Missing data are commonly encountered using multilocus, fragment‐based (dominant) fingerprinting methods, such as random amplified polymorphic DNA (RAPD) or amplified fragment length polymorphism (AFLP). Data sets containing missing data have been analysed by eliminating those bands or samples with missing data, assigning values to missing data or ignoring the problem. Here, we present a method that uses random assignments of band presence–absence to the missing data, implemented by the computer program famd (available from http://homepage.univie.ac.at/philipp.maria.schlueter/famd.html), for analyses based on pairwise similarity and Shannon's index. When missing values group in a data set, sample or band elimination is likely to be the most appropriate action. However, when missing values are scattered across the data set, minimum, maximum and average similarity coefficients are a simple means of visualizing the effects of missing data on tree structure. Our approach indicates the range of values that a data set containing missing data points might generate, and forces the investigator to consider the effects of missing values on data interpretation.

It has been proposed that the diversification of the MADS-box gene family of transcription factors has played a major role in the radiation of land plants. This suggestion is based on the critical roles that these genes play in plant development and the apparent coincidence of key duplication events with major radiations, such as the establishment of the B and C lineages concurrent with the evolution of the seed plants. On a more recent scale, it is also possible that subsequent duplication events have contributed to later morphological diversifications. In order to investigate this possibility, we are studying the evolution of homologs of the petal and stamen identity genes APETALA3 (AP3) and PISTILLATA (PI) in the Ranunculaceae. In this family, the AP3 and PI lineages have undergone many duplication events at every phylogenetic level. Early duplications gave rise to three paralogous AP3 lineages, which are found throughout the family. In contrast, numerous duplications have occurred relatively recently in the PI lineage. We outline a hypothesis that these duplications have played a role in the evolution of the unique types of petaloid organs in the Ranunculaceae and present preliminary expression data supporting such a scenario.

Aim  Plants in islands have often evolved through adaptive radiation, providing the classical model of evolution of closely related species each with strikingly different morphological and ecological features and with low levels of genetic divergence. We emphasize the importance of an alternative (anagenetic) model of evolution, whereby a single island endemic evolves from a progenitor and slowly builds up genetic variation through time. Location  Continental and oceanic islands. Methods  We surveyed 2640 endemic angiosperm species in 13 island systems of the world, both oceanic and continental, for anagenetic and cladogenetic patterns of speciation. Genetic data were evaluated from a progenitor and derivative species pair in Ullung Island, Korea, and Japan. Results  We show that the anagenetic model of evolution is much more important in oceanic islands than previously believed, accounting for levels of endemic specific diversity from 7% in the Hawaiian Islands to 88% in Ullung Island, Korea, with a mean for all islands of 25%. Examination of an anagenetically derived endemic species in Ullung Island reveals genetic (amplified fragment length polymorphism) variation equal or nearly equal to that of its continental progenitor. Main conclusions  We hypothesize that, during anagenetic speciation, initial founder populations proliferate, and then accumulate genetic variation slowly through time by mutation and recombination in a relatively uniform environment, with drift and/or selection yielding genetic and morphological divergence sufficient for the recognition of new species. Low‐elevation islands with low habitat heterogeneity are highly correlated with high levels of anagenetic evolution, allowing prediction of levels of the two models of evolution from these data alone. Both anagenetic and adaptive radiation models of speciation are needed to explain the observed levels of specific and genetic diversity in oceanic islands.

Floral isolation is a form of prepollination reproductive isolation mediated by floral morphology (morphological isolation) and pollinator behavior (ethological isolation). Here we review mechanisms and evolutionary consequences of floral isolation in various pollination systems. Furthermore, we compare key features of floral isolation, i.e., pollinator sharing and specialization in pollination, in different orchid pollination systems. In orchid pollination, pollinator sharing is generally low, indicating strong floral isolation. The pollinators' motivation to visit flowers (specifically) can be due to both foraging or reproductive behavior. In both types of behavior, innate preferences for floral signals can be quickly overruled by learning. In pollination systems in which reproductive behavior of pollinators triggers flower visits, lower pollinator sharing was evident compared with systems with foraging behavior, probably because pollinators displaying reproductive behavior show higher fidelity in their visitation patterns. Orchids pollinated through reproductive behavior also use fewer pollinators than orchids pollinated through foraging behavior. No association between specialization and pollinator sharing was found. Thus, generalized pollination does not impede floral isolation, as orchids with many pollinators may nonetheless have low pollinator sharing. Specialization in pollination was, however, linked to orchid species richness in our analysis. Flower size, spur, and column morphology are most important for morphological isolation, and floral scent is most important for ethological isolation. These traits may be based on few genes, implying that floral isolation can be brought about by few genes of large effect.

