagellariaceae, Restionaceae, and Join-villeaceae);Flagellaria served as the outgroup for the purpose of cladogram rooting. Among the grasses, 24 tribes and all 16 subfamilies of grasses recognized by various modern authors were sampled. Transformations of structural characters are mapped onto the phylogenetic hypotheses generated by the analysis, and interpreted with respect to biogeography and the evolution of wind pollination in the grass family. A major goal of the study was to test the monophyly of several putatively natural groups, including Bambusoideae, Pooideae, Arundinoideae, and the “PACC clade” (the latter comprising subfamilies Panicoideae, Arundinoideae, Chloridoideae, and Centothecoideae), as well as to analyze the phylogenetic structure within these groups and others. Several genera of controversial placement (Amphipogon, Anisopogon, Anomochloa, Brachyelytrum, Diarrhena, Eremitis, Ehrharta, Lithachne, Lygeum, Nardus, Olyra, Pharus, andStreptochaeta) also were included, with the goal of determining their phylogenetic affinities. The two character sets were analyzed separately, and a simultaneous analysis of the combined matrices also was conducted. The combined data set also was analyzed using homoplasy-implied weights. Among major results of the combined unweighted analysis were resolution of a sister-group relationship betweenJoinvillea and Poaceae; resolution of a clade comprisingAnomochloa andStreptochaeta as the sister of all other grasses, withPharus the next group to diverge from the lineage that includes all remaining grasses; and resolution of other taxa often assigned to Bambusoideae s.l. (includingEhrharta and Oryzeae, and excluding a few other taxa as noted) as a paraphyletic assemblage, within which is nested a clade that consists ofBrachyelytrum, the PACC clade (includingAmphipogon), and Pooideae (including Brachypodieae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). Within the PACC clade,Aristida is identified as the sister of all other elements of the group; Chloridoideae, Centothecoideae, and Panicoideae are each resolved as monophyletic, the latter two being sister-groups; and the remaining Arundinoid elements constitute a paraphyletic group within which are nested these three subfamilies. Within the Pooideae, four “core tribes” (Bromeae, Hordeeae [i.e., Triticeae], Agrostideae [i.e., Aveneae], andPoeae, the latter includingSesleria) are resolved as a monophyletic group that is nested among the remaining elements of the subfamily (Brachypodieae, Meliceae, Stipeae,Anisopogon, Diarrhena, Lygeum, andNardus). A second principal goal of the analysis was to identify structural synapomorphies of clades. Among the synapomorphies identified for some of the major clades are the following: gain of a 6.4 kb inversion in the chloroplast genome inJoinvillea and the grasses; reduction to 1 ovule per pistil, gain of a lateral “grass-type” embryo, and gain of an inversion around the gene trnT in the chloroplast genome in the grasses; loss of arm cells in the clade that consists ofBrachyelytrum, Pooideae, and the PACC clade; loss of the epiblast and gain of an elongate mesocotyl internode in the PACC clade; gain of proximal female-sterile florets in female-fertile spikelets, gain of overlapping embryonic leaf margins, and gain ofPanicum- type endosperm starch grains in the clade that comprises Centothecoideae and Panicoideae; and loss of the scutellar tail of the embryo in Pooideae (in one of two alternative placements of Pooideae among other groups). These findings are consistent with an origin and early diversification of grasses as forest understory herbs, followed by one or more radiations into open habitats, concomitant with multiple origins of C₄ photosynthesis and specialization for wind pollination.     

Molecular phylogeny ofIva (Asteraceae,Heliantheae) based on chloroplast DNA restriction site variation

Iva s.str. (comprising ten species) was examined by cpDNA restriction site variation to determine phyletic relationships within the group. The results were compared with relationships proposed from other data. A total of 86 restriction site mutations was detected, 47 of which proved phylogenetically informative. A single most parsimonious tree was obtained using both Wagner and Dollo parsimony. The tree revealed three main lineages that are congruent with the three chromosome lineages (base numbers of x = 16, 17, 18). The monophyly of the x = 16 and 18 groups was supported strongly by molecular data, while the monophyly of x = 17 lineage was only supported moderately. Relationships among the three lineages indicate that the sect.Iva is paraphyletic because sect.Linearbractea is nested within it. Both morphological data and the secondary chemical data are in agreement with the proposed cpDNA phylogeny. Because of this agreement, sect.Iva is revised such that,I. axillaris was excluded and positioned within the newly proposed sect.Rhizoma. Patterns and rates of cpDNA evolution were also examined. The results indicated an uneven evolution in the chloroplast genome with different rates of cpDNA evolution in at least a few species ofIva. However, the evolutionary clock hypothesis can not be rejected within most of the lineages inIva.     

