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The work was supported by a grant from the Spanish Ministerio de Ciencia e Innovación, PID2020-119163 GB-I00, and SG benefited from a Ramón y Cajal contract (RYC-2014–16608), both funded by MCIN/AEI/10.13039/501100011033., Introduction Materials and methods Results and discussion Data availability References Acknowledgements Funding Author information Ethics declarations Additional information Rights and permissions About this article

The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel ‘Genotype’ module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated ‘Expression’ module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.

PREMISE State‐sponsored weather stations became ubiquitous by the 1880s, yet many old climate data and phenological observations still need to be digitized and made accessible. METHODS We here make available flowering times for 450 species of herbs and shrubs gathered in 1844 by Carl Friedrich Philipp von Martius (1794–1868), director of the Munich Botanical Garden. The data formed part of the world’s third‐oldest phenological monitoring network as we explain in a brief overview of the history of such networks. Using data from one of the world’s oldest continuously functioning weather stations, Hohenpeißenberg, we relate temperature to flowering in three species with short flowering times and herbarium collections made since 1844 within the city’s perimeter, namely, Anemone patens, A. pulsatilla, and Arum maculatum. RESULTS Mean advances in flowering dates were 1.3–2.1 days/decade or 3.2–4.2 days/1°C warming. These advances are in keeping with similar advances in other European herbs during more recent periods. CONCLUSIONS Future studies might use the 1844 flowering data made available here as a source of information on the availability of particular flowers for specialized pollinators including insects looking for oviposition sites, such as the Psychoda flies that become trapped in Arum inflorescences. Another use of Martius’s 1844 data would be their incorporation into larger‐scale analyses of flowering in southern‐central Europe., American Journal of Botany, 108 (4), ISSN:1914-2016, ISSN:0002-9122

Iconographic evidence from Egypt suggests that watermelon pulp was consumed there as a dessert by 4,360 BP. Earlier archaeobotanical evidence comes from seeds from Neolithic settlements in Libya, but whether these were watermelons with sweet pulp or other forms is unknown. We generated genome sequences from 6,000- and 3,300-year-old seeds from Libya and Sudan, and from worldwide herbarium collections made between 1824 and 2019, and analyzed these data together with resequenced genomes from important germplasm collections for a total of 131 accessions. Phylogenomic and population-genomic analyses reveal that (1) much of the nuclear genome of both ancient seeds is traceable to West African seed-use “egusi-type” watermelon (Citrullus mucosospermus) rather than domesticated pulp-use watermelon (Citrullus lanatus ssp. vulgaris); (2) the 6,000-year-old watermelon likely had bitter pulp and greenish-white flesh as today found in C. mucosospermus, given alleles in the bitterness regulators ClBT and in the red color marker LYCB; and (3) both ancient genomes showed admixture from C. mucosospermus, C. lanatus ssp. cordophanus, C. lanatus ssp. vulgaris, and even South African Citrullus amarus, and evident introgression between the Libyan seed (UMB-6) and populations of C. lanatus. An unexpected new insight is that Citrullus appears to have initially been collected or cultivated for its seeds, not its flesh, consistent with seed damage patterns induced by human teeth in the oldest Libyan material.

In 1917, sex chromosomes in plants were discovered in a liverwort with hetermorphic U and V chromosomes. Such heteromorphy is unexpected because, unlike the XY chromosomes in diploid-dominant plants, in haploid-dominant plants the female U and the male V chromosomes experience largely symmetrical potential recombination environments. Here we use molecular cytogenetics and super-resolution microscopy to study Frullania dilatata, a liverwort with one male and two female sex chromosomes. We applied a pipeline to Illumina sequences to detect abundant types of repetitive DNA and developed FISH probes to microscopically distinguish the sex chromosomes. We also determined the phenotypic population sex ratio because biased ratios have been reported from other liverworts with heteromorphic sex chromosomes. Populations had male-biased sex ratios. The sex chromosomes are monocentric, and of 14 probes studied (eight satellites, five transposable elements and one plastid region), four resulted in unique signals that differentiated the sex chromosomes from the autosomes and from each other. One FISH probe selectively marked the centromeres of both U chromosomes, so we could prove that during meiosis each U chromosome associates with one of the opposite telomeres of the V chromosome, resulting in a head-to-head trivalent. The similarity of the two U chromosomes to each other in size and in their centromere FISH signal positions points to their origin via a non-disjunction event (aneuploidy), which would fit with the general picture of sex chromosomes rarely crossing-over and being prone to suffer from non-disjunction.

Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J. cathayensis, J. mandshurica, and hybrids between J. cathayensis and J. mandshurica). Based on 151 whole-genome sequences of the relevant taxa, we discovered that all J. hopeiensis individuals are first-generation hybrids, with the time for the onset of gene flow estimated as 370,000 years, implying both strong postzygotic barriers and the presence of J. regia in China by that time. Six inversion regions enriched for genes associated with pollen germination and pollen tube growth may be involved in the postzygotic barriers that prevent sexual reproduction in the hybrids. Despite its long-recurrent origination and distinct traits, J. hopeiensis does not appear on the way to speciation.

Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages and that J. cinerea resulted from massive introgression from an immigrating Asian butternut into the genome of an American black walnut. Approximate Bayesian Computation modeling placed the hybrid origin in the late Pliocene, ∼3.45 My, with both parental lineages since having gone extinct in Europe.

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding., Molecular Biology and Evolution, 38 (10), ISSN:0737-4038, ISSN:1537-1719

Natural history collections are leading successful large-scale projects of specimen digitization (images, metadata, DNA barcodes), thereby transforming taxonomy into a big data science. Yet, little effort has been directed towards safeguarding and subsequently mobilizing the considerable amount of original data generated during the process of naming 15,000–20,000 species every year. From the perspective of alpha-taxonomists, we provide a review of the properties and diversity of taxonomic data, assess their volume and use, and establish criteria for optimizing data repositories. We surveyed 4113 alpha-taxonomic studies in representative journals for 2002, 2010, and 2018, and found an increasing yet comparatively limited use of molecular data in species diagnosis and description. In 2018, of the 2661 papers published in specialized taxonomic journals, molecular data were widely used in mycology (94%), regularly in vertebrates (53%), but rarely in botany (15%) and entomology (10%). Images play an important role in taxonomic research on all taxa, with photographs used in >80% and drawings in 58% of the surveyed papers. The use of omics (high-throughput) approaches or 3D documentation is still rare. Improved archiving strategies for metabarcoding consensus reads, genome and transcriptome assemblies, and chemical and metabolomic data could help to mobilize the wealth of high-throughput data for alpha-taxonomy. Because long-term—ideally perpetual—data storage is of particular importance for taxonomy, energy footprint reduction via less storage-demanding formats is a priority if their information content suffices for the purpose of taxonomic studies. Whereas taxonomic assignments are quasifacts for most biological disciplines, they remain hypotheses pertaining to evolutionary relatedness of individuals for alpha-taxonomy. For this reason, an improved reuse of taxonomic data, including machine-learning-based species identification and delimitation pipelines, requires a cyberspecimen approach—linking data via unique specimen identifiers, and thereby making them findable, accessible, interoperable, and reusable for taxonomic research. This poses both qualitative challenges to adapt the existing infrastructure of data centers to a specimen-centered concept and quantitative challenges to host and connect an estimated \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$ \le $\end{document}2 million images produced per year by alpha-taxonomic studies, plus many millions of images from digitization campaigns. Of the 30,000–40,000 taxonomists globally, many are thought to be nonprofessionals, and capturing the data for online storage and reuse therefore requires low-complexity submission workflows and cost-free repository use. Expert taxonomists are the main stakeholders able to identify and formalize the needs of the discipline; their expertise is needed to implement the envisioned virtual collections of cyberspecimens. [Big data; cyberspecimen; new species; omics; repositories; specimen identifier; taxonomy; taxonomic data.]

