Species relationships and divergence times in beeches: new insights from the inclusion of 53 young and old fossils in a birth-death clock model.

The fossilized birth-death (FBD) model can make use of information contained in multiple fossils representing the same clade, and we here apply this model to infer divergence times in beeches (genus Fagus), using 53 fossils and nuclear sequences for all nine species. We also apply FBD dating to the fern clade Osmundaceae, with about 12 living species and 36 fossils. Fagus nuclear sequences cannot be aligned with those of other Fagaceae, and we therefore use Bayes factors to choose among alternative root positions. The crown group of Fagus is dated to 53 (62-43) Ma; divergence of the sole American species to 44 (51-39) Ma and divergence between Central European F. sylvatica and Eastern Mediterranean F. orientalis to 8.7 (20-1.8) Ma, unexpectedly old. The FBD model can accommodate fossils as sampled ancestors or as extinct or unobserved lineages; however, this makes its raw output, which shows all fossils on short or long branches, problematic to interpret. We use hand-drawn depictions and a bipartition network to illustrate the uncertain placements of fossils. Inferred speciation and extinction rates imply approximately 5× higher evolutionary turnover in Fagus than in Osmundaceae, fitting a hypothesized low turnover in plants adapted to low-nutrient conditions.This article is part of the themed issue 'Dating species divergences using rocks and clocks'.

Escape from extreme specialization: passionflowers, bats and the sword-billed hummingbird.

A striking example of plant/pollinator trait matching is found between Andean species of Passiflora with 6-14-cm-long nectar tubes and the sword-billed hummingbird, Ensifera ensifera, with up to 11-cm-long bills. Because of the position of their anthers and stigmas, and self-incompatibility, these passionflower species depend on E. ensifera for pollination. Field observations show that the bird and plant distribution match completely and that scarcity of Ensifera results in reduced passionflower seed set. We here use nuclear and plastid DNA sequences to investigate how often and when these mutualisms evolved and under which conditions, if ever, they were lost. The phylogeny includes 26 (70%) of the 37 extremely long-tubed species, 13 (68%) of the 19 species with tubes too short for Ensifera and four of the seven bat-pollinated species for a total of 43 (69%) of all species in Passiflora supersection Tacsonia (plus 11 outgroups). We time-calibrated the phylogeny to infer the speed of any pollinator switching. Results show that Tacsonia is monophyletic and that its stem group dates to 10.7 Ma, matching the divergence at 11.6 Ma of E. ensifera from its short-billed sister species. Whether pollination by short-billed hummingbirds or by Ensifera is the ancestral condition cannot be securely inferred, but extremely long-tubed flowers exclusively pollinated by Ensifera evolved early during the radiation of the Tacsonia clade. There is also evidence of several losses of Ensifera dependence, involving shifts to bat pollination and shorter billed birds. Besides being extremely asymmetric-a single bird species coevolving with a speciose plant clade-the Ensifera/Passiflora system is a prime example of a specialized pollinator not driving plant speciation, but instead being the precondition for the maintenance of isolated populations (through reliable seed set) that then underwent allopatric speciation.

Molecular cytogenetics (FISH, GISH) of Coccinia grandis : a ca. 3 myr-old species of cucurbitaceae with the largest Y/autosome divergence in flowering plants.

The independent evolution of heteromorphic sex chromosomes in 19 species from 4 families of flowering plants permits studying X/Y divergence after the initial recombination suppression. Here, we document autosome/Y divergence in the tropical Cucurbitaceae Coccinia grandis, which is ca. 3 myr old. Karyotyping and C-value measurements show that the C. grandis Y chromosome has twice the size of any of the other chromosomes, with a male/female C-value difference of 0.094 pg or 10% of the total genome. FISH staining revealed 5S and 45S rDNA sites on autosomes but not on the Y chromosome, making it unlikely that rDNA contributed to the elongation of the Y chromosome; recent end-to-end fusion also seems unlikely given the lack of interstitial telomeric signals. GISH with different concentrations of female blocking DNA detected a possible pseudo-autosomal region on the Y chromosome, and C-banding suggests that the entire Y chromosome in C. grandis is heterochromatic. During meiosis, there is an end-to-end connection between the X and the Y chromosome, but the X does not otherwise differ from the remaining chromosomes. These findings and a review of plants with heteromorphic sex chromosomes reveal no relationship between species age and degree of sex chromosome dimorphism. Its relatively small genome size (0.943 pg/2C in males), large Y chromosome, and phylogenetic proximity to the fully sequenced Cucumis sativus make C. grandis a promising model to study sex chromosome evolution.

