Reto Nyffeler

Contemporaneous and recent radiations of the world's major succulent plant lineages.

The cacti are one of the most celebrated radiations of succulent plants. There has been much speculation about their age, but progress in dating cactus origins has been hindered by the lack of fossil data for cacti or their close relatives. Using a hybrid phylogenomic approach, we estimated that the cactus lineage diverged from its closest relatives ≈35 million years ago (Ma). However, major diversification events in cacti were more recent, with most species-rich clades originating in the late Miocene, ≈10–5 Ma. Diversification rates of several cactus lineages rival other estimates of extremely rapid speciation in plants. Major cactus radiations were contemporaneous with those of South African ice plants and North American agaves, revealing a simultaneous diversification of several of the worlds major succulent plant lineages across multiple continents. This short geological time period also harbored the majority of origins of C4 photosynthesis and the global rise of C4 grasslands. A global expansion of arid environments during this time could have provided new ecological opportunity for both succulent and C4 plant syndromes. Alternatively, recent work has identified a substantial decline in atmospheric CO2 ≈15–8 Ma, which would have strongly favored C4 evolution and expansion of C4-dominated grasslands. Lowered atmospheric CO2 would also substantially exacerbate plant water stress in marginally arid environments, providing preadapted succulent plants with a sharp advantage in a broader set of ecological conditions and promoting their rapid diversification across the landscape.

Phylogenetic relationships in the cactus family (Cactaceae) based on evidence from trnK/ matK and trnL-trnF sequences

Cacti are a large and diverse group of stem succulents predominantly occurring in warm and arid North and South America. Chloroplast DNA sequences of the trnK intron, including the matK gene, were sequenced for 70 ingroup taxa and two outgroups from the Portulacaceae. In order to improve resolution in three major groups of Cactoideae, trnL-trnF sequences from members of these clades were added to a combined analysis. The three exemplars of Pereskia did not form a monophyletic group but a basal grade. The well-supported subfamilies Cactoideae and Opuntioideae and the genus Maihuenia formed a weakly supported clade sister to Pereskia. The parsimony analysis supported a sister group relationship of Maihuenia and Opuntioideae, although the likelihood analysis did not. Blossfeldia, a monotypic genus of morphologically modified and ecologically specialized cacti, was identified as the sister group to all other Cactoideae. The tribe Cacteae was found to be sister to a largely unresolved clade comprising the genera Calymmanthium, Copiapoa, and Frailea, as well as two large and well-supported clades. Browningia sensu stricto (excluding Castellanosia), the two tribes Cereeae and Trichocereeae, and parts of the tribes Notocacteae and Rhipsalideae formed one clade. The distribution of this group is largely restricted to South America. The other clade consists of the columnar cacti of Notocacteae, various genera of Browningieae, Echinocereeae, and Leptocereeae, the tribes Hylocereeae and Pachycereeae, and Pfeiffera. A large portion of this latter group occurs in Central and North America and the Caribbean.

Phylogenetic relationships of Malvatheca (Bombacoideae and Malvoideae; Malvaceae sensu lato) as inferred from plastid DNA sequences.

Previous molecular phylogenetic analyses have revealed that elements of the former families Malvaceae sensu stricto and Bombacaceae together form a well-supported clade that has been named Malvatheca. Within Malvatheca, two major lineages have been observed; one, Bombacoideae, corresponds approximately to the palmate-leaved Bombacaceae, and the other, Malvoideae, includes the traditional Malvaceae (the mallows or Eumalvoideae). However, the composition of these two groups and their relationships to other elements of Malvatheca remain a source of uncertainty. Sequence data from two plastid regions, ndhF and trnK/matK, from 34 exemplars of Malvatheca and six outgroups were analyzed. Parsimony, likelihood, and Bayesian analyses of the sequence data provided a well-resolved phylogeny except that relationships among five lineages at the base of Malvatheca are poorly resolved. Nonetheless, a 6-bp insertion in matK suggests that Fremontodendreae is sister to the remainder of Malvatheca. Our results suggest that the Malvoideae originated in the Neotropics and that a mangrove taxon dispersed across the Pacific from South America to Australasia and later radiated out of Australasia to give rise to the ca. 1700 living species of Eumalvoideae. Local clock analyses imply that the plastid genome underwent accelerated molecular evolution coincident with the dispersal out of the Americas and again with the radiation into the three major clades of Eumalvoideae.