About 15,000 angiosperms are dioecious, but the mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here, we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped, and the transmission patterns of SNPs were then analyzed. In the &gt, 1300 sex-linked genes studied, maximum X-Y divergence was 0.13&ndash, 0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.

Some ~15.000 angiosperms are dioecious, but mechanisms of sex determination in plants remain poorly understood. In particular, how Y chromosomes evolve and degenerate, and whether dosage compensation evolves as a response, are matters of debate. Here we focus on Coccinia grandis, a dioecious cucurbit with the highest level of X/Y heteromorphy recorded so far. We identified sex-linked genes using RNA sequences from a cross and a model-based method termed SEX-DETector. Parents and F1 individuals were genotyped and the transmission patterns of SNPs then analysed. In the >1300 sex-linked genes studied, X-Y divergence was 0.13 - 0.17, and substantial Y degeneration is implied by an average Y/X expression ratio of 0.63 and an inferred gene loss on the Y of ~40%. We also found reduced Y gene expression being compensated by elevated expression of corresponding genes on the X and an excess of sex-biased genes on the sex chromosomes. Molecular evolution of sex-linked genes in C. grandis is thus comparable to that in Silene latifolia, another dioecious plant with a strongly heteromorphic XY system, and cucurbits are the fourth plant family in which dosage compensation is described, suggesting it might be common in plants.

The three bryophyte lineages have longy-lived gametophytes that are either bisexual, producing both male- and female gametes, or sexually specialized and then producing only one type of gamete. Phylogenies suggest repeated evolutionary switches between these systems, implying that bryophyte sex chromosomes may have been gained and lost repeatedly. How this occurred is poorly understood, even though plant sex chromosomes were first discovered in liverworts. We explain how the sex chromosomes of haploid-dominant organisms are distinct from the better-studied X-Y and Z-W systems in the tree of life, summarise what is known about their distribution and genetic composition, and present new cytogenetic data for Frullania dilatata and Plagiochila asplenioides, the former with two U chromosomes and one V chromosome, the latter with one U chromosome and two V chromosomes; male and female C-values in F. dilatata are correspondingly asymmetric (the C-value of P. asplenioides is only known for female nuclei). So far, there is a lack of high-throughput sequencing, quantification, and in situ study of the repetitive DNA, organellar DNA, and transposable elements, and it is therefore not known what causes the size difference of U and V chromosomes from the autosomes or each other. Heterochromatin was also first discovered in bryophytes, but its function in their sex regulation has not been addressed. Studies of bryophyte sex chromosomes with combined cytogenetic and genomic approaches are fundamental for fuller understanding of s sex chromosome evolution across the tree of life.

Our understanding of the evolution of plant sex chromosomes is increasing rapidly due to high-throughput sequencing data and phylogenetic and molecular-cytogenetic approaches that make it possible to infer the evolutionary direction and steps leading from homomorphic to heteromorphic sex chromosomes. Here, we focus on four species of Coccinia, a genus of 25 dioecious species, including Coccinia grandis, the species with the largest known plant Y chromosome. Based on a phylogeny for the genus, we selected three species close to C. grandis to test the distribution of eight repetitive elements including two satellites, and several plastid and mitochondrial probes, that we had previously found to have distinct accumulation patterns in the C. grandis genome. Additionally, we determined C-values and performed immunostaining experiments with (peri-)centromere-specific antibodies on two species (for comparison with C. grandis). In spite of no microscopic chromosomal heteromorphism, single pairs of chromosomes in male cells of all three species accumulate some of the very same repeats that are enriched on the C. grandis Y chromosome, pointing to either old (previous) sex chromosomes or incipient (newly arising) ones, that is, to sex chromosome turnover. A 144-bp centromeric satellite repeat (CgCent) that characterizes all C. grandis chromosomes except the Y is highly abundant in all centromeric regions of the other species, indicating that the centromeric sequence of the Y chromosome diverged very recently.

Premise The proportion of woody dicots with toothed leaves increases toward colder regions, a relationship used to reconstruct past mean annual temperatures. Recent hypotheses explaining this relationship are that (1) leaves in colder regions are thinner, requiring thick veins for support and water supply, with the resulting craspedodromous venation leading to marginal teeth (support–supply hypothesis) or that (2) teeth are associated with the packing of leaf primordia in winter buds (bud‐packing hypothesis). Methods We addressed these hypotheses by examining leaf thickness, number of primordia in buds, growing season length (mean annual temperature, MAT), and other traits in 151 deciduous woody species using georeferenced occurrences and a Bayesian model controlling for phylogeny. We excluded evergreen species because longer leaf life spans correlate with higher leaf mass per area, precluding the detection of independent effects of leaf thickness on leaf‐margin type. Results The best model predicted toothed leaves with 94% accuracy, with growing season length the strongest predictor. Neither leaf thickness nor number of leaves preformed in buds significantly influenced margin type, rejecting the support–supply and bud‐packing hypotheses. Conclusions A direct selective benefit of leaf teeth via a carbon gain early in the spring as proposed by Royer and Wilf (2006) would match the strong correlation between toothed species occurrence and short growing season found here using Bayesian hierarchical models. Efforts should be directed to physiological work quantifying seasonal photosynthate production in toothed and nontoothed leaves., American Journal of Botany, 106 (11), ISSN:1914-2016, ISSN:0002-9122

PREMISE Parasitic plants with large geographic ranges, and different hosts in parts of their range, may acquire horizontally transferred genes (HGTs), which might sometimes leave a footprint of gradual host and range expansion. Cynomorium coccineum, the only member of the Saxifragales family Cynomoriaceae, is a root holoparasite that occurs in water-stressed habitats from western China to the Canary Islands. It parasitizes at least 10 angiosperm families from different orders, some of them only in parts of its range. This parasite therefore offers an opportunity to trace HGTs as long as parasite-host pairs can be obtained and sequenced. METHODS By sequencing mitochondrial, plastid, and nuclear loci from parasite-host pairs from throughout the parasite's range and with prior information from completely assembled mitochondrial and plastid genomes, we detected 10 HGTs of five mitochondrial genes. RESULTS The 10 HGTs appear to have occurred sequentially as C. coccineum expanded from East to West. Molecular-clock models yield Cynomorium stem ages between 66 and 156 Myr, with relaxed clocks converging on 66-67 Myr. Chinese Sapindales, probably Nitraria, were the first source of transferred genes, followed by Iranian and Mediterranean Caryophyllales. The most recently acquired gene appears to come from a Tamarix host in the Iberian Peninsula. CONCLUSIONS Data on HGTs that have accumulated over the past 15 years, along with this discovery of multiple HGTs within a single widespread species, underline the need for more whole-genome data from parasite-host pairs to investigate whether and how transferred copies coexist with, or replace, native functional genes.

