Niklas Wikström

Phylogeny of Lycopodiaceae (Lycopsida) and the Relationships of Phylloglossum drummondii Kunze Based on rbcL Sequences

A cladistic analysis based on rbcL sequences from a representative sample of 12 species yields a single most parsimonious tree that supports monophyly of Lycopodiaceae, Lycopodium, and Lycopodiella. Huperzia is resolved as paraphyletic to the morphologically divergent, monotypic Australasian Phylloglossum. The Huperzia-Phylloglossum clade is strongly supported and is sister group to a Lycopodium-Lycopodiella clade. These results provide the first clear evidence for the relationships of the problematic Phylloglossum drummondii. Profound differences in life cycle and morphology between Phylloglossum and other Lycopodiaceae are interpreted in terms of pedomorphosis (specifically, progenesis) and are viewed as adaptive responses to drought and brush fire. Our results show that rbcL sequence divergence among neotropical species of the supposedly ancient genus Huperzia is extremely low and that additional data will be necessary to resolve relationships among epiphytes and ground-living species. These surprisingly low levels of sequence divergence indicate that most living species diversity within Lycopodiaceae is of relatively recent origin Our results are consistent with a late Cretaceous or early Tertiary origin and diversification of epiphytic species within Huperzia, and these events may be linked to the diversification of angiosperms.

Epiphytism and terrestrialization in tropicalHuperzia (Lycopodiaceae)

A phylogenetic analysis ofHuperzia (Lycopodiaceae) documents a single origin of epiphytism and multiple reversals to a terrestrial habit in the Neotropics. Epiphytism evolved prior to the final rifting of South America and Africa, but the origin of most modern species diversity probably postdates the Mid Cretaceous diversification of flowering plants. In this respect, the evolution ofHuperzia parallels that of many other Neotropical epiphytic groups. In the Andes, alpine terrestrial species are shown to have evolved from montane epiphytes, an event that correlates well with regional orogenesis during the Miocene. Species from Australia, New Zealand, and Tasmania show diverse relationships with SE Asian groups. Results also indicate that long distance, transoceanic dispersal is rare in these homosporous plants — accounting for less than 5% of species distributions — and that convergence in strobilus and branch morphology is widespread among Paleotropical and Neotropical epiphytes. The phylogenetic analysis is based on a sample of 63 species (c. 15% total species diversity) and data from a c. 1.1kb region of noncoding (intron and spacer sequences) plastid DNA located between thetrnL andtrnF genes.

Schizaeaceae: a phylogenetic approach

Schizaeaceae fossils have been documented throughout Mesozoic and Cenozoic deposits, but our understanding of this fossil record is hampered by uncertainties with respect to the relationships of living species. To start building a phylogenetic framework for the family, an initial phylogenetic analysis of living species using plastid rbcL nucleotide sequence data is conducted. The analysis supports Schizaea s. lat. and Lygodium monophyly, but Anemia is resolved as paraphyletic to Mohria. In the Anemia/Mohria clade, monophyly of subgenus Anemiorrhiza is supported, but Coptophyllum is resolved as paraphyletic to subgenus Anemia. In Schizaea s. lat., both Schizaea s. str. and Actinostachys are well supported and Microschizaea is grouped with Schizaea s. str., although only one Microschizaea species (Schizaea pusilla) was included. These results are largely congruent with previous morphology-based analyses. In Lygodium however, results presented contrast with recent morphological analyses highlighting the problems of identifying Lygodium subgeneric groups. Using the resulting phylogeny as a framework, putative relationships of fossil species are discussed, tentative minimum age estimates for generic crown group diversifications are made, and possible conclusions with respect to the origins of habit and habitat preferences are discussed. The fossil evidence indicates that subgeneric groups within the Anemia/Mohria clade are comparatively ancient, originating during the Early Cretaceous, and the putative placement of fossil Anemia within the crown group of living subgenus Anemiorrhiza would indicate that their calcareous habitat preference may be a relic feature that has persisted ever since the Early Cretaceous. Lygodium on the other hand appears to have passed through a diversity bottleneck. Modern species diversity probably originated in the Neogene, and the earliest fossil evidence for the origin of their vining and trailing habit comes from the placement of Miocene fossil Lygodium within the crown group of living species.

