John G. Conran

Plastid genomes and deep relationships among the commelinid monocot angiosperms

The commelinid monocots comprise the orders Arecales (A), Commelinales (C), Poales sensu Angiosperm Phylogeny Group III (APGIII) (P), Zingiberales (Z), plus the unplaced family Dasypogonaceae (D), collectively containing numerous economically and ecologically important species and encompassing enormous morphological diversity. Commelinids are supported as monophyletic based on anatomy and molecular data; however, relationships among major commelinid groupings conflict among previous studies, representing a long‐standing problem in monocot systematics, with major implications for interpretations of character evolution. In more recent analyses, with whole‐plastome sampling largely focused on Poales, areas of conflict remain, suggesting the need for closer investigation of relationships and support. Here, we increased sampling of plastomes among non‐Poalean commelinid orders to investigate deep nodal support. Analysis of 83 plastid genes recovered relationships as ((A, D) (ZC, P)) with robust support, regardless of reconstruction method (parsimony/likelihood). However, conflict among genes was evident when grouped by genomic region. Cumulative analyses of genes ranked by decreasing numbers of informative characters indicated continued fluctuation in support, even as small genes were added to a nearly complete matrix, contrary to the expected pattern of stabilization in support. Topology tests among major commelinid groups suggested that the data were not powerful enough to reject all alternatives. This study provides clues to the limits of the plastid genome for resolving deep relationships among the commelinid monocots.

Generic relationships within and between the gymnosperm families Podocarpaceae and Phyllocladaceae based on an analysis of the chloroplast gene rbcL

Analysis of sequences of the chloroplast gene rbcL for 76 taxa of Podocarpaceae (representing all genera except Parasitaxus) and five species of Phyllocladaceae were undertaken with respect to their relationships to each other and to 28 coniferalean outgroup taxa from seven families. The results indicate that Podocarpaceae are polyphyletic unless expanded to include Phyllocladaceae. Within Podocarpaceae, Sundacarpus is placed in a clade with Prumnopitys, and Falcatifolium is paraphyletic as a basal grade to Dacrydium. Phyllocladus is in an unresloved clade with Halocarpus, Manoao/Lagarostrobos and Prumnopitys/Sundacarpus. The separation of Afrocarpus from Podocarpus and its placement instead as sister to Nageia and Retrophyllum is supported. Podocarpus s. str. is monophyletic, with both subgenera identified, albeit poorly supported. The analysis placed Lepidothamnus and Saxegothaea in an unresolved basal polytomy within the family. There were no clear outgroup relationships with the family. These results differ from the morphological clades found by Kelch (1997), and disagree strongly with his 18S-sequence-based phylogeny (Kelch 1998). However, jackknife support values indicate that although the genera are well supported, relationships both within and between them are not, suggesting that intergeneric relationships in the family require further study. There is also some congruence between our results and those of the gymnosperm 18S study by Chaw et al. (1997), although their study included only three Podocarpaceae and one Phyllocladaceae species.

New Zealand Eocene, Oligocene and Miocene Macrofossil and Pollen Records and Modern Plant Distributions in the Southern Hemisphere