Using a Null Model to Recognize Significant Co-Occurrence Prior to Identifying Candidate Areas of Endemism

EDMONDS, D., AND J. EIDINOW. 2001. Wittgenstein’s poker. HarperCollins, New York. EDWARDS, A. W. F. 1992. Likelihood. Expanded edition. Johns Hopkins Univ. Press, Baltimore, Maryland. FAITH, D. P. 1999. Review of Error and the growth of experimental knowledge. Syst. Biol. 48:675–679. FAITH, D. P., AND W. H. TRUEMAN. 2001. Towards an inclusive philosophy for phylogenetic inference. Syst. Biol. 50:331–350. FARRIS, S. J. 1983. The logical basis of phylogenetic analysis. Pages 7–36 in Advances in cladistics, Volume 2 (N. I. Platnick and V. A. Funk, eds.). Columbia Univ. Press, New York. FARRIS, J. S., A. G. KLUGE, AND J. M. CARPENTER. 2001. Popper and likelihood versus “Popper*.” Syst. Biol. 50:438–444. GAFFNEY, E. S. 1979. An introduction to the logic of phylogeny reconstruction. Pages 79–111 in Phylogenetic analysis and paleontology (J. Cracraft and N. Eldredge, eds.). Columbia Univ. Press, New York. GLOCK, H.-J. 2000. A Wittgenstein dictionary. Blackwell, Oxford, U.K. GOODMAN, N. 2001. The new riddle of induction. Pages 215–224 in Analytic philosophy, an anthology (A. P. Martinich and D. Sosa, eds.). Blackwell, Oxford, U.K. HEMPEL, C. G. 1965. Studies in the logic of explanation. Pages 245–295 in Aspects of scientific explanation and other essays in the philosphy of science (C. G. Hempel, ed.). Free Press, New York. HEMPEL, C. G. 2001. Laws and their role in scientific explanation. Pages 201–214 in Analytic philosophy, an anthology (A. P. Martinich and D. Sosa, eds.). Blackwell, Oxford, U.K. HUNG, T. 1992. Ayer and the Vienna Circle. Pages 279–300 in The philosophy of A. J. Ayer (L. E. Hahn, ed.). Open Court, La Salle, Illinois. KLUGE, A. 2001a. Parsimony with and without scientific justification. Cladistics 17:199–210. KLUGE, A. G. 2001b. Philosophical conjectures and their refutation. Syst. Biol. 50:322–330. KLUGE, A. G., AND J. S. FARRIS. 1969. Qualitative phyletics and the evolution of anurans. Syst. Zool. 18:1–32. KORNER, S. 1959. Conceptual thinking. A logical enquiry. Dover, New York. KORNER, S. 1970. Erfahrung und Theorie. Suhrkamp, Frankfurt am Main, Germany. KRIPKE, S. 2002. Naming and necessity. Blackwell, Oxford, U.K. LAKATOS, I. 1974. Falsification and the methodology of scientific research programs. Pages 91–196 in Criticism and the growth of knowledge (I. Lakatos and A. Musgrave, eds.). Cambridge Univ. Press, Cambridge, U.K. LAUDAN, L., AND J. LEPLIN. 2002. Empirical equivalence and underdetermination. Pages 362–384 in Philosophy of science. Contemporary readings (Y. Balashov and A. Rosenberg, eds.). Routledge, London. MAYHALL, C. W. 2002. On Carnap. Wadsworth, Belmont, California. NAGEL, E. 1971. Principles of the theory of probability. Pages 341–422 in Foundations of the Unity of Science, Volume I (O. Neurath, R. Carnap, and C. Morris, eds.). Univ. Chicago Press, Chicago.