The 23 species of mycoheterotrophic or exoparasitic land plants (from 15 genera and 6 families) studied so far all retain a minimal set of 17 of the normally 116 plastome genes. Only Rafflesia lagascae, an endoparasite concealed in its host except when flowering, has been reported as perhaps lacking a plastome, although it still possesses plastid-like compartments. We analyzed two other endoparasites, the African Apodanthaceae Pilostyles aethiopica and the Australian Pilostyles hamiltonii, both living inside Fabaceae. Illumina and 454 data and Sanger resequencing yielded circularized plastomes of 11,348 and 15,167 bp length, with both species containing five possibly functional genes (accD, rps3, rps4, rrn16, rrn23) and two/three pseudogenes (rpoC2 in P. aethiopica and rpl2 and rps12 in both species; rps12 may be functional in P. hamiltonii). Previously known smallest land plant plastomes contain 27-29 genes, making these Apodanthaceae plastomes the most reduced in size and gene content. A similar extent of divergence might have caused the plastome of Rafflesia to escape detection. The higher plastome degeneration in both these families of endoparasites, Rafflesiaceae and Apodanthaceae, of similar high age, compared with exoparasites points to a difference of plastome function between those two modes of parasitic life.

It is plausible that specialized ecological interactions constrain geographic ranges. We address this question in neotropical bees, Centris and Epicharis, that collect oils from flowers of Calceolariaceae, Iridaceae, Krameriaceae, Malpighiaceae, Plantaginaceae, or Solanaceae, with different species exploiting between one and five of these families, which either have epithelial oil glands or hair fields. We plotted the level of oil-host specialization on a clock-dated phylogeny for 22 of the 35 species of Epicharis and 72 of the 230 species of Centris (genera that are not sister genera) and calculated geographic ranges (km(2) ) for 23 bee species based on collection data from museum specimens. Of the oil-offering plants, the Malpighiaceae date to the Upper Cretaceous, whereas the other five families are progressively younger. The stem and crown groups of the two bee genera date to the Cretaceous, Eocene, and Oligocene. Shifts between oil hosts from different families are common in Centris, but absent in Epicharis, and the direction is from flowers with epithelial oil glands to flowers with oil hairs, canalized by bees' oil-collecting apparatuses, suitable for piercing epithelia or mopping oil from hair fields. With the current data, a link between host specialization and geographic range size could not be detected.

Mutualisms could be evolutionarily unstable, with changes in partner abundances or in the spatial context of interactions potentially promoting their dissolution. We test this prediction using the defense mutualisms between species of the Neotropical genus Cecropia and Azteca ants. A new, multigene phylogeny with representatives of all five genera of Cecropieae (most of them from the Neotropics) and half of the 61 species of Cecropia shows the West African endemic Musanga (2 spp.) as sister to Cecropia, implying dispersal from the Neotropics to Africa, with a molecular clock suggesting that this occurred about 23 Mya. Cecropia, a genus of neotropical pioneer trees, started diversifying ca. 8 Mya. We infer a single origin of specialized symbiosis with Azteca within Cecropia, eight complete losses of this symbiosis, and a potential partner shift involving the replacement of Azteca by Neoponera luteola ants. Niche space modeling based on geo-referenced occurrences of over 9000 collections representing 58 of the 61 species of Cecropia, together with several comparative analyses, implies that mutualism loss is concentrated at high altitudes and on Caribbean islands, with the surprisingly frequent breakdowns potentially facilitated by low species-specificity of interacting Cecropia and Azteca mutualists.

Combining molecular cytogenetics and phylogenetic modelling of chromosome number change can shed light on the types of evolutionary changes that may explain the haploid numbers observed today. Applied to the monocot family Araceae, with chromosome numbers of 2n = 8 to 2n = 160, this type of approach has suggested that descending dysploidy has played a larger role than polyploidy in the evolution of the current chromosome numbers. To test this, we carried out molecular cytogenetic analyses in 14 species from 11 genera, using probes for telomere repeats, 5S rDNA and 45S rDNA and a plastid phylogenetic tree covering the 118 genera of the family, many with multiple species. We obtained new chromosome counts for six species, modelled chromosome number evolution using all available counts for the family and carried out fluorescence in situ hybridization with three probes (5S rDNA, 45S rDNA and Arabidopsis-like telomeres) on 14 species with 2n = 14 to 2n = 60. The ancestral state reconstruction provides support for a large role of descending dysploidy in Araceae, and interstitial telomere repeats (ITRs) were detected in Anthurium leuconerum, A. wendlingeri and Spathyphyllum tenerum, all with 2n = 30. The number of ITR signals in Anthurium (up to 12) is the highest so far reported in angiosperms, and the large repeats located in the pericentromeric regions of A. wendlingeri are of a type previously reported only from the gymnosperms Cycas and Pinus. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177, 15–26.

A major concern in molecular clock dating is how to use information from the fossil record to calibrate genetic distances from DNA sequences. Here we apply three Bayesian dating methods that differ in how calibration is achieved— "node dating" (ND) in BEAST, "total evidence" (TE) dating in MrBayes, and the "fossilized birth-death" (FBD) in FDPPDiv— to infer divergence times in the royal ferns. Osmundaceae have 16-17 species in four genera, two mainly in the Northern Hemisphere and two in South Africa and Australasia; they are the sister clade to the remaining leptosporangiate ferns. Their fossil record consists of at least 150 species in ∼17 genera. For ND, we used the five oldest fossils, whereas for TE and FBD dating, which do not require forcing fossils to nodes and thus can use more fossils, we included up to 36 rhizomes and frond compression/impression fossils, which for TE dating were scored for 33 morphological characters. We also subsampled 10%, 25%, and 50% of the 36 fossils to assess model sensitivity. FBD-derived divergence ages were generally greater than those inferred from ND; two of seven TE-derived ages agreed with FBD-obtained ages, the others were much younger or much older than ND or FBD ages. We prefer the FBD-derived ages because they best fit the Osmundales fossil record (including Triassic fossils not used in our study). Under the preferred model, the clade encompassing extant Osmundaceae (and many fossils) dates to the latest Paleozoic to Early Triassic; divergences of the extant species occurred during the Neogene. Under the assumption of constant speciation and extinction rates, the FBD approach yielded speciation and extinction rates that overlapped those obtained from just neontological data. However, FBD estimates of speciation and extinction are sensitive to violations in the assumption of continuous fossil sampling; therefore, these estimates should be treated with caution. (Bayesian inference; fossilized birth-death dating; molecular clock calibration; node dating; total evidence dating; royal ferns.)