The modern New Zealand flora has a relatively low number of families and genera in relation to land area, but well-preserved macrofossils and pollen from three sites in southern New Zealand suggest that the floras in Eocene, Oligocene and Miocene times were much more diverse at the generic level. At Pikopiko, Southland, a late Eocene in situ forest with fern understory was dominated by conifers, Casuarinaceae, Lauraceae, Nothofagus, Proteaceae, and mesothermal angiosperms including palms (aff. Calamus), Sapindaceae: Cupaniae and Picrodendraceae. At Newvale Mine, Southland, a leaf bed within a thick lignite seam represents leaf fossils preserved in a late Oligocene oligotrophic bog. This site demonstrates that Agathis, Dacrycarpus, Dacrydium, Halocarpus, Microcachrys, Podocarpus and Phyllocladus coexisted with diverse angiosperms including Nothofagus, Gymnostoma, Cunoniaceae, Ericaceae, Sapindaceae and several Proteaceae. Pollen data add Meliaceae, Myrtaceae, Onagraceae and Rubiaceae to the flora. At Foulden Maar, Otago, mummified leaves and flowers, including several with in situ pollen, demonstrate the existence of a diverse flora surrounding an Early Miocene lake. This site contains numerous monocot macrofossils including Astelia, Cordyline, Ripogonum and Typha, as well as the oldest fossils known for Orchidaceae and Luzuriagaceae. This flora was dominated by Lauraceae with affinities to Cryptocarya and Litsea, but other families include Araliaceae, Cunoniaceae, Elaeocarpaceae, Euphorbiaceae sensu lato, Menispermaceae, Myrsinaceae, Myrtaceae, Onagraceae, Proteaceae and Sterculiaceae. Many ferns, conifers, and Nothofagus are from lineages with Gondwanan ancestors, whereas other taxa show links to Australia (e.g., Gyrostemonaceae), New Caledonia (e.g., Beauprea) and South America (e.g., Luzuriaga, Fuchsia). Many of these taxa are now extinct in New Zealand, and therefore indicate much wider biogeographic ranges for many families and genera in the past.

New Circumscriptions and a New Family of Asparagoid Lilies: Genera Formerly included in Anthericaceae

Both molecular and morphological data have indicated that the family Anthericaceae sensu lato is polyphyletic. For example, some members have successive microsporogenesis, while others have simultaneous microsporogenesis. Anthericaceae and Lomandraceae are here formally recircumscribed. Anthenicaceae sensu stricto now includes only eight genera. Lomandraceae has fifteen genera in two informal groups: the Lomandra-group and the arthropodioids, representing genera formerly in four different families. The tribe Boryeae is raised to family status (Boryaceae). A broad concept of Phormiaceae is presented, including all the genera with trichotomosulcate pollen and Hemerocallis. The relationships of other genera are discussed. New observations on ovule structure are presented, together with a summary of existing evidence necessitating rearrangements of these taxa.

Phylogenetic relationships within the ‘core’ Laureae (Litsea complex, Lauraceae) inferred from sequences of the chloroplast gene matK and nuclear ribosomal DNA ITS regions

Abstract.A phylogenetic analysis of the ‘core’ Laureae (Litsea complex) was conducted using the chloroplast gene matK and nuclear ribosomal DNA ITS sequences to investigate generic relationships and boundaries within the complex. Despite low genetic divergence for matK, rooting of the tree with Sassafras resulted in Iteadaphne as the basal member of the complex and five resolved clades: a Neolitsea clade and then Laurus, Parasassafras, Litsea and Lindera clades in a large polytomy with unresolved Lindera sections plus Umbellularia. A combined analysis of the data (identical to the ITS results) provided a more resolved phylogeny of the Laureae, with four major lineages: the Laurus, Litsea, Lindera and Actinodaphne II clades. These clades also appear to reflect the importance of inflorescence structure and ontogeny within the Laureae, as well as data from cuticular micromorphology, but there was no support for traditional generic characters such as 2- versus 4- celled anthers. As a result, genera such as Actinodaphne, Litsea, Neolitsea and Lindera were polyphyletic in all analyses. Parasassafras was related to Sinosassafras by the matK data, but distant from it in the ITS and combined analyses.

Plastid phylogenomics and molecular evolution of Alismatales

Past phylogenetic studies of the monocot order Alismatales left several higher‐order relationships unresolved. We addressed these uncertainties using a nearly complete genus‐level sampling of whole plastid genomes (gene sets representing 83 protein‐coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter‐ and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister‐group of the rest of the order, one likelihood analysis indicated a contrasting Araceae‐sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral‐state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae.