The evolution and loss of oil-offering flowers: new insights from dated phylogenies for angiosperms and bees.

The interactions between bees that depend on floral oil for their larvae and flowers that offer oil involve an intricate mix of obligate and facultative mutualisms. Using recent phylogenies, new data on oil-offering Cucurbitaceae, and molecular-dating, we ask when and how often oil-offering flowers and oil-foraging bees evolved, and how frequently these traits were lost in the cause of evolution. Local phylogenies and an angiosperm-wide tree show that oil flowers evolved at least 28 times and that floral oil was lost at least 36-40 times. The oldest oil flower systems evolved shortly after the K/T boundary independently in American Malpighiaceae, tropical African Cucurbitaceae and Laurasian Lysimachia (Myrsinaceae); the ages of the South African oil flower/oil bee systems are less clear. Youngest oil flower clades include Calceolaria (Calceolariaceae), Iridaceae, Krameria (Krameriaceae) and numerous Orchidaceae, many just a few million years old. In bees, oil foraging evolved minimally seven times and dates back to at least 56 Ma (Ctenoplectra) and 53 Ma (Macropis). The co-occurrence of older and younger oil-offering clades in three of the four geographical regions (but not the Holarctic) implies that oil-foraging bees acquired additional oil hosts over evolutionary time. Such niche-broadening probably started with exploratory visits to flowers resembling oil hosts in scent or colour, as suggested by several cases of Muellerian or Batesian mimicry involving oil flowers.

A sex-linked SCAR marker in Bryonia dioica (Cucurbitaceae), a dioecious species with XY sex-determination and homomorphic sex chromosomes.

Genetic crosses between the dioecious Bryonia dioica (Cucurbitaceae) and the monoecious B. alba in 1903 provided the first clear evidence for Mendelian inheritance of dioecy and made B. dioica the first organism for which XY sex-determination was experimentally proven. Applying molecular tools to this system, we developed a sex-linked sequence-characterized amplified region (SCAR) marker for B. dioica and sequenced it for individuals representing the full geographic range of the species from Scotland to North Africa. For comparison, we also sequenced this marker for representatives of the dioecious B. cretica, B. multiflora and B. syriaca, and monoecious B. alba. In no case did any individual, male or female, yield more than two haplotypes. In northern Europe, we found strong linkage between our marker and sex, with all Y-sequences being identical to each other. In southern Europe, however, the linkage between our marker and sex was weak, with recombination detected within both the X- and the Y-homologues. Population genetic analyses suggest that the SCAR marker experienced different evolutionary pressures in northern and southern Europe. These findings fit with phylogenetic evidence that the XY system in Bryonia is labile and suggest that the genus may be a good system in which to study the early steps of sex chromosome evolution.

The evolution of dioecy, heterodichogamy, and labile sex expression in Acer.

