Gregory M. Plunkett

Evolutionary Patterns in Apiaceae: Inferences Based on matK Sequence Data

Phylogenetic relationships among the genera of Apiaceae are poorly understood, and the commonly employed systems of classification of this family are widely regarded as artificial. The understand- ing of evolutionary relationships in Apiaceae has been hampered by difficulties in interpreting traditional taxonomic characters, especially fruit characters. A cladistic analysis of 53 sequences from the chloroplast gene matK was used to provide a phylogenetic perspective for interpreting evolutionary patterns and relationships in Apiaceae. Results of the analysis of mnatK sequence data are in conflict with the subfamilial and tribal treatment of Cerceau-Larrival, as well as the tribal system of Drude. matK sequence data do support much of Drudes subfamilial system, suggesting subfamilies Apioideae and Saniculoideae are largely monophyletic. The saniculoid genus Lagoecia, however, is found among the apioids and should perhaps be transferred to that subfamily. Three of the apioid genera analyzed (Bupleurum, Anginon, and Heteromorpha) are placed in basally-branching clades within subfamily Apioideae. This topology, along with evidence from morphology, anatomy, geographic distribution, and insertions and deletions in matK sequences, suggests that subfamily Apioideae may have originated in southern Africa from woody, simple-leaved ancestors. Relationships among the remaining taxa of Apioideae agree largely with other recent molecular studies, and suggest that the carpological characters used to construct older systems of classification have been prone to parallel evolution.

Tribes and clades within apiaceae subfamily apioideae: The contribution of molecular data

Phylogenetic analyses of chloroplast gene ( rbc L, mat K), intron ( rpl 16, rps 16, rpo C1) and nuclear ribosomal DNA internal transcribed spacer (ITS) sequences and chloroplast DNA restriction sites, with supplementary data from variation in size of the chloroplast genome inverted repeat, have been used to elucidate major clades within Apiaceae ( Umbelliferae ) subfamily Apioideae Drude. This paper summarizes the results of previously published molecular cladistic analyses and presents a provisional classification of the subfamily based on taxonomic congruence among the data sets. Ten tribes ( Aciphylleae M. F. Watson & S. R. Downie, Bupleureae Spreng., Careae Baill., Echinophoreae Benth., Heteromorpheae M. F. Watson & S. R. Downie, Oenantheae Dumort., Pleurospermeae M. F. Watson & S. R. Downie, Pyramidoptereae Boiss., Scandiceae Spreng. and Smyrnieae Spreng.) are erected or confirmed as monophyletic, with Scandiceae comprising subtribes Daucinae Dumort., Scandicinae Tausch and Torilidinae Dumort. Seven additional clades are also recognized but have yet to be treated formally, and at least 23 genera examined to date are of dubious tribal or clade placement. The utility of these different molecular markers for phylogenetic inference in Apioideae is compared based on maximum parsimony analyses of subsets of previously published molecular data sets. Of the six loci sequenced, the ITS region is seen to be evolving most rapidly and rbc L is the most conservative. Intermediate in rate of evolution are mat K and the three chloroplast introns; with rpl 16 and rps 16 evolving slightly faster than mat K or rpo C1. The analysis of restriction sites, however, provided 2–4 times more parsimony informative characters than any single DNA locus sequenced, with estimates of divergence just slightly lower than that of the ITS region. The trees obtained from separate analyses of these reduced data sets are consistent with regard to the major clades inferred and the relationships among them. Similar phylogenies are obtained by combining data or combining trees, representing the supermatrix and supertree approaches to phylogenetic analysis, respectively. The inferred relationship among the tribes and informally recognized major clades within Apioideae is presented.

The Evolution of Araliaceae: A Phylogenetic Analysis Based on ITS Sequences of Nuclear Ribosomal DNA

Abstract Phylogenetic analyses of ITS sequence data from 70 species and 40 genera of Araliaceae (representing all major lineages within the “core group” of the family) do not support the widely used traditional division of Araliaceae into three tribes. Tribe Aralieae (characterized by imbricate petals) is found nested within a paraphyletic Schefflerieae (whose taxa have valvate petals). There are, however, two large monophyletic groups comprising most araliad genera: the ”Aralia-Polyscias-Pseudopanax group” (which includes Aralia, Meryta, Munroidendron, Panax, Pentapanax, Polyscias, Pseudopanax, Reynoldsia, Sciadodendron, Tetraplasandra, and their close allies), and the ”Eleutherococcus-Dendropanax-Schefflera group” (including Brassaiopsis, Dendropanax, Eleutherococcus, Fatsia, Hedera, Oreopanax, Schefflera, Sinopanax, and their close allies). The ITS trees also permit a re-evaluation of several taxonomically important morphological characters (e.g., petal aestivation, leaf architecture, carpel number, and habit), and provide the opportunity to assess traditional generic delimitations in the family. Four of the largest genera appear to be either polyphyletic (Schefflera, Pseudopanax) or paraphyletic (Aralia, Polyscias), but further studies will be needed to fully re-define these complex taxa. Outgroup comparisons and the placement of Astrotricha and Osmoxylon (in basally-branching lineages in Araliaceae) help to confirm a paleotropical origin of the family. The ITS topologies suggest that biogeographic radiations into different tropical/subtropical regions and into the north and south temperate regions occurred early in the history of core Araliaceae. Temperate taxa have arisen several times independently from tropical and subtropical relatives, although a few subtropical taxa may be found nested within temperate clades (e.g., Pentapanax within Aralia). Migrations between the Old and New Worlds are also suggested for several taxa, including Aralia, Panax, Oplopanax, and the Sinopanax—Oreopanax generic pair. Communicating Editor: Alan Whittemore