Relationships of Lycopodium and Lycopodiella Based on Combined Plastid rbcL Gene and trnL Intron Sequence Data

Abstract The relationships of Lycopodium and Lycopodiella (Lycopodiaceae) were investigated based on two plastid data sets (rbcL gene and trnL intron) from a representative sample of 21 species. Separate and combined analyses of the data reveal consistent patterns of relationship. There is strong support for monophyly of Lycopodium and Lycopodiella. There is also support for monophyly of species groups or sections sensu Øllgaard (Lycopodium, Diphasium, Magellanica, Complanata, Lycopodiella, and Campylostachys). The combined data provide new evidence of relationships between subgeneric groups. In Lycopodium, section Pseudodiphasium groups with section Magellanica, section Obscura groups with section Diphasium, and section Annotina groups with section Lycopodium. In Lycopodiella, sections Lateristachys and Caroliniana group with section Campylostachys and this group is sister to section Lycopodiella. Tentative calibration of the phylogenetic tree using fossil evidence indicates a minimum age of Early Jurassic (208 Myr) for the split between Lycopodium and Lycopodiella. Reticulate fossil spores from Upper Permian records are potentially of Lycopodium affinity and indicate that early cladogenesis in Lycopodium may be even older. An evaluation of biogeographic and phylogenetic patterns in these two genera shows a striking difference from that in Huperzia. Sections within Lycopodium and Lycopodiella have broad geographic distributions, whereas molecular data partition the much larger Huperzia group into predominantly neotropical and paleotropical clades. Communicating Editor: Alan Whittemore

Phylogeny of Isoetes (Lycopsida): resolving basal relationships using rbcL sequences

The phylogenetic relationships of Isoetes (Isoetaceae) were investigated by means of a cladistic analysis using plastid rbcL sequences and a representative sample of 18 species. The analysis supports a basal split in Isoetes separating two main groups, one including aquatic species from South America (I. bradei and I. amazonica) and West Africa (I. kersii and I. schweinfurthii), and the other including aquatic, amphibious and terrestrial species representing all major continents. Higher level relationships remain unresolved, but supported groups do conflict with previous morphology-based hypotheses. Comparatively low levels of sequence divergence indicate that the use of more rapidly evolving regions will be required to resolve higher level relationships. The phylogenetically isolated nature of Isoetes will in such analyses make standard outgroup comparisons problematic, and results presented here will in this respect prove important by providing support for choosing among alternative rooting options.

A Revised Time Tree of the Asterids : Establishing a Temporal Framework For Evolutionary Studies of the Coffee Family (Rubiaceae)

Divergence time analyses in the coffee family (Rubiaceae) have all relied on the same Gentianales crown group age estimate, reported by an earlier analysis of the asterids, for defining the upper age bound of the root node in their analyses. However, not only did the asterid analysis suffer from several analytical shortcomings, but the estimate itself has been used in highly inconsistent ways in these Rubiaceae analyses. Based on the original data, we here reanalyze the divergence times of the asterids using relaxed-clock models and 14 fossil-based minimum age constraints. We also expand the data set to include an additional 67 taxa from Rubiaceae sampled across all three subfamilies recognized in the family. Three analyses are conducted: a separate analysis of the asterids, which completely mirrors the original asterid analysis in terms of taxon sample and data; a separate analysis of the Gentianales, where the result from the first analysis is used for defining a secondary root calibration point; and a combined analysis where all taxa are analyzed simultaneously. Results are presented in the form of a time-calibrated phylogeny, and age estimates for asterid groups, Gentianales, and major groups of Rubiaceae are compared and discussed in relation to previously published estimates. Our updated age estimates for major groups of Rubiaceae provide a significant step forward towards the long term goal of establishing a robust temporal framework for the divergence of this biologically diverse and fascinating group of plants.

Historical Biogeography of the Predominantly Neotropical Subfamily Cinchonoideae (Rubiaceae): Into or Out of America?

The Rubiaceae is the fifth largest plant family and is found on all continents, mostly in (sub-)tropical regions. Despite a large representation of Rubiaceae in the Paleotropics, the subfamily Cinchonoideae has its primary distribution in the Neotropics. Within the Cinchonoideae only two tribes, Naucleeae and Hymenodictyeae, have Paleotropical centers of distribution. In this study, we used information from five chloroplast DNA markers and fossil data to investigate when the subfamily was established in the Neotropics as well as major subsequent dispersal events within and out of the Neotropics and within the Paleotropics. Our results show that the ancestor of Cinchonoideae and its sister, Ixoroideae, was present in South America during the Late Cretaceous. Dispersal to Central America was estimated to occur during the Early Paleocene, and subsequent dispersals to the Caribbean islands occurred during the Oligocene–Miocene. The ancestor of Naucleeae and Hymenodictyeae dispersed to the Paleotropics no later than the Eocene, and the findings of fossils of Cephalanthus in Europe and western Siberia support its presence in the boreotropical forests. Long-distance, trans-Pacific dispersal during the Miocene was indicated for the remaining Paleotropical Cinchonoideae.