The northern hemisphere tree genus Acer comprises 124 species, most of them monoecious, but 13 dioecious. The monoecious species flower dichogamously, duodichogamously (male, female, male), or in some species heterodichogamously (two morphs that each produce male and female flowers but at reciprocal times). Dioecious species cannot engage in these temporal strategies. Using a phylogeny for 66 species and subspecies obtained from 6600 nucleotides of chloroplast introns, spacers, and a protein-coding gene, we address the hypothesis (Pannell and Verdú, Evolution 60: 660-673. 2006) that dioecy evolved from heterodichogamy. This hypothesis was based on phylogenetic analyses (Gleiser and Verdú, New Phytol. 165: 633-640. 2005) that included 29-39 species of Acer coded for five sexual strategies (duodichogamous monoecy, heterodichogamous androdioecy, heterodichogamous trioecy, dichogamous subdioecy, and dioecy) treated as ordered states or as a single continuous variable. When reviewing the basis for these scorings, we found errors that together with the small taxon sample, cast doubt on the earlier inferences. Based on published studies, we coded 56 species of Acer for four sexual strategies, dioecy, monoecy with dichogamous or duodichogamous flowering, monoecy with heterodichogamous flowering, or labile sex expression, in which individuals reverse their sex allocation depending on environment-phenotype interactions. Using Bayesian character mapping, we infer an average of 15 transformations, a third of them involving changes from monoecy-cum-duodichogamy to dioecy; less frequent were changes from this strategy to heterodichogamy; dioecy rarely reverts to other sexual systems. Contra the earlier inferences, we found no switches between heterodichogamy and dioecy. Unexpectedly, most of the species with labile sex expression are grouped together, suggesting that phenotypic plasticity in Acer may be a heritable sexual strategy. Because of the complex flowering phenologies, however, a concern remains that monoecy in Acer might not always be distinguishable from labile sex expression, which needs to be addressed by long-term monitoring of monoecious trees. The 13 dioecious species occur in phylogenetically disparate clades that date back to the Late Eocene and Oligocene, judging from a fossil-calibrated relaxed molecular clock.

Melastomeae come full circle: biogeographic reconstruction and molecular clock dating.

Rhexia, with 11 species in the Coastal Plain province of North America, is the only temperate zone endemic of the tropical eudicot family Melastomataceae. It is a member of the only pantropical tribe of that family, Melastomeae. Based on the chloroplast gene ndhF, we use a fossil-calibrated molecular clock to address the question of the geographic origin and age of Rhexia. Sequences from 37 species in 21 genera representing the tribe's geographical range were analyzed together with five outgroups. To obtain better clade support, another chloroplast region, the rpl16 intron, was added for 24 of the species. Parsimony analysis of the combined data and maximum-likelihood analysis of ndhF alone indicate that the deepest split is between Rhexia plus its sister group, a small Central American genus, and all other Melastomeae. Old World Melastomeae are monophyletic and nested within New World Melastomeae. Although likelihood-ratio tests of clock and nonclock substitution models for the full or moderately pruned datasets rejected the clock, these models yielded identical topologies (for 30 taxa) with few significantly different branch lengths as assessed by a Student's t-test. Age estimates obtained were 22 million years ago (Mya) for the divergence of Rhexia from its sister group, 12 Mya for the dispersal of Melastomeae from the New World to West Africa, and 1 Mya for the diversification of Melastoma in Southeast Asia. The only other genus of Melastomeae to have reached Southeast Asia from Africa or Madagascar is Osbeckia. The age and geographic distribution of fossils, which come from Miocene sites throughout Eurasia, suggest that Melastomeae once ranged from Eurasia across Beringia to North America from whence they reached South America and subsequently Africa and Southeast Asia. Climate deterioration led to their extinction in the Northern Hemisphere, with Rhexia possibly surviving in Coastal Plain refugia.

Historical biogeography of Melastomataceae: the roles of Tertiary migration and long-distance dispersal.