Gene trees of holoparasitic plants usually show distinctly longer branch lengths than seen in photosynthetic closest relatives. Such substitution rate jumps have made it difficult to infer the absolute divergence times of parasites. An additional problem is that parasite clades often lack a fossil record. Using nuclear and mitochondrial DNA sequences of Apodanthaceae, a worldwide family of endoparasites living inside Fabaceae and Salicaceae, we compared several dating approaches: (i) an uncorrelated lognormal (UCLN) model calibrated with outgroup fossils, (ii) ages of host lineages as a maximal age in an UCLN model, (iii) user-assigned local clocks, and (iv) outgroup-fossil-calibrated random local clocks (RLC) with varying prior probabilities on the number of permitted rate changes (RLCu and RLCp models), a variable that has never been explored. The resulting dated phylogenies include all 10 species of the family, three in Australia, one in Iran, one in Africa, and the remainder in the Americas. All clock models infer a drastic rate jump between nonparasitic outgroups and Apodanthaceae, but since they distribute the rate heterogeneity differently, they result in much-different age estimates. Bayes factors using path and stepping-stone sampling indicated that the RLCp model fit poorly, while for matR, topologically unconstrained RLCu and UCLN models did not differ significantly and for 18S, the UCLN model was preferred. Under the equally well fitting models, the Apodanthaceae appear to be a relatively old clade, with a stem age falling between 65 and 81 my, the divergence of Apodanthes from Pilostyles between 36 and 57 my ago, and the crown age of the Australian clade 8–18 my ago. In our study system, host-age calibrations did not yield well-constrained results, but they may work better in other parasite clades. For small data sets where statistical convergence can be reached even with complex models, random local clocks should be explored as an alternative to the exclusive reliance on UCLN clocks.

The economically most important group of bees is the “corbiculates”, or pollen basket bees, some 890 species of honeybees (Apis), bumblebees (Bombus), stingless bees (Meliponini), and orchid bees (Euglossini). Molecular studies have indicated that the corbiculates are closest to the New World genera Centris, with 230 species, and Epicharis, with 35, albeit without resolving the precise relationships. Instead of concave baskets, these bees have hairy hind legs on which they transport pollen mixed with floral oil, collected with setae on the anterior and middle legs. We sampled two-thirds of all Epicharis, a third of all Centris, and representatives of the four lineages of corbiculates for four nuclear gene regions, obtaining a well-supported phylogeny that has the corbiculate bees nested inside the Centris/Epicharis clade. Fossil-calibrated molecular clocks, combined with a biogeographic reconstruction incorporating insights from the fossil record, indicate that the corbiculate clade arose in the New World and diverged from Centris 84 (72–95) mya. The ancestral state preceding corbiculae thus was a hairy hind leg, perhaps adapted for oil transport as in Epicharis and Centris bees. Its replacement by glabrous, concave baskets represents a key innovation, allowing efficient transport of plant resins and large pollen/nectar loads and freeing the corbiculate clade from dependence on oil-offering flowers. The transformation could have involved a novel function of Ubx, the gene known to change hairy into smooth pollen baskets in Apis and Bombus.

Absolute times from calibrated DNA phylogenies can be used to infer lineage diversification, the origin of new ecological niches, or the role of long distance dispersal in shaping current distribution patterns. Molecular-clock dating of non-vascular plants, however, has lagged behind flowering plant and animal dating. Here, we review dating studies that have focused on bryophytes with several goals in mind, (i) to facilitate cross-validation by comparing rates and times obtained so far; (ii) to summarize rates that have yielded plausible results and that could be used in future studies; and (iii) to calibrate a specieslevel phylogeny for Nothoceros, a model for plastid genome evolution in hornworts. Including the present work, there have been 18 molecular clock studies of liverworts, mosses, or hornworts, the majority with fossil calibrations, a few with geological calibrations or dated with previously published plastid substitution rates. Over half the studies cross-validated inferred divergence times by using alternative calibration approaches. Plastid substitution rates inferred for ‘‘bryophytes’’ are in line with those found in angiosperm studies, implying that bryophyte clock models can be calibrated either with published substitution rates or with fossils, with the two approaches testing and cross-validating each other. Our phylogeny of Nothoceros is based on 44 accessions representing all suspected species and a matrix of six markers of nuclear, plastid, and mitochondrial DNA. The results show that Nothoceros comprises 10 species, nine in the Americas and one in New Zealand (N. giganteus), with the divergence between the New Zealand species and its Chilean sister species dated to the Miocene and therefore due to long-distance dispersal. Based on the new tree, we formally transfer two species of Megaceros into Nothoceros, resulting in the new combinations N. minarum (Nees) J.C. Villarreal and N. schizophyllus (Gottsche ex Steph.) J.C. Villarreal, and we also newly synonymize eight names described in Megaceros.

The lily family Colchicaceae consists of geophytic herbs distributed on all continents except the Neotropics. It is particularly diverse in southern Africa, where 80 of the 270 species occur. Colchicaceae exhibit a wide range of ploidy levels, from 2n = 14 to 2n = 216. To understand where and how this cytogenetic diversity arose, we generated multilocus phylogenies of the Colchicaceae and the Colchicum clade that respectively included 85 or 137 species plus relevant outgroups. To infer the kinds of events that could explain the observed numbers in the living species (dysploidy, polyploidization, or demi-duplication, i.e. fusion of gametes of different ploidy), we compared a series of likelihood models on phylograms, penalized likelihood ultrametric trees, and relaxed clock chronograms that contained the 58 or 112 species with published chromosome counts. While such models involve simplification and cannot address the processes behind chromosomal rearrangements, they can help frame questions about...

The circumscription of the five to eight species of Luffa, as well as their correct names, have long been problematic. Experts on the genus, most recently C. Heiser and C. Jeffrey, have disagreed on the number of species in the New World and the application of the name L. operculata, which in turn affected the names L. quinquefida and L. sepium. Heiser used classic biosystematic methods, including experimental crossing, to infer species boundaries, but neither researcher had today's option of using DNA sequences for this purpose. We sequenced 51 accessions of Luffa, representing the geographic range of the genus and as much as possible topotypical or type material. Phylogenies from four non-coding plastid regions and the nuclear ribosomal DNA spacer region show that eight clades of specimens have geographic-morphological coherence. Heiser's view that Luffa has three species in the New World is supported, and there are four species in tropical and subtropical Asia. Australia has an endemic species...