The closest relatives of cacti: insights from phylogenetic analyses of chloroplast and mitochondrial sequences with special emphasis on relationships in the tribe Anacampseroteae

Recent molecular and morphological systematic investigations revealed that the cacti are most closely related to Anacampseroteae, Portulaca and Talinum of the family Portulacaceae (ACPT clade of suborder Portulacineae). A combined analysis of ndhF, matK, and nad1 sequence data from the chloroplast and the mitochondrial genomes indicates that the tribe Anacampseroteae is the sister group of the family Cactaceae. This clade, together with Portulaca, is well characterized by the presence of axillary hairs or scales. Relationships within Anacampseroteae are characterized by a grade of five species of Grahamia s.l. from North and South America, and Grahamia australiana is found to be sister to the genera Anacampseros and Avonia. A comparison of vegetative characteristics indicates an evolutionary transition from woody subshrubs to dwarf perennial and highly succulent herbs during the diversification of Anacampseroteae. Available evidence from the present investigation as well as from previously published studies suggests that a revised classification of Portulacineae on the basis of inferred phylogenetic relationships might consist of a superfamily that includes Cactaceae and the three genera Anacampseros s.l. (including Avonia and Grahamia s.l.), Portulaca, and Talinum (including Talinella), either referred to three monogeneric families or to a paraphyletic family Portulacaceae*.

Living under temporarily arid conditions - succulence as an adaptive strategy

Summary: Succulence is an adaptive strategy that allows plants to remain active during seasonal water shortage. The term was first used formally by Johann (Jean) Bauhin in 1619 to refer to plants with thick, juicy leaves. Its subsequent use and selected definitions are critically discussed, including concepts such as utilizable water, caudiciforms and pachycauls, and root succulence. A unified definition of succulence considers aspects of morphology and anatomy, ecology, and physiology. Stem succulence and the “cactus life form” are used to illustrate the parallel evolution of functional adaptations in morphology, and to contrast the obvious external similarities with the widely variable internal architecture, including the participation of different stem tissues in water storage.

Phylogenetic relationships of the durians (Bombacaceae-Durioneae or /Malvaceae/Helicteroideae/Durioneae) based on chloroplast and nuclear ribosomal DNA sequences

The circumscription and phylogenetic position of the tribe Durioneae (Bombacaceae or /Malvaceae/Helicteroideae) was investigated by supplementing a previously publishedndhF data set. The present analysis supports a narrow conception of Durioneae (excludingCamptostemon andPapuodendron) and confirms a close relationship withHelicteres, Reevesia, Ungeria, andTriplochiton (all of traditional Sterculiaceae). Phylogenetic relationships within Durioneae were inferred from a combined analysis ofndhF and ITS sequences. These data suggest thatNeesia is sister to a clade comprising all other five genera of core Durioneae, and thatCoelostegia +Kostermansia form a clade that is sister toCullenia +Boschia +Durio. Various morphological features support these relationships. However, characters usually considered diagnostic for the entirety of Durioneae, such as a densely lepidote lower leaf surface and uni- or polylocular anthers, appear to be apomorphic within this clade. Likewise, spiny fruits and large arils covering the seeds are not plesiomorphic for Durioneae, in contradiction to Corners classic Durian Theory. The phylogeny suggests that bat- and bird-pollination evolved from beetle-pollination and that this transition was coincident with extensive androecial modification. Similarities due to convergent evolution of floral traits in relation to pollination by birds and mammals probably account for the erroneous, traditional placement of Durioneae in Bombacaceae.

Variations On A Theme: Repeated Evolution Of Succulent Life Forms In the Portulacineae (Caryophyllales)

Abstract The succulent life form is a tried and true strategy for plants living in arid environments. It has evolved in many distantly related lineages comprising 12,500 species from 70 flowering plant families and has spawned remarkable radiations. Three major groups are generally recognized: (1) stem succulents (that is, leafless cactus-like growth forms), (2) leaf succulents, and (3) caudiciform and pachycaul succulents. All three lifeform groups are represented in the relatively small suborder Portulacineae. Here we suggest that this diversity provides a unique opportunity to evaluate early cactus evolution within a richer contextual framework. We briefly review what we know about the phylogenetic relationships within the suborder Portulacineae (that is, Basellaceae, Cactaceae, Didiereaceae, and Portulacaceae) and the morphology and ecology of all major Portulacineae lineages. We then outline what we believe to be key areas for future research on these understudied plants and discuss several hypothetical “pre-adaptations” and conditions in ancestral Portulacineae that may have promoted the repeated evolution of unusual succulent life forms.