Melastomataceae and Memecylaceae are pantropically distributed sister groups for which an ndhF gene phylogeny for 91 species in 59 genera is here linked with Eurasian and North American fossils in a molecular clock approach to biogeographical reconstruction. Nine species from the eight next-closest families are used to root phylogenetic trees obtained under maximum likelihood criteria. Melastomataceae comprise ∼3000 species in the neotropics, ∼1000 in tropical Asia, 240 in Africa, and 225 in Madagascar in 150-166 genera, and the taxa sampled come from throughout this geographic range. Based on fossils, ranges of closest relatives, tree topology, and calibrated molecular divergences, Melastomataceae initially diversified in Paloecene/Eocene times in tropical forest north of the Tethys. Their earliest (Eocene) fossils are from northeastern North America, and during the Oligocene and Miocene melastomes occurred in North America as well as throughout Eurasia. They also entered South America, with earliest (Oligocene) South American fossils representing Merianieae. One clade (Melastomeae) reached Africa from the neotropics 14-12 million years ago and from there spread to Madagascar, India, and Indochina. Basalmost Melastomataceae (Kibessieae, Astronieae) are species-poor lineages restricted to Southeast Asia. However, a more derived Asian clade (Sonerileae/Dissochaeteae) repeatedly reached Madagascar and Africa during the Miocene and Pliocene. Contradicting earlier hypotheses, the current distribution of Melastomataceae is thus best explained by Neogene long-distance dispersal, not Gondwana fragmentation.

Molecular phylogenetics of Melastomataceae and Memecylaceae: implications for character evolution.

Melastomataceae are among the most abundant and diversified groups of plants throughout the tropics, but their intrafamily relationships and morphological evolution are poorly understood. Here we report the results of parsimony and maximum likelihood (ML) analyses of cpDNA sequences from the rbcL and ndhF genes and the rpl16 intron, generated for eight outgroups (Crypteroniaceae, Alzateaceae, Rhynchocalycaceae, Oliniaceae, Penaeaceae, Myrtaceae, and Onagraceae) and 54 species of melastomes. The sample represents 42 of the family's currently recognized ∼150 genera, the 13 traditional tribes, and the three subfamilies, Astronioideae, Melastomatoideae, and Memecyloideae (= Memecylaceae DC.). Parsimony and ML yield congruent topologies that place Memecylaceae as sister to Melastomataceae. Pternandra, a Southeast Asian genus of 15 species of which five were sampled, is the first- branching Melastomataceae. This placement has low bootstrap support (72%), but agrees with morphological treatments that placed Pternandra in Melastomatacaeae because of its acrodromal leaf venation, usually ranked as a tribe or subfamily. The interxylary phloem islands found in Memecylaceae and Pternandra, but not most other Melastomataceae, likely evolved in parallel because Pternandra resembles Melastomataceae in its other wood characters. A newly discovered plesiomorphic character in Pternandra, also present in Memecylaceae, is a fibrous anther endothecium. Higher Melastomataceae lack an endothecium as do the closest relatives of Melastomataceae and Memecylaceae. The next deepest split is between Astronieae, with anthers opening by slits, and all remaining Melastomataceae, which have anthers opening by pores. Within the latter, several generic groups, corresponding to traditional tribes, receive solid statistical support, but relationships among them, with one exception, are different from anything predicted on the basis of morphological data. Thus, Miconieae and Merianieae are sister groups, and both are sister to a trichotomy of Bertolonieae, Microlicieae + Melastomeae, and Dissochaeteae + Blakeeae. Sonerileae/Oxysporeae are nested within Dissochaeteae, Rhexieae within Melastomeae, and African and Asian Melastomeae within neotropical Melastomeae. These findings have profound implications for our understanding of melastome morphological evolution (and biogeography), implying, for example, that berries evolved from capsules minimally four times, stamen connectives went from dorsally enlarged to basal/ventrally enlarged, and loss of an endothecium preceded poricidal dehiscence.

Repeated evolution of dioecy from monoecy in Siparunaceae (Laurales).

Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yielded almost identical topologies, which were used to trace the evolution of the two sexual systems. The African species, which is dioecious, was sister to all neotropical species, and the monoecious species formed a grade basal to a large dioecious Andean clade. Dioecy evolved a second time within the monoecious grade. Geographical mapping of 6,496 herbarium collections from all species sorted by sexual system showed that monoecy is confined to low-lying areas (altitude < 700 m) in the Amazon basin and southern Central America. The only morphological trait with a strong phylogenetic signal is leaf margin shape (entire or toothed), although this character also correlates with altitude, probably reflecting selection on leaf shapes by temperature and rainfall regimes. The data do not reject the molecular clock, and branch lengths suggest that the shift to dioecy in the lowlands occurred many million years after the shift to dioecy in the ancestor of the Andean clade.