• Premise of the study: The Foulden Maar lake sediments in Otago, South Island, New Zealand, date to the earliest Miocene and provide an important picture of the diversity of the Australasian biota, paleoecology, and climate at a time when New Zealand had a smaller land area than today. The diverse rainforest contains many taxa now restricted to Australia, New Caledonia, or South America. The presence of Luzuriaga-like fossils in these deposits is important for understanding Alstroemeriaceae evolution and the biogeography of genera shared between New Zealand and South America.• Methods: Leaves and a flower with in situ pollen that resemble extant Luzuriaga are described and placed phylogenetically. Geographic range information and a molecular clock model for the Alstroemeriaceae were used to investigate possible biogeographic scenarios and the influence of the new fossil on inferred divergence times.• Key results: Luzuriaga peterbannisteri Conran, Bannister, Mildenh., & D.E.Lee sp. nov. represents the first macrofossil record for Alstroemeriaceae. An associated Luzuriaga-like flower with in situ fossil pollen of Liliacidites contortus Mildenh. & Bannister sp. nov. is also described. The biogeographic analysis suggests that there have been several dispersal events across the Southern Ocean for the genus, with the fossil representing a now-extinct New Zealand lineage.• Conclusions: Luzuriaga was present in Early Miocene New Zealand, indicating a long paleogeographic history for the genus, and L. peterbannisteri strengthens biogeographic connections between South America and Australasia during the Oligocene and earliest Miocene.

Most plant–pollinator interactions are mutualistic, involving rewards provided by flowers or inflorescences to pollinators. Antagonistic plant–pollinator interactions, in which flowers offer no rewards, are rare and concentrated in a few families including Araceae. In the latter, they involve trapping of pollinators, which are released loaded with pollen but unrewarded. To understand the evolution of such systems, we compiled data on the pollinators and types of interactions, and coded 21 characters, including interaction type, pollinator order, and 19 floral traits. A phylogenetic framework comes from a matrix of plastid and new nuclear DNA sequences for 135 species from 119 genera (5342 nucleotides). The ancestral pollination interaction in Araceae was reconstructed as probably rewarding albeit with low confidence because information is available for only 56 of the 120–130 genera. Bayesian stochastic trait mapping showed that spadix zonation, presence of an appendix, and flower sexuality were correlated with pollination interaction type. In the Araceae, having unisexual flowers appears to have provided the morphological precondition for the evolution of traps. Compared with the frequency of shifts between deceptive and rewarding pollination systems in orchids, our results indicate less lability in the Araceae, probably because of morphologically and sexually more specialized inflorescences.

Studies over the past ten years have shown that the crown groups of most conifer genera are only about 15-25 Ma old. The genus Picea (spruces, Pinaceae), with around 35 species, appears to be no exception. In addition, molecular studies of co-existing spruce species have demonstrated frequent introgression. Perhaps not surprisingly therefore previous phylogenetic studies of species relationships in Picea, based mostly on plastid sequences, suffered from poor statistical support. We therefore generated mitochondrial, nuclear, and further plastid DNA sequences from carefully sourced material, striking a balance between alignability with outgroups and phylogenetic signal content. Motif duplications in mitochondrial introns were treated as characters in a stochastic Dollo model; molecular clock models were calibrated with fossils; and ancestral ranges were inferred under maximum likelihood. In agreement with previous findings, Picea diverged from its sister clade 180 million years ago (Ma), and the most recent common ancestor of today's spruces dates to 28 Ma. Different from previous analyses though, we find a large Asian clade, an American clade, and a Eurasian clade. Two expansions occurred from Asia to North America and several between Asia and Europe. Chinese P. brachytyla, American P. engelmannii, and Norway spruce, P. abies, are not monophyletic, and North America has ten, not eight species. Divergence times imply that Pleistocene refugia are unlikely to be the full explanation for the relationships between the European species and their East Asian relatives. Thus, northern Norway spruce may be part of an Asian species complex that diverged from the southern Norway spruce lineage in the Upper Miocene, some 6 Ma, which can explain the deep genetic gap noted in phylogeographic studies of Norway spruce. The large effective population sizes of spruces, and incomplete lineage sorting during speciation, mean that the interspecific relationships within each of the geographic clades require further studies, especially based on genomic information and population genetic data.

SUMMARY Comparisons of closely related species are needed to understand the fine-scale dynamics of retrotransposon evolution in flowering plants. Towards this goal, we classified the long terminal repeat (LTR) retrotransposons from six diploid and one tetraploid species of Orobanchaceae. The study species are the autotrophic, non-parasitic Lindenbergia philippensis (as an out-group) and six closely related holoparasitic species of Orobanche [O. crenata, O. cumana, O. gracilis (tetraploid) and O. pancicii] and Phelipanche (P. lavandulacea and P. ramosa). All major plant LTR retrotransposon clades could be identified, and appear to be inherited from a common ancestor. Species of Orobanche, but not Phelipanche, are enriched in Ty3/Gypsy retrotransposons due to a diversification of elements, especially chromoviruses. This is particularly striking in O. gracilis, where tetraploidization seems to have contributed to the Ty3/Gypsy enrichment and led to the emergence of seven large species-specific families of chromoviruses. The preferential insertion of chromoviruses in heterochromatin via their chromodomains might have favored their diversification and enrichment. Our phylogenetic analyses of LTR retrotransposons from Orobanchaceae also revealed that the Bianca clade of Ty1/Copia and the SMART-related elements are much more widely distributed among angiosperms than previously known.

A growing body of evidence is pointing to an important role of horizontal gene transfer (HGT) in the evolution of higher plants. However, reports of HGTs of transposable elements (TEs) in plants are still scarce and only one case is known of a class II transposon horizontally transferred between grasses. To investigate possible TE transfers in dicots, we performed transcriptome screening in the obligate root parasite Phelipanche aegyptiaca (Orobanchaceae), data-mining in the draft genome assemblies of four other Orobanchaceae, gene cloning, gene annotation in species with genomic information and a molecular phylogenetic analysis. We discovered that the broomrape genera Phelipanche and Orobanche acquired two related nuclear genes (christened BO transposase genes), a new group of the hAT superfamily of class II transposons, from Asian Sisymbrieae or a closely related tribe of Brassicaceae, by HGT. The collinearity of the flanking genes, lack of a classic border structure and low expression levels suggest that BO transposase genes cannot transpose in Brassicaceae, whereas they are highly expressed in P. aegyptiaca.

Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites' occurrence. Cynomorium has large genomes of 13.70-13.61 (Italy) to 13.95-13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.

Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA, including 16 mobile elements. The size of the Y chromosome is largely due to the accumulation of certain repeats, such as members of the Ty1/copia and Ty3/gypsy superfamilies, an unclassified element and a satellite, but also plastome- and chondriome-derived sequences. An abundant tandem repeat with a unit size of 144 bp stains the centromeres of the X chromosome and the autosomes, but is absent from the Y centromere. Immunostaining with pericentromere-specific markers for anti-histone H3Ser10ph and H2AThr120ph revealed a Y-specific extension of these histone marks. That the Y centromere has a different make-up from all the remaining centromeres raises questions about its spindle attachment, and suggests that centromeric or pericentromeric chromatin might be involved in the suppression of recombination.