Infrafamilial classifications and characters in Araliaceae: Insights from the phylogenetic analysis of nuclear (ITS) and plastid (trnL-trnF) sequence data

Abstract.Traditional classifications of Araliaceae have stressed a relatively small number of morphological characters in the circumscription of infrafamilial groups (usually recognized as tribes). These systems remain largely untested from a phylogenetic perspective, and only a single previous study has explicitly explored intergeneric relationships throughout this family. To test these infrafamilial classification systems, parsimony and Bayesian-inference analyses were conducted using a broad sampling of 107 taxa representing 37 (of the 41) genera currently recognized in core Araliaceae, plus five outgroup genera. Data were collected from two molecular markers, the internal transcribed spacers (ITS) of the nuclear rRNA genes and the intron and intergenic spacer found in the trnL-trnF region of the chloroplast genome. The results suggest that there are three major lineages of Araliaceae, and that these lineages generally correspond with the centers of diversity for the family. The Aralia and Asian Palmate groups are centered primarily in eastern and southeastern Asia, whereas the Polyscias-Pseudopanax group is found throughout the Pacific and Indian Ocean basins. Several poorly resolved lineages are placed at the base of core Araliaceae, and the geographic distributions of these clades are consistent with a hypothesized rapid radiation of Araliaceae, possibly correlated with the breakup of Gondwanaland. Comparison of molecular results with the traditional systems of classification shows almost no congruence, indicating that they inadequately reflect phylogenetic relationships. Moreover, the morphological characters employed in these classifications appear to be highly homoplastic, and are thus of little utility at the infrafamilial level.

Major lineages within Apiaceae subfamily Apioideae: a comparison of chloroplast restriction site and DNA sequence data.

Traditional sources of taxonomic characters in the large and taxonomically complex subfamily Apioideae (Apiaceae) have been confounding and no classification system of the subfamily has been widely accepted. A restriction site analysis of the chloroplast genome from 78 representatives of Apioideae and related groups provided a data matrix of 990 variable characters (750 of which were potentially parsimony-informative). A comparison of these data to that of three recent DNA sequencing studies of Apioideae (based on ITS, rpoCl intron, and matK sequences) shows that the restriction site analysis provides 2.6-3.6 times more variable characters for a comparable group of taxa. Moreover, levels of divergence appear to be well suited to studies at the subfamilial and tribal levels of Apiaceae. Cladistic and phenetic analyses of the restriction site data yielded trees that are visually congruent to those derived from the other recent molecular studies. On the basis of these comparisons, six lineages and one paraphyletic grade are provisionally recognized as informal groups. These groups can serve as the starting point for future, more intensive studies of the subfamily.

Recent advances in understanding Apiales and a revised classification

Despite the long history of recognising the angiosperm order Apiales as a natural alliance, the circumscription of the order and the relationships among its constituent groups have been troublesome. Recent studies, however, have made great progress in understanding phylo- genetic relationships in Apiales. Although much of this recent work has been based on molecular data, the results are congruent with other sources of data, including morphology and geography. A unified picture of relationships has now emerged regarding the delimitation of Apiales, which includes a core group of four families (Apiaceae, Araliaceae, Myodocarpaceae, Pittosporaceae) to which three small families are also added (Griseliniaceae, Torricelliaceae and Pennantiaceae). After a brief review of recent advances in each of the major groups, a revised classification of the order is presented, which includes the recognition of the new suborder Apiineae (comprising the four core families) and two new subfamilies within Apiaceae (Azorelloideae and Mackinlayoideae).