Pollination by flies, bees, and beetles of Nuphar ozarkana and N. advena (Nymphaeaceae).

Nuphar comprises 13 species of aquatic perennials distributed in the temperate Northern Hemisphere. The European species N. lutea and N. pumila in Norway, the Netherlands, and Germany are pollinated by bees and flies, including apparent Nuphar specialists. This contrasts with reports of predominant beetle pollination in American N. advena and N. polysepala. We studied pollination in N. ozarkana in Missouri and N. advena in Texas to assess whether (1) there is evidence of pollinator shifts associated with floral-morphological differences between Old World and New World species as hypothesized by Padgett, Les, and Crow (American Journal of Botany 86: 1316-1324. 1999) and (2) whether beetle pollination characterizes American species of Nuphar. Ninety-seven and 67% of flower visits in the two species were by sweat bees, especially Lasioglossum (Evylaeus) nelumbonis. Syrphid fly species visiting both species were Paragus sp., Chalcosyrphus metallicus, and Toxomerus geminatus. The long-horned leaf beetle Donacia piscatrix was common on leaves and stems of N. ozarkana but rarely visited flowers. Fifteen percent of visits to N. advena flowers were by D. piscatrix and D. texana. The beetles' role as pollinators was investigated experimentally by placing floating mesh cages that excluded flies and bees over N. advena buds about to open and adding beetles. Beetles visited 40% of the flowers in cages, and flowers that received visits had 69% seed set, likely due to beetle-mediated geitonogamy of 1st-d flowers. Experimentally outcrossed 1st-d flowers had 62% seed set, and open-pollinated flowers 76%; 2nd-d selfed or outcrossed flowers had low seed sets (9 and 12%, respectively). Flowers are strongly protogynous and do not self spontaneously. Flowers shielded from pollinators set no seeds. A comparison of pollinator spectra in the two Old World and three New World Nuphar species studied so far suggests that the relative contribution of flies, bees, and beetles to pollen transfer in any one population depends more on these insects' relative abundances (and in the case of Donacia, presence) and alternative food sources than on stamen length differences between Old World and New World pond-lilies.

Timing transantarctic disjunctions in the Atherospermataceae (Laurales): evidence from coding and noncoding chloroplast sequences.

Previous studies of the small Southern Hemisphere family Atherospermataceae have drawn contradictory conclusions regarding the number of transantarctic disjunctions and role of transoceanic dispersal in its evolution. Clarification of intergeneric relationships is critical to resolving (1) whether the two Chilean species, Laurelia sempervirens and Laureliopsis philippiana, are related to different Austral-Pacific species, implying two transantarctic disjunctions as suggested by morphology; (2) where the group is likely to have originated; and (3) whether observed disjunctions reflect the breakup of Gondwana. We analyzed chloroplast DNA sequences from six regions (the rbcL gene, the rpl16 intron, and the trnL-trnF, trnT-trnL, psbA-trnH, and atpB-rbcL spacer regions; for all six regions, 4,372 bp) for all genera and most species of Atherospermataceae, using parsimony and maximum likelihood (ML). The family's sister group, the Chilean endemic Gomortega nitida (Gomortegaceae), was used to root the tree. Parsimony and ML yielded identical single best trees that contain three well-supported clades (> or = 75% bootstrap): Daphnandra and Doryphora from south-eastern Australia; Atherosperma and Nemuaron from Australia-Tasmania and New Caledonia, respectively; and Laurelia novac-zelandiac and Laureliopsis philippiana from New Zealand and Chile, respectively. The second Chilean species, Laurelia sempervirens, is sister to this last clade. Likelihood ratio testing did not reject the molecular clock assumption for the rbcL data, which can therefore be used for divergence time estimates. The atherosperm fossil record, which goes back to the Upper Cretaceous, includes pollen, wood, and leaf fossils from Europe, Africa, South America, Antarctica, New Zealand, and Tasmania. Calibration of rbcL substitution rates with the fossils suggests an initial diversification of the family at 100-140 million years ago (MYA), probably in West Gondwana, early entry into Antarctica, and long-distance dispersal to New Zealand and New Caledonia at 50-30 MYA by the ancestors of L. novae-zelandiae and Nemuaron.