PREMISE OF THE STUDY: Caricaceae include six genera and 34 species, among them papaya, a model species in plant sex chromosome research. The family was held to have a conserved karyotype with 2n = 18 chromosomes, an assumption based on few counts. We examined the karyotypes and genome size of species from all genera to test for possible cytogenetic variation. METHODS: We used fluorescent in situ hybridization using standard telomere, 5S, and 45S rDNA probes. New and published data were combined with a phylogeny, molecular clock dating, and C values (available for similar to 50% of the species) to reconstruct genome evolution. KEY RESULTS: The African genus Cylicomorpha, which is sister to the remaining Caricaceae (all neotropical), has 2n = 18, as do the species in two other genera. A Mexican clade of five species that includes papaya, however, has 2n = 18 (papaya), 2n = 16 (Horovitzia cnidoscoloides), and 2 n = 14 (Jarilla caudata and J. heterophylla;third Jarilla not counted), with the phylogeny indicating that the dysploidy events occurred similar to 16.6 and similar to 5.5 million years ago and that Jarilla underwent genome size doubling (similar to 450 to 830-920 Mbp/haploid genome). Pericentromeric interstitial telomere repeats occur in both Jarilla adjacent to 5S rDNA sites, and the variability of 5S rDNA sites across all genera is high. CONCLUSIONS: On the basis of outgroup comparison, 2n = 18 is the ancestral number, and repeated chromosomal fusions with simultaneous genome size increase as a result of repetitive elements accumulating near centromeres characterize the papaya clade. These results have implications for ongoing genome assemblies in Caricaceae.

Papaya (Carica papaya) is a crop of great economic importance, and the species was among the first plants to have its genome sequenced. However, there has never been a complete species-level phylogeny for the Caricaceae, and the crop's closest relatives are therefore unknown. We investigated the evolution of the Caricaceae based on sequences from all species and genera, the monospecific Carica, African Cylicomorpha with two species, South American Jacaratia and Vasconcellea with together c. 28 species, and Mexican/Guatemalan Jarilla and Horovitzia with four species. Most Caricaceae are trees or shrubs; the species of Jarilla, however, are herbaceous. We generated a matrix of 4711 nuclear and plastid DNA characters and used maximum likelihood (ML) and Bayesian analysis to infer species relationships, rooting trees on the Moringaceae. Divergence times were estimated under relaxed and strict molecular clocks, using different subsets of the data. Ancestral area reconstruction relied on a ML approach. The deepest split in the Caricaceae occurred during the Late Eocene, when the ancestor of the Neotropical clade arrived from Africa. In South America, major diversification events coincide with the Miocene northern Andean uplift and the initial phase of the tectonic collision between South America and Panama resulting in the Panamanian land bridge. Carica papaya is sister to Jarilla/Horovitzia, and all three diverged from South American Caricaceae in the Oligocene, 27 (22-33) Ma ago, coincident with the early stages of the formation of the Panamanian Isthmus. The discovery that C. papaya is closest to a clade of herbaceous or thin-stemmed species has implications for plant breeders who have so far tried to cross papaya only with woody highland papayas (Vasconcellea).

 Premise of the study: Understanding the fl exibility of monocot genomes requires a phylogenetic framework, which so far is available for few of the ca. 2800 genera. Here we use a molecular tree for the South American genus Alstroemeria to place karyological information, including fl uorescent in situ hybridization (FISH) signals, in an explicit evolutionary context.  Methods: From a phylogeny based on plastid, nuclear, and mitochondrial sequences for most species of Alstroemeria , we selected early-branching (Chilean) and derived (Brazilian) species for which we obtained 18S-25S and 5S rDNA FISH signals; we also analyzed chromosome numbers, 1C-values, and telomere FISH signals (in two species).  Key results: Chromosome counts for Alstroemeria cf. rupestris and A. pulchella confi rm 2 n = 16 as typical of the genus, which now has chromosomes counted for 29 of its 78 species. The rDNA sites are polymorphic both among and within species, and interstitial telomeric sites in Alstroemeria cf. rupestris suggest chromosome fusion.  Conclusions: In spite of a constant chromosome number, closely related species of Alstroemeria differ drastically in their rDNA, indicating rapid increase, decrease, or translocations of these genes. Previously proposed Brazilian and Chilean karyotype groups are not natural, and the n = 8 chromosomes in Alstroemeria compared to n = 9 in its sister genus Bomarea may result from a Robertsonian fusion.

We used next-generation sequencing to characterize the genomes of nine species of Orobanchaceae of known phylogenetic relationships, different life forms, and including a polyploid species. The study species are the autotrophic, nonparasitic Lindenbergia philippensis, the hemiparasitic Schwalbea americana, and seven nonphotosynthetic parasitic species of Orobanche (Orobanche crenata, Orobanche cumana, Orobanche gracilis (tetraploid), and Orobanche pancicii) and Phelipanche (Phelipanche lavandulacea, Phelipanche purpurea, and Phelipanche ramosa). Ty3/Gypsy elements comprise 1.93%–28.34% of the nine genomes and Ty1/Copia elements comprise 8.09%–22.83%. When compared with L. philippensis and S. americana, the nonphotosynthetic species contain higher proportions of repetitive DNA sequences, perhaps reflecting relaxed selection on genome size in parasitic organisms. Among the parasitic species, those in the genus Orobanche have smaller genomes but higher proportions of repetitive DNA than those in Phelipanche, mostly due to a diversification of repeats and an accumulation of Ty3/ Gypsy elements. Genome downsizing in the tetraploid O. gracilis probably led to sequence loss across most repeat types.

Hallucinogenic or toxic species of Brunfelsia (Solanaceae: Petunieae) are important in native cultures throughout South America, and the genus also contains several horticulturally important species. An earlier morphological revision of the c. 50 species recognized three main groups, one consisting of the 23 Antillean species, another of southern South American and Andean species, and a third of species from the Amazon Basin and Guiana Shield. Based on plastid and nuclear DNA sequences from up to 65 accessions representing 80% of the species, we generated a phylogeny and a calibrated chronogram for Brunfelsia to infer clade expansion and shifts in pollinators and fruit types. Brunfelsia flowers offer nectar, and attract lepidoptera, hummingbirds, or bees; the fruits are dry or fleshy. Our results imply that Brunfelsia is 16-21 Myr old and entered the Antilles from South America early during its history, with subsequent expansion along the island arc. The ancestor of the Antillean clade was hawk-moth-pollinated and had fleshy capsules, perhaps facilitating dispersal by birds. The only shift to hummingbird pollination occurred on Cuba, which also harbors the largest single radiation, with 11 species (10 included in our study) that apparently arose over the past 4 Myr. Jamaica, Hispaniola, and Puerto Rico each sustained smaller radiations. The data also reveal at least one new species.