Evolutionary diversification of continuous traits: phylogenetic tests and application to seed size in the California flora

Evolutionary diversification of a phenotypic trait reflects the tempo and mode of trait evolution, as well as the phylogenetic topology and branch lengths. Comparisons of trait variance between sister groups provide a powerful approach to test for differences in rates of diversification, controlling for differences in clade age. We used simulation analyses under constant rate Brownian motion to develop phylogenetically based F-tests of the ratio of trait variances between sister groups. Random phylogenies were used for a generalized evolutionary null model, so that detailed internal phylogenies are not required, and both gradual and speciational models of evolution were considered. In general, phylogenetically structured tests were more conservative than corresponding parametric statistics (i.e., larger variance ratios are required to achieve significance). The only exception was for comparisons under a speciational evolutionary model when the group with higher variance has very low sample size (number of species). The methods were applied to a large data set on seed size for 1976 species of California flowering plants. Seven of 37 sister-group comparisons were significant for the phylogenetically structured tests (compared to 12 of 37 for the parametric F-test). Groups with higher diversification of seed size generally had a greater diversity of fruit types, life form, or life history as well. The F-test for trait variances provides a simple, phylogenetically structured approach to test for differences in rates of phenotypic diversification and could also provide a valuable tool in the study of adaptive radiations.

Evolutionary plant radiations: where, when, why and how?

Radiations generating exceptionally diverse clades are a fundamental component of evolutionary diversification across all organismal groups. For plants, radiations have occurred in many different geographical and ecological settings, many different plant lineages, and atmany different times over the last 400 million years. This prevalence means that working out the causes, mechanisms and outcomes of radiations is central to understanding the evolution of plant diversity. This Special Issue of New Phytologist focuses on plant radiations and contains 19 papers spanning a vibrant mix of conceptual, methodological and empirical contributions. These papers result from the Symposium, Plant Evolutionary Radiations: Where, When, Why and How?, which took place in Z€ urich (Switzerland), 13–14 June 2014 (http://www. systbot.uzh.ch/static/congresses/radiations/). The complementary primary data that inform us about evolutionary diversification – fossils and time-calibrated molecular phylogenies – are amply represented in this Special Issue, with landmark studies using either both in combination or just one type of information. Macro-evolutionary studies have proliferated massively in recent years with the development of time-calibrated molecular phylogenies. For the first time these are revealing what had been suspected for a long time: the existence of extensive diversification rate heterogeneity through time, among lineages, and in different geographical and ecological settings. As a result, in the last decade, investigating the patterns and processes of radiations has become both possible and highly topical, and research in this area has been developing very rapidly. This Special Issue summarizes the current state of play aboutWhere,When,Why and How plant radiations happened, and the significant progress that has beenmade over the last few years since these questions were last posed (Linder, 2008). In light of these advances it is interesting to reflect upon what constitutes a radiation. This is an old and well-trodden debate (Givnish, 1997, in this issue, pp. 297–303; Sanderson, 1998; Donoghue & Sanderson, pp. 260–274) not least because the term radiation can encompass a wide spectrum of concepts. Few would disagree that most radiations involve elements of both adaptive (phenotypic trait or ecological) diversification and lineage (species) diversification (Sanderson, 1998; Donoghue & Sanderson, pp. 260–274; Losos & Mahler, 2010; but see Givnish, pp. 297–303). Somewould argue that radiationsmust constitute rapid episodes of species and/or trait diversification. The ability to quantify rates of evolution and locate rate shifts across phylogenies more precisely (reviewed by Stadler, 2013; Morlon, 2014), opens up opportunities to understand the interplay between species and trait diversification on a scale not previously envisaged (e.g. Venditti et al., 2011; Rabosky et al., 2013). With these more powerful insights come possibilities to define radiations more objectively and quantitatively (e.g. Drummond et al., 2012), but also in more specific and restrictive ways (Bouchenak-Khelladi et al., pp. 313–326; Donoghue & Sanderson, pp. 260–274). This new era of quantitative analyses argues for retaining a broad concept of what constitutes a radiation – as adopted in this Special Issue – whilst recognizing the finer conceptual distinctions, many particular types of radiations (e.g. adaptive radiation, non-adaptive radiation,mixedmodel radiations, explosive species diversification, super radiation, semi-replicated radiations, progressive radiations, convergent radiations), the potential continuities across these definitional spectra (Olsen & Arroyo-Santos, 2009), and the diverse evolutionary processes underlying radiations (Givnish, pp. 297–303).