Phylotranscriptomic analysis and genome evolution of the Cypripedioideae (Orchidaceae).

PREMISE OF THE STUDY: The slipper orchids (Cypripedioideae) are a morphologically distinct subfamily of Orchidaceae. They also have some of the largest genomes in the orchids, which may be due to polyploidy or some other mechanism of genome evolution. We generated 10 transcriptomes and incorporated existing RNA-seq data to infer a multilocus nuclear phylogeny of the Cypripedioideae and to determine whether a whole-genome duplication event (WGD) correlated with the large genome size of this subfamily. Knowing more about timing of ancient polyploidy events can help us understand the evolution of one of the most species-rich plant families. METHODS: Transcriptome data were used to identify low-copy orthologous genes to infer a phylogeny of Orchidaceae and to identify paralogs to place any WGD events on the species tree. KEY RESULTS: Our transcriptome phylogeny confirmed relationships published in previous studies that used fewer markers but incorporated more taxa. We did not find a WGD event at the base of the slipper orchids; however, we did identify one on the Orchidaceae stem lineage. We also confirmed the presence of a previously identified WGD event deeper in the monocot phylogeny. CONCLUSIONS: Although WGD has played a role in the evolution of Orchidaceae, polyploidy does not appear to be responsible for the large genome size of slipper orchids. The conserved set of 