Alocasia comprises over 113 species of rainforest understorey plants in Southeast Asia, the Malesian region, and Australia. Several species, including giant taro, Alocasia macrorrhizos, and Chinese taro, Alocasia cucullata, are important food plants or ornamentals. We investigated the biogeography of this genus using plastid and nuclear DNA sequences (5200 nucleotides) from 78 accessions representing 71 species, plus 25 species representing 16 genera of the Pistia clade to which Alocasia belongs. Divergence times were inferred under strict and relaxed clock models, and ancestral areas with Bayesian and maximum likelihood approaches. Alocasia is monophyletic and sister to Colocasia gigantea from the SE Asian main- land, whereas the type species of Colocasia groups with Steudnera and Remusatia, requiring taxonomic realignments. Nuclear and plastid trees show topological conflict, with the nuclear tree reflecting morphological similarities, the plastid tree species' geographic proximity, suggesting chloroplast capture. The ancestor of Alocasia diverged from its mainland sister group c. 24 million years ago, and Borneo then played a central role in the expansion of Alocasia: 11–13 of 18–19 inferred dispersal events originated on Borneo. The Philippines were reached from Borneo 4–5 times in the Late Miocene and Early Pliocene, and the Asian mainland 6–7 times in the Pliocene. Domesticated giant taro originated on the Philippines, Chinese taro on the Asian mainland.

The tribe Delphinieae (Ranunculaceae) comprises two species-rich genera, Aconitum and Delphinium, the latter including Consolida and Aconitella. The 650–700 species are distributed in Eurasia and North America; three species occur on tropical African mountains. Maximum likelihood analyses of 2088 aligned nucleotides of plastid and nuclear sequences obtained from up to 185 species of Delphinieae from throughout the geographic range (plus relevant outgroups) show that three short-lived (facultative annual or biennial) Mediterranean species belonging to Delphinium subgenus Staphisagria are the sister clade to all other Delphinieae, implying that Staphisagria needs to be raised to genus status if Delphinium and Aconitum are to become mutually monophyletic. Molecular clock dating suggests an origin of the sampled Delphinieae in the Early Oligocene (c. 32.3 Ma) and expansion to North America of Aconitum and Delphinium around 3.3 and 2.9 Ma ago, respectively; the East African Mts. were reached by long-distance dispersal some 2.4 Ma ago, coincident with the major uplift of the East African Rift system. The ancestral growth form of the Delphinieae could not be reconstructed, but Late Miocene bursts in diversification rates in the Himalayan and southwestern Chinese clades of Aconitum and Delphinium appear to be associated with transitions from short-lived to long-lived life histories.

Deceptive flowers exploit pollinators by signalling the presence of a reward without providing it. At the core of this phenomenon is mimicry, which results in insects thinking something that is not true – in other words, cognitive misclassification of floral signals by insects. This definition, adopted by Steven Johnson and Florian Schiestl in their book on floral mimicry, excludes camouflage and crypsis, which do not involve detection and cognitive misclassification. To discover mimicry requires field observations of interactions in natural settings, combined with knowledge of insect life histories, sensory perception, and cognition. Early work on mimicry in plants focused on orchids mimicking bee or wasp sexual pheromones (Kullenberg 1961) or orchids mimicking fungi (Vogel 1973), but most of the research covered in this book came out after the 1980s, with studies on plant mimicry now apparently making up 30% of all publications dealing with biological mimicry. Mimicry today is studied on every biological level from genomes to populations, and Floral Mimicry is a well-written book that is the first to cover all aspects of the topic. This article is protected by copyright. All rights reserved

†Background and Aims For 84 years, botanists have relied on calculating the highest common factor for series of haploid chromosome numbers to arrive at a so-called basic number, x. This was done without consistent (reproducible) reference to species relationships and frequencies of different numbers in a clade. Likelihood models that treat polyploidy, chromosome fusion and fission as events with particular probabilities now allow reconstruction of ancestral chromosome numbers in an explicit framework. We have used a modelling approach to reconstruct chromosome number change in the large monocot family Araceae and to test earlier hypotheses about basic numbers in the family. †Methods Using a maximum likelihood approach and chromosome counts for 26 % of the 3300 species of Araceae and representative numbers for each of the other 13 families of Alismatales, polyploidization events and single chromosome changes were inferred on a genus-level phylogenetic tree for 113 of the 117 genera of Araceae. †Key Results The previously inferred basic numbers x ¼ 14 and x ¼ 7 are rejected. Instead, maximum likelihood optimization revealed an ancestral haploid chromosome number of n ¼ 16, Bayesian inference of n ¼ 18. Chromosome fusion (loss) is the predominant inferred event, whereas polyploidization events occurred less frequently and mainly towards the tips of the tree. †Conclusions The bias towards low basic numbers (x) introduced by the algebraic approach to inferring chromosome number changes, prevalent among botanists, may have contributed to an unrealistic picture of ancestral chromosome numbers in many plant clades. The availability of robust quantitative methods for reconstructing ancestral chromosome numbers on molecular phylogenetic trees (with or without branch length information), with confidence statistics, makes the calculation of x an obsolete approach, at least when applied to large clades.

Molecular phylogenetic analyses based on numerous plant accessions have shown that Cucumis comprises 25 species in Asia, the Malesian region, and Australia, rather than just two as traditionally thought. Among the 25 species several are new, and here we describe four from tropical Australia. The new species C. costatus, C. queenslandicus , C. umbellatus , and C. variabilis are illustrated, their distri- butions are mapped based on 7-50 collections per species, and information is provided on habitats and conservation status. We also vali- date C. althaeoides comb. nov. and C. argenteus comb. nov., update the description of C. picrocarpus , and provide a key to the 11 native and naturalized species of Cucumis occurring in Australia and eastern Malesia. The Australasian species diversity of Cucumis , a genus that until recently was held to be essentially African, is of interest also because Australia harbours the sister species to the commercially important melon, C. melo . Keywords—Cucumis picrocarpus , melon , morphological characters , phylogenetics , sequencing herbarium specimens , taxonomy.

Phyllanthus comprises approximately 1,270 species, making it one of the world's largest plant genera. Molecular data so far are of limited value for understanding Phyllanthus because of the sheer size of the genus. They can, however, help sort-out cryptic species and provide information on the origin of suspected introduced species. One of the seemingly most widespread species is P. reticulatus, which has been recorded from Asia, Australia, Africa, and Jamaica. The name is based on a mixed collection from tropical Asia now in the Lamarck herbarium, and we lectotypify it here. We use nuclear ITS sequences to test the broad treatment of P. reticulatus in recent floras, identify records of “P. reticulatus” from Africa, and investigate the origin of P. reticulatus on Jamaica. A maximum likelihood tree for accessions of P. reticulatus from throughout its supposed range (plus relevant outgroups) shows that the Jamaican plants represent the Asian species, that the African plants called P. reticulatus be...