Phylogenetic relationships of subtribe Ecliptinae (Asteraceae: Heliantheae) based on chloroplast DNA restriction site data

Phylogenetic analysis of chloroplast DNA restriction site data for 76 of the 302 genera of Heliantheae sensu lato using 16 restriction endonucleases reveals that subtribe Ecliptinae is polyphyletic and that its genera are distributed in four different lineages. The ecliptinous genera Squamopappus, Podachaenium, Verbesina, and Tetrachyron (of the Neurolaeninae), along with other members of subtribe Neurolaeninae are the basalmost clades of the paleaceous Heliantheae. The mostly temperate species of subtribe Ecliptinae (exemplified by Balsamorhiza, Borrichia, Chrysogonum, Engelmannia, Silphium, Vigethia, and Wyethia) are strongly nested in a clade with the Mesoamerican monotypic genus Rojasianthe as basal. The genera characterized by marcescent ray corollas traditionally classified in subtribe Zinniinae constitute a strongly supported group sister to Acmella, Spilanthes, and Salmea. The largest clade of ecliptinous genera is the most recently derived group within Heliantheae sampled. This large group of mostly Neotropical lowland genera (variously characterized by their winged cypselae, foliaceous phyllaries, and opposite phyllotaxy and exemplified by Perymenium, Wedelia, and Zexmenia) has been and continues to be the most challenging group from a taxonomic standpoint. The study provides new insights as to their relationships that will have a positive impact in future monographic studies of the group. The genera of the Espeletiinae form a monophyletic clade and are sister to members of the Milleriinae and Melampodiinae. This result is consistent with their traditional taxonomic placement with genera such as Smallanthus with which they share a tendency for functionally staminate disc flowers. The phylogenetically enigmatic genus Montanoa is sister to Melampodium. Members of subtribe Galinsoginae are clustered in two main lineages that correspond to the traditional division of the subtribe based on pappus characteristics. There is no support for the monophyly of subtribe Galinsoginae, and the same results indicate some of its genera are paraphyletic.     

Phylogenetic relationships in the genusStylosanthes (Leguminosae) based upon chloroplast DNA variation

A detailed analysis of chloroplast DNA restriction fragment length variation was undertaken to reconstruct the maternal phylogeny of 18 taxa from both sections of the papilionoid tropical forage legume genusStylosanthes. Data were analysed by means of the computer program PAUP, using an heuristic search with Wagner parsimony. The resulting cladogram dividedStylosanthes into four separate clades, which comprised: (i) theS. guianensis complex and related species (i.e.S. gracilis, S. grandifolia andS. montevidensis); (ii)S. hispida, tetraploidS. hamata s. l.,S. sympodialis, S. humilis, S. leiocarpa, S. angustifolia and certain accesions ofS. scabra; (iii)S. calcicola, S. viscosa, diploidS. hamata s. str., andS. fruticosa, plus accessions ofS. scabra, S. capitata and one accession ofS. grandifolia; and (iv)S. macrocephala and other accessions ofS. capitata not included within clade 3. Results are generally congruent with previously established interspecific relationships and, moreover, enabled identification of putative maternal progenitors for four tetraploid taxa:S. humilis was identified as a likely maternal parent of bothS. sympodialis andS. hamata s. l.,S. viscosa as a maternal parent ofS. scabra, andS. macrocephala as a maternal parent ofS. capitata.     

Phylogenetic patterns in the genus Manihot (Euphorbiaceae) inferred from analyses of nuclear and chloroplast DNA regions

From a phylogenetic perspective, the genus Manihot can be considered as an orphan group of plants, and the scientific knowledge acquired has been mainly related to cassava, one of the most important crops in poor tropical countries. The goal of the majority of evolutionary studies in the genus has been to decipher the domestication process and identify the closest relatives of cassava. Few investigations have focused on wild Manihot species, and the phylogeny of the genus is still unclear. In this study the DNA sequence variation from two chloroplast regions, the nuclear DNA gene G3pdh and two nuclear sequences derived from the 3'-end of two cassava ESTs, were used in order to infer the phylogenetic relationships among a subset of wild Manihot species, including two species from Cnidoscolus as out-groups. Maximum parsimony and Bayesian analyses were conducted for each data set and for a combined matrix due to the low variation of each region when analyzed independently. A penalized likelihood analysis of the chloroplast region trnL-trnF, calibrated with various age estimates for genera in the Euphorbiaceae extracted from the literature was used to determine the ages of origin and diversification of the genus. The two Mesoamerican species sampled form a well-defined clade. The South American species can be grouped into clades of varying size, but the relationships amongst them cannot be established with the data available. The age of the crown node of Manihot was estimated at 6.6 million years ago. Manihot esculenta varieties do not form a monophyletic group that is consistent with the possibility of multiple introgressions of genes from other wild species. The low levels of variation observed in the DNA regions sampled suggest a recent and explosive diversification of the genus, which is confirmed by our age estimates.     

Phylogenetic analysis of Hordeum (Poaceae) as inferred by nuclear rDNA ITS sequences

Hordeum (Poaceae, Triticeae) occurs with 31 species worldwide in temperate regions, with the exception of Australasia. About 50% of the species are polyploids (4x, 6x) or occur as di- and polyploid forms. To analyze the phylogenetic relationships among diploid and polyploid taxa of the genus the nuclear rDNA internal transcribed spacer region (ITS) was analyzed for 91 accessions, representing all Hordeum species, together with 10 outgroup species. PCR products were either directly sequenced (outgroups) or cloned and eight clones per individual were analyzed. Phylogenetic analysis revealed four major clades that concur with the four genome groups in Hordeum (H, I, Xa, and Xu). Allopolyploids, putative autopolyploids, and species groups within the closely related H-genome clade could be identified. The ITS data indicate times of independent evolution of paralogous rDNA clusters on different chromosomes intermitted by sweeps of homogenization among these clusters and bi-directional homogenization of the clusters in diploids. Penalized likelihood analysis revealed an age of about 12 million years (my) for the genus and indicated the start of a rapid radiation in the H-genome group about 2.5 my ago in South America and Asia.     