Floral isolation is an important

SummaryEpisodes of rapid speciation provide unique insights into evolutionary processes underlying species radiations and patterns of biodiversity. Here we investigated the radiation of sexually deceptive bee orchids (Ophrys).Based on a time-calibrated phylogeny and by means of ancestral character reconstruction and divergence time estimation, we estimated the tempo and mode of this radiation within a state-dependent evolutionary framework.It appears that, in the Pleistocene, the evolution of Ophrys was marked by episodes of rapid diversification coinciding with shifts to different pollinator types: from wasps to Eucera bees to Andrena and other bees. An abrupt increase in net diversification rate was detected in three clades. Among these, two phylogenetically distant lineages switched from Eucera to Andrena and other bees in a parallel fashion and at about the same time in their evolutionary history.Lack of early radiation associated with the evolution of the key innovation of sexual deception suggests that Ophrys diversification was mainly driven by subsequent ecological opportunities provided by the exploitation of novel pollinator groups, encompassing many bee species slightly differing in their sex pheromone communication systems, and by spatiotemporal fluctuations in the pollinator mosaic.

The orchids Ophrys sphegodes and O. exaltata are reproductively isolated from each other by the attraction of two different, highly specific pollinator species. For pollinator attraction, flowers chemically mimic the pollinators' sex pheromones, the key components of which are alkenes with different double-bond positions. This study identifies genes likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturase (SAD) homologs. The expression of two isoforms, SAD1 and SAD2, is flower-specific and broadly parallels alkene production during flower development. SAD2 shows a significant association with alkene production, and in vitro assays show that O. sphegodes SAD2 has activity both as an 18:0-ACP Δ 9 and a 16:0-ACP Δ 4 desaturase. Downstream metabolism of the SAD2 reaction products would give rise to alkenes with double-bonds at position 9 or position 12, matching doublebond positions observed in alkenes in the odor bouquet of O. sphegodes. SAD1 and SAD2 show evidence of purifying selection before, and positive or relaxed purifying selection after gene duplication. By contributing to the production of species-specific alkene bouquets, SAD2 is suggested to contribute to differential pollinator attraction and reproductive isolation among these species. Taken together, these data are consistent with the hypothesis that SAD2 is a florally expressed barrier gene of large phenotypic effect and, possibly, a genic target of pollinator-mediated selection.acyl-acyl carrier protein desaturase | isolation genes | pollination | speciation R eproductive isolation is a central topic in the study of evolution, its origin and maintenance being critical for the process of speciation. This statement is especially true for ecological speciation, in which divergent selection pressures on key traits drive the establishment of reproductive isolation even in the absence of geographic barriers to gene flow (1). This process fits the genic view of speciation, in which only few loci of large effect may be responsible for species differentiation, whereas gene flow is possible throughout the rest of the genome (2, 3). In practice, the challenge in studying these processes is identifying the traits under divergent selection and their genetic basis (1). In plants with strong pollinator-mediated reproductive isolation (floral isolation), however, key floral traits are direct targets of selection (1, 4). By identifying the molecular mechanisms underlying these traits, genes directly involved in reproductive isolation (so-called "barrier" or "isolation" genes) or even speciation can be identified (3-5).Strong floral isolation and high pollinator specificity make sexually deceptive orchids an excellent system for identifying barrier genes (4, 6). Rewardless orchids of the genus Ophrys attract male insects by sexual mimicry, inducing mating attempts of pollinators with flowers, whereby pollen is transferred. The key component to this system is the chemical mimicry of the pollinator female's sex pheromone (7, 8), a ...

In plants, pollinator adaptation is considered to be a major driving force for floral diversification and speciation. However, the genetic basis of pollinator adaptation is poorly understood. The orchid genus Ophrys mimics its pollinators' mating signals and is pollinated by male insects during mating attempts. In many species of this genus, chemical mimicry of the pollinators' pheromones, especially of alkenes with different double-bond positions, plays a key role for specific pollinator attraction. Thus, different alkenes produced in different species are probably a consequence of pollinator adaptation. In this study, we identify genes that are likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturases (SAD), in three closely related Ophrys species, O. garganica, O. sphegodes, and O. exaltata. Combining floral odor and gene expression analyses, two SAD homologs (SAD1/2) showed significant association with the production of (Z)-9- and (Z)-12-alkenes that were abundant in O. garganica and O. sphegodes, supporting previous biochemical data. In contrast, two other newly identified homologs (SAD5/6) were significantly associated with (Z)-7-alkenes that were highly abundant only in O. exaltata. Both molecular evolutionary analyses and pollinator preference tests suggest that the alkenes associated with SAD1/2 and SAD5/6 are under pollinator-mediated divergent selection among species. The expression patterns of these genes in F1 hybrids indicate that species-specific expression differences in SAD1/2 are likely due to cis-regulation, while changes in SAD5/6 are likely due to trans-regulation. Taken together, we report a genetic mechanism for pollinator-mediated divergent selection that drives adaptive changes in floral alkene biosynthesis involved in reproductive isolation among Ophrys species.