Expansion and Contraction of the Chloroplast Inverted Repeat in Apiaceae Subfamily Apioideae

Abstract Chloroplast DNA (cpDNA) restriction site maps for 113 species of Apiaceae (Umbelliferae) and the allied families Araliaceae and Pittosporaceae were constructed for two enzymes and examined for variation in position of JLB, the junction between the large single copy and inverted repeat regions that is typically contained within the ribosomal protein S10 operon. With the exception of one large clade in Apiaceae subfamily Apioideae, all species possess a JLB indistinguishable from that found in the vast majority of angiosperms. Within this large clade, however, at least one expansion and seven different contractions of the IR relative to the tobacco JLB were detected, each ranging in size from ∼1–16 kb. Five of the junction shifts are parsimony informative, and three support major clades delimited in earlier phylogenetic studies. In light of cladograms based on previous studies of restriction site and DNA sequencing data, the IR appears to have expanded and contracted a minimum of ten times during the evolution of Apioideae, with several presumably identical size variants occurring in parallel. The frequency and large size of JLB shifts in Apioideae cpDNAs are unprecedented among angiosperms, indicating that the subfamily represents a model system to study the mechanisms leading to large-scale expansions and contractions of the IR. Communicating Editor: Jeff H. Rettig

The demise of subfamily Hydrocotyloideae (Apiaceae) and the re-alignment of its genera across the entire order Apiales.

As circumscribed by Drude, the umbellifer subfamily Hydrocotyloideae posed a major hindrance to resolving the phylogeny of order Apiales. Previous studies have suggested its polyphyly, but have not had sufficient sampling to address the issue fully. To put an end to the out-dated concept of Hydrocotyloideae, we investigated the placement of 40 of the 42 genera once placed in the subfamily, using extensive taxon sampling across the entire order. Molecular phylogenies were constructed using plastid sequences of the rpl16 intron and the trnD-trnT regions and revealed at least six hydrocotyloid lineages dispersed across both families Apiaceae and Araliaceae. The most speciose of these clades corresponds to the recently erected subfamily Azorelloideae. Another lineage includes genera grouped in Mackinlayoideae, where relationships are well resolved. Platysace appears paraphyletic with respect to Homalosciadium, and their placement is well supported as a basal lineage in Apiaceae. The type genus, Hydrocotyle, belongs to a supported clade in Araliaceae. The placements of Hermas as sister to a clade consisting of Apiaceae subfamilies Apioideae and Saniculoideae, and of Choritaenia as sister to Lichtensteinia in a clade with affinities to both Apioideae and Saniculoideae, calls into question the circumscriptions of the two subfamilies. Finally, plastid data suggest that many former hydrocotyloid genera are non-monophyletic (e.g., Azorella, Schizeilema, and Eremocharis) and are in dire need of additional phylogenetic and taxonomic studies.

Phylogenetic Relationships in the Heterosporous Fern Genus Azolla (Azollaceae) Based on DNA Sequence Data from Three Noncoding Regions

The taxonomic history of Azolla (Azollaceae) is long and complex. Previous studies have employed morphological, cytological, and molecular data in an attempt to circumscribe the seven extant species, but none has been completely successful. In this study, we employ DNA sequence data from three noncoding regions, two derived from the plastid genome (the atpB‐rbcL and trnL‐trnF regions) and a third from the internal transcribed spacers of the nuclear rRNA genes. Cladistic analyses of these data confirm the division of Azolla into two major clades, corresponding to the traditional classification of the genus into sections Azolla and Rhizosperma. Moreover, the monophyly of A. pinnata plus A. nilotica (sect. Rhizosperma) contradicts newer classifications of the family, in which these species were placed in different subgenera. In section Azolla, DNA sequence data support several past reports in suggesting that A. rubra and A. filiculoides are distinct species and that A. caroliniana is distinct from both A. microphylla and A. mexicana. However, distinct lineages representing A. microphylla and A. mexicana were not found, and these plants appear to represent a single evolutionary lineage.

Generic relationships in Araliaceae: looking into the crystal ball

Our understanding of relationships among Apiales and within Araliaceae has progressed considerably in the last decade thanks to numerous molecular phylogenetic studies. It is now clear that traditional infrafamilial systems of classification of Araliaceae fail to reflect evolutionary relationships and that the morphological features on which they were based exhibit high levels of homoplasy. Recent studies have provided a very different picture of relationships in the family, and are rapidly converging on a consensus that allows us to review the status of the 41 genera currently recognised in Araliaceae and to consider alternative circumscriptions for those that are not monophyletic. Twenty-four small and medium-sized genera are unlikely to be modified, whereas five others ( Dendropanax , Oreopanax , Osmoxylon , Pseudopanax and Sinopanax ) may require changes in circumscription. The status of four other small genera is not yet clear, but the two largest genera will require considerable re-alignments: Polyscias (c. 150 spp.), which is paraphyletic with respect to six other genera, and the polyphyletic genus Schefflera (c. 650-900 spp.), which represents five geographically distinct clades. While it is still too early to make formal taxonomic changes to these genera, current evidence suggests that Polyscias sensu lato will likely be realigned into 5–8 geographically coherent genera, while Schefflera sensu lato will be split into 10–16 genera.