Phylogeny of Hedyotis L. (Rubiaceae Spermacoceae): Redefining a complex Asian-Pacific assemblage

The genus Hedyotis (Rubiaceae: Spermacoceae) has long served as a repository for tropical herbaceous species that do not fit readily into other genera. Circumscribed broadly the genus becomes a highly heterogeneous assembly, but relationships of Hedyotis have been difficult to resolve and it has proven very difficult to circumscribe the genus in a more narrow sense. Here we present Bayesian phylogenetic analyses of Hedyotis using plastid (rps16, petD) and nuclear (ITS, ETS) sequence data to resolve monophyletic lineages, to test former taxonomic hypotheses, and to revise the taxa within a well-supported evolutionary framework. Four hundred and sixty-seven sequences representing 129 accessions, never previously included in any phylogenetic analyses, are newly reported. Hedyotis, as previously circumscribed, is polyphyletic, but all investigated species, except for Hedyotis coronaria, are resolved in one of three well-supported monophyletic groups. The largest clade includes all investigated species of Hedyotis from the Indian subcontinent as well as three groups of species with primarily Chinese distributions. The type species of Hedyotis (H. fruticosa) is resolved with the Indian subcontinent species and following previous suggestions this group is referred to as Hedyotis s.str. Species currently recognized under the generic names Metabolos and Pleiocraterium are resolved in Hedyotis s.str. The second-largest group comprises a series of smaller, but well-supported, clades including the Leptopetalum clade, the genus Kadua, an unnamed group distributed in Asia and the Pacific, and a large Asian group referred to here as the ExallagelDimetia clade. The third group includes a few SE Asian Hedyotis, as well as all investigated species of the genus Neanotis. Hedyotis coronaria is not closely related to other species from Asia and is resolved with Spern2acoce hispida. The analyses indicate that diplophragmous capsules and fruticosa-type seeds occur outside of Hedyotis s.str., and several species suggested to have these features are resolved in the ExallagelDimetia clade. Species suggested to have indehiscent capsules, a feature used by Bremekamp to characterize the genus Exallage, are also resolved in both the ExallagelDimetia clade and in Hedyotis s.str., but a close examination indicates that the capsules are not truly indehiscent in the Hedyotis s.str. species. One species of Metabolos and one species of Pleiocraterium are given new species names, and one species of Pleiocrateriam is transferred to Hedyotis and three species of Hedyotis are transferred to Neanotis.

The Hedyotis-Oldenlandia complex (Rubiaceae: Spermacoceae) in Asia and the Pacific : Phylogeny revisited with new generic delimitations

Hedyotis and related genera (here called the Hedyotis-Oldenlandia complex) are highly debated groups in the Rubiaceae family with no consensus to date on their generic delimitations. The present study focuses on Asian-Pacific taxa from these groups and aims at resolving taxonomic inconsistencies by describing monophyletic genera within the complex. The generic circumscriptions presented in our study are based on the phylogenetic trees of nuclear (ITS, ETS) and plastid (petD, rps16) sequence data inferred using Bayesian and maximum likelihood methods. Morphological key features of the group such as habit, fruit type, seed form, and pollen type are studied and compared with the phylogeny to characterize the clades. Based on these results, the Asian-Pacific members are placed in 14 monophyletic groups across the Hedyotis-Oldenlandia complex. Of these, we accept and circumscribe 13 monophyletic genera: Debia, Dentella, Dimetia, Edrastima, Exallage, Hedyotis, Involucrella, Kadua, Kohautia, Leptopetalum, Neanotis, Oldenlandia, and Scleromitrion. Two of these, Debia and Involucrella, are here described as new genera.

Inferring geographic range evolution of a pantropical tribe in the coffee family (Lasiantheae, Rubiaceae) in the face of topological uncertainty

In this study we explore what historical biogeographic events are responsible for the wide and disjunct distribution of extant species in Lasiantheae, a pantropical group of trees and shrubs in the coffee family. Three of the genera in the group, Lasianthus, Saldinia, and Trichostachys, are found to be monophyletic, while there are indications that the fourth, Ronabea, is paraphyletic. We also address how the uncertainty in topology and divergence times affects the level of confidence in the biogeographic reconstruction. A data set consisting of chloroplast and nuclear ribosomal DNA data was analyzed using a Bayesian relaxed molecular clock approach to estimate phylogenetic relationships and divergence times, and the dispersal-extinction-cladogenesis (DEC) method to reconstruct geographic range evolution. Our results show that the Lasiantheae stem lineage originated in the neotropics, and the group expanded its range to the palaeotropics during the Eocene, either by continental migration through the boreotropics or by transatlantic long-distance dispersal. Two cases of Oligocene/Miocene over water-dispersal were also inferred, once from the paleotropics to the neotropics within Lasianthus, and once to Madagascar, concurrent with the origin of Saldinia. A lot of the diversification within Lasianthus took place during the Miocene and may have been influenced by climatic factors such as a period of markedly warm and moist climate in Asia and the aridification of the interior of the African continent. When biogeographic reconstructions were averaged over a random sample of 1000 dated phylogenies, the confidence in the biogeographic reconstruction decreased for most nodes, compared to when a single topology was used. A good understanding of phylogenetic relationships is necessary to understand the biogeographic history of a group, bit since the phylogeny is rarely completely known it is important to include phylogenetic uncertainty in biogeographic analysis. For nodes where the resolution is uncertain, the use of a single best topology as a basis for biogeographic analysis will result in inflated confidence in a biogeographic reconstruction which may be just one of several possible reconstructions.