Circumscription and phylogeny of the Laurales: evidence from molecular and morphological data.

The order Laurales comprises a few indisputed core constituents, namely Gomortegaceae, Hernandiaceae, Lauraceae, and Monimiaceae sensu lato, and an equal number of families that have recently been included in, or excluded from, the order, namely Amborellaceae, Calycanthaceae, Chloranthaceae, Idiospermaceae, and Trimeniaceae. In addition, the circumscription of the second largest family in the order, the Monimiaceae, has been problematic. I conducted two analyses, one on 82 rbcL sequences representing all putative Laurales and major lineages of basal angiosperms to clarify the composition of the order and to determine the relationships of the controversal families, and the other on a concatenated matrix of sequences from 28 taxa and six plastid genome regions (rbcL, rpl16, trnT-trnL, trnL-trnF, atpB-rbcL, and psbA-trnH) that together yielded 898 parsimony-informative characters. Fifteen morphological characters that play a key role in the evolution and classification of Laurales were analyzed on the most parsimonious molecular trees as well as being included directly in the analysis in a total evidence approach. The resulting trees strongly support the monophyly of the core Laurales (as listed above) plus Calycanthaceae and Idiospermaceae. Trimeniaceae form a clade with Illiciaceae, Schisandraceae, and Austrobaileyaceae, whereas Amborellaceae and Chloranthaceae represent isolated clades that cannot be placed securely based on rbcL alone. Within Laurales, the deepest split is between Calycanthaceae (including Idiospermaceae) and the remaining six families, which in turn form two clades, the Siparunaceae (Atherospermataceae-Gomortegaceae) and the Hernandiaceae (Monimiaceae s.str. [sensu stricto]-Lauraceae). Monimiaceae clearly are polyphyletic as long as they include Atherospermataceae and Siparunaceae. Several morphological character state changes are congruent with the molecular tree: (1) Calycanthaceae have disulculate tectate-columellate pollen, while their sister clade has inaperturate thin-exined pollen, with the exception of Atherospermataceae, which have columellate but meridionosulcate or disulcate pollen. (2) Calycanthaceae have two ventral ovules while their sister clade has solitary ovules. Within this sister clade, the Hernandiaceae (Lauraceae-Monimiaceae) have apical ovules, while the Siparunaceae (Atherospermataceae-Gomortegaceae) are inferred to ancestrally have basal ovules, a condition lost in Gomortega, the only lauralean genus with a syncarpous ovary. (3) Calycanthaceae lack floral nectaries (except for isolated nectarogeneous fields on the inner tepals), while their sister clade ancestrally has paired nectar glands on the filaments. Filament glands were independently lost in higher Monimiaceae and in Siparunaceae concomitant with pollinator changes away from nectar-foraging flies and bees to non-nectar feeding beetles and gall midges. (4) Disporangiate stamens with anthers dehiscing by two apically hinged valves are ancestral in Siparunaceae-(Atherospermataceae-Gomortegaceae) and evolved independently within Hernandiaceae and Lauraceae. Depending on the correct placement of Calycanthaceae-like fossil flowers, tetrasporangiate anthers with valvate dehiscence (with the valves laterally hinged) may be ancestral in Laurales and lost in modern Calycanthaceae and Monimiaceae.

Oligomeric hydrolysable tannins from Tibouchina multiflora.

Two hydrolysable tannins, nobotanin O and nobotanin P, were isolated from the leaf extract of Tibouchina multiflora (Melastomataceae) and their dimeric and tetrameric structures elucidated on the basis of spectral data and chemical correlations with nobotanin B and K, respectively. Thirteen known hydrolysable tannins including nobotanins A, B, C and J, which are oligomers characteristic of the Melastomataceae, were also isolated.