Chloroplast-DNA restriction site analysis in the genus Bromus (Poaceae)

Chloroplast DNA (cpDNA) restriction site variation was examined in 32 species, representing five subgenera, of Bromus (Poaceae). Thirty-seven phylogenetically informative restriction sites were detected. Cladistic analysis of the restriction site data produced a single most-parsimonious tree of 50 steps. The cladogram indicated two major clades within the genus. One clade included B. trinii of subgenus Neobromus and species of subgenus Ceratochloa. The other was composed of subgenera Festucaria, Stenobromus, and Bromus. Within the second clade, species of subgenus Festucaria appeared in three lineages. The second clade also contained an assemblage of species belonging to subgenera Stenobromus and Bromus in a separate lineage. There was very little resolution of relationships in this assemblage since several species appeared individually in separate lineages. The cpDNA phylogenetic hypothesis did not separate species of subgenera Stenobromus and Bromus into well-defined clades as circumscribed by morphology and cytogenetics. The cpDNA tree is in agreement with the phylogenetic scheme based on traditional data in that: 1) subgenera Neobromus and Ceratochloa were the first to diverge, while Bromus and Stenobromus diverged later; 2) within the genus Bromus species with small chromosomes are ancestral; and 3) subgenera Bromus and Stenobromus probably originated from similar ancestors as Festucaria. The tree based on cpDNA data does not support that: 1) subgenera Neobromus and Ceratochloa did not have a common origin; 2) subgenus Festucaria is monophyletic; and 3) subgenera Stenobromus and Bromus are distinct entities. The mean nucleotide sequence divergence values between pairs of subgenera ranged from p = 0.0 to 0.9. These values suggest that cpDNA evolution in Bromus is slow.     

A phylogenetic analysis of chloroplast DNA restriction site variation inPoaceae subfam.Pooideae

A phylogenetic analysis was conducted on chloroplast DNA restriction site variation in 34 genera of grasses (familyPoaceae), including 28 genera from subfam.Pooideae (representing tribesAveneae, Brachypodieae, Bromeae, Meliceae, Poeae, Stipeae, andTriticeae) and representatives of three other subfamilies,Arundinoideae, Oryzoideae, andPanicoideae. Analyses of all 34 genera always distinguishedPooideae as monophyletic, regardless of which nonpooid genus functioned as outgroup; six separate analyses of all 28 pooid genera, each including one of the six nonpooid genera as outgroup, resolved five identically-constituted clades withinPooideae (in four cases), or (in the other two cases) yielded results that were less well resolved, but not in conflict with those of the other four analyses. The four best-resolved analyses distinguishedMeliceae as the earliest diverging lineage withinPooideae, andStipeae as the next. Above the point of divergence ofStipeae is a dichotomy between supertribeTriticodae (including tribesBrachypodieae, Bromeae, andTriticeae), and a clade comprisingPoeae andAveneae. The analysis supports some tribal realignments, specifically the assignment ofBriza, Chascolytrum, Microbriza, andTorreyochloa toAveneae, andArctagrostis, Catabrosa, andSesleria toPoeae. The analysis also suggests that the pooid spikelet (i.e., glumes shorter than lemmas and florets two or more) is plesiomorphic inPooideae, and that spikelets with one floret, and those with glumes longer than the first lemma, each have evolved more than once withinPooideae. Results also indicate that small chromosomes and chromosome numbers based on x=c. 10–12 are plesiomorphic withinPooideae. Alternative states of these characters (chromosomes large, chromosome numbers based on x=7) are interpreted as synapomorphies or parallelisms of clades that includeTriticodae, Aveneae, andPoeae. Lanceolate lodicule shape may be a synapomorphy of the clade that includesStipeae, Triticodae, Aveneae, andPoeae, and loss of lodicule vascularization a synapomorphy of the entirePooideae.     

Chloroplast DNA variation in the genusSecale (Poaceae)

The chloroplast genomes of 44 accessions ofSecale were surveyed for restriction site polymorphisms. The accessions were chosen to represent the geographic as well as taxonomic range of the genus. Using 12 restriction enzymes a total of 348 sites were detected. Twenty-nine mutation sites were phylogenetically informative and used in a cladistic analysis. Further, a 0.1 kb insertion separatedSecale from the outgroup species. Only the annual speciesS. sylvestre was distinct from the rest of the taxa. Cultivated rye together with both wild annual and wild perennial accessions were mixed among each other. Sequence divergence (p) among taxa ofSecale was low, varying from 0.000 to 0.005, suggesting a rather recent origin of the genus.     

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.