The biogeographical history of several important vegetables is still unclear. In the gourd family, Cucurbitaceae, this applies to melon and cucumber, but also to many species of more regional importance. Cucumeropsis mannii is cultivated in West Tropical Africa for its nutritious seeds. Family-wide phylogenetic analyses suggested that it is closest to Posadaea sphaerocarpa from Central and South America, the seeds of which are also eaten and the fruit of which is made into bowls. To reconstruct these species' historical biogeography, we sequenced six plastid markers and the nuclear ribosomal ITS region for several accessions of both species, plus all relevant outgroups. Morphological traits were studied in 102 herbarium specimens representing both species. A 5,155 nucleotide-long matrix of chloroplast and nuclear DNA contained a single informative mutation in a poly-C region of nuclear ITS among six accessions that covered the species' native ranges. Next-closest species differed in all plastid markers and by ≥34 mutations in ITS1 and ITS2. Study of the morphology revealed a possible small difference in fruit shape (cylindrical-ovate versus spherical), presumably resulting from human selection on the African populations. The closest out- groups Melancium and Melothria are endemic to the neotropics, and maximum likelihood area reconstruction indicates that Cucumeropsis mannii also originated there. The near-absence of genetic and morphological differentiation implies that gene flow between Cucumeropsis manni and Posadaea sphaerocarpa stopped relatively recently, and taxonomically they should (or could) be treated as one species. Transport of seeds during the transatlantic slave trade is a possible scenario, although we cannot reject natural dispersal.

 Premise of the study : Flower heating is known from a few species in 11 of the c. 450 families of flplants. Flowers in these families produce heat metabolically and are adapted to beetles or fl as pollinators. Here, we focus on the Schisandraceae, an American/Asian plant family known to exhibit fl ower heating in some species, but not others, raising the question of the adaptive function of heat production.  Methods : We used fi eld observations, experiments, and ancestral trait reconstruction on a molecular phylogeny for Schisandraceae that includes the investigated species.  Key results : At least two Chinese species of Illicium are exclusively pollinated by gall midges that use the fl owers as brood sites (not for pollen feeding). Continuous monitoring of fltemperatures revealed that the highest temperatures were attained after the fl owers ’ sexual functions were over, and experiments showed that post-anthetic warming benefi ted larval development, not fruit development. Midge larvae in flwith trimmed tepals (and hence a lower temperature) died, but fruit set ratios remained unchanged. Based on the DNA phylogeny, gall midge pollination evolved from general fl y/beetle pollination several times in Schisandraceae, with some species adapted to flmidges, others to pollen-feeding midges.  Conclusions : Flower heating may be an ancestral trait in Schisandraceae that became co-opted in species pollinated by fl breeding midges requiring long-persistent warm chambers for larval development.

UNLABELLED PREMISE OF THE STUDY The Cucurbitaceae genus Cayaponia comprises ∼60 species that occur from Uruguay to the southern United States and the Caribbean; C. africana occurs in West Africa and on Madagascar. Pollination is by bees or bats, raising the question of the evolutionary direction and frequency of pollinator shifts. Studies that investigated such shifts in other clades have suggested that bat pollination might be an evolutionary end point. • METHODS Plastid and nuclear DNA sequences were obtained for 50 accessions representing 30 species of Cayaponia and close relatives, and analyses were carried out to test monophyly, infer divergence times, and reconstruct ancestral states for habitat preferences and pollination modes. • KEY RESULTS The phylogeny shows that Cayaponia is monophyletic as long as Selysia (a genus with four species from Central and South America) is included. The required nomenclatural transfers are made in this paper. African and Madagascan accessions of C. africana form a clade that is part of a polytomy with Caribbean and South American species, and the inferred divergence time of 2-5 Ma implies a transoceanic dispersal event from the New World to Africa. The ancestral state reconstructions suggest that Cayaponia originated in tropical forests from where open savannas were reached several times and that bee pollination arose from bat pollination, roughly concomitant with the shifts from forests to savanna habitats. • CONCLUSIONS Cayaponia provides the first example of evolutionary transitions from bat to bee pollination as well as another instance of transoceanic dispersal from the New World to Africa.

The bitter gourd genus Momordica comprises 47 species in Africa and 12 in Asia and Australia. All have unisexual flowers, and of the African species, 24 are dioecious, 23 monoecious, while all Asian species are dioecious. Maximum likelihood analyses of 6257 aligned nucleotides of plastid, mitochondrial and nuclear DNA obtained for 122 accessions of Momordica and seven outgroups show that Momordica is monophyletic and consists of 11 well-supported clades. Monoecy evolved from dioecy seven times independently, always in Africa and mostly in savanna species with low population densities. Leaky dioecy, with occasional fruit-producing males, occurs in two African species and might be the first step in an evolutionary transition towards monoecy. Dated biogeographic analyses suggest that Momordica originated in tropical Africa and that the Asian species are the result of one long-distance dispersal event about 19 million years ago. The pantropical vegetable Momordica charantia is of African, not Asian origin as had previously been suggested.

We describe and illustrate the new species Fevillea anomalosperma from the semideciduous forests of northwestern Bolivia. Analysis of chloroplast DNA sequences representing most genera of Cucurbitaceae, including Fevillea with four of its seven species, supports placing the new species in Fevillea despite its small (10–11.5 × 7.5–10 mm, 2–3 mm thick), flattened, and highly sculptured seeds, which are unusual in the genus. The molecular phylogeny also revealed that the recent sinking of the monotypic genus Anisosperma into Fevillea is not justified.

Several hundred angiosperm genera range from Africa to Asia and Australia, among them Bridelia (Phyllanthaceae), with ca. 40 species, including commercially important timber trees. We here use nuclear and chloroplast DNA sequences from herbarium material, plus new collections from China, to test the monophyly of Bridelia and to infer the geologic times when it acquired its disjunct range. For the Southeast Asian mainland, within-species sampling, including material collected close to the type localities, allowed testing current species concepts. Based on a sample of 114 chloroplast matK sequences of Phyllanthaceae, Bridelia is monophyletic and sister to an Asian clade which requires resurrecting an older generic name to make the African Cleistanthus monophyletic. Within Bridelia, gene trees from the combined data (3,177 aligned nucleotides from 25 species of Bridelia plus outgroups) agree with most morphological species boundaries. Exceptions are that B. tomentosa must include B. harmandii and B. curtisii to become monophyletic and that B. fordii is distinct from B. retusa. The topology, together with relaxed clock divergence times, implies that Bridelia dispersed from tropical Asia to Africa once or twice between 10 and 1.85 million years ago (Ma). Australia was reached, probably from New Guinea, at least twice, both times ca. 2 Ma. Together with earlier studies, there are now at least eight cases of Neogene long distance dispersal between Africa and Asia (followed by speciation), with no directional bias apparent so far.