Phylogeny and historical biogeography of Isodon (Lamiaceae): Rapid radiation in south-west China and Miocene overland dispersal into Africa

Rapid organismal radiations occurring on the Qinghai-Tibetan Plateau (QTP) and the mechanisms underlying Asia-Africa intercontinental disjunctions have both attracted much attention from evolutionary biologists. Here we use the genus Isodon (Lamiaceae), a primarily East Asian lineage with disjunct species in central and southern Africa, as a case study to shed light upon these processes. The molecular phylogeny and biogeographic history of Isodon were reconstructed using sequences of three plastid markers, the nuclear ribosomal internal transcribed spacer (nrITS), and a low-copy nuclear gene (LEAFY intron II). The evolution of chromosome numbers in this genus was also investigated using probabilistic models. Our results support a monophyletic Isodon that includes the two disjunct African species, both of which likely formed through allopolyploidy. An overland migration from Asia to Africa through Arabia during the early Miocene is proposed as the most likely explanation for the present disjunct distribution of Isodon. The opening of the Red Sea in the middle Miocene may appear to have had a major role in disrupting floristic exchange between Asia and Africa. In addition, a rapid radiation of Isodon was suggested to occur in the late Miocene. It corresponds with one of the major uplifts of the QTP and subsequent aridification events. Our results support the hypothesis that geological and climatic events play important roles in driving biological diversification of organisms distributed in the QTP area.

Family distributions in the Liliiflorae and their biogeographical implications

The Liliiflorae sensu Dahlgren, Clifford & Yeo (1985) represent ninety-one tribes in between forty-eight and fifty-six families and five orders worldwide, many of which are of restricted distribution, making them an ideal subject for biogeographic study. In order to evaluate the Liliifloraes usefulness as phytogeographic indicators, Ecogeographic Pattern comparisons (EP) and Parsimony Area of Endemicity (PAE) analyses were applied to Takhtajans (1969) biogeographic regions, using the Liliiflorae as characters. These procedures involved agglomerative clustering, multi-dimensional scaling and minimum spanning tree and parsimony analyses of the regions. The results indicate that the Liliiflorae have several centres of diversity: N and E Australia, the Cape and Madagascar and the SE Asian and Indian regions. Africa and India showed affinities with northern regions, whereas the southern Oceanian and Australasian regions were associated more with South America, although there were also links to Asia through the spread of both Laurasian and Gondwanan lily taxa into adjacent regions. The Liliiflorae show clear northern and southern taxon associations which may prove useful in the future for the re-evaluation of their past histories, as their traditional phylogenetic relationships are redefined radically by ongoing molecular systematic research.

Systematic root anatomy of Asparagales and other monocotyledons

Root anatomy of several taxa of Asparagales and some taxa formerly included in Asparagales is described in a systematic context together with a literature review. The presence of a dimorphic outer layer with long and short cells is widespread in monocotyledons, indicating that it originated early in the monocot lineage, but whereas this layer is rhizodermal in most monocotyledons, in Asparagales and Araceae it is usually hypodermal. There may be a correlation between the presence of a velamen or a persistent rhizodermis in many Asparagales and Araceae and the presence of a dimorphic hypodermal layer. Many other root anatomical characters, such as the presence of vascular bundles in the central pith and a multi-layered sclerenchymatous cylinder, are probably xeromorphic and developed convergently.

Early Eocene Ripogonum (Liliales: Ripogonaceae) leaf macrofossils from southern Australia

We present evidence that fossil leaves from an early Eocene estuarine mudstone deposit at Lowana Road in western Tasmania include the oldest records of the extant monocot genus, Ripogonum (Ripogonaceae). These fossils are similar to the extant eastern Australian and Papua New Guinean R. album R.Br. and New Zealand R. scandens J.R. et G.Forst., and are described as a new species, R. tasmanicum Conran, R.J.Carp. & G.J.Jord. The venation, cuticular and other leaf features of this fossil are included in a morphology-based phylogenetic analysis for the genus, and character evolution is discussed in relation to the ecology of the extant species and the palaeoenvironments of known Ripogonaceae fossil sites. The fossil (albeit on leaf characters) was placed close to the base of a black-fruited, Australian endemic Ripogonum clade. This suggests that the family have a long and conservative evolutionary history in association with moist forests, with the fossil locality showing palaeoclimate similar to the environments that most Ripogonum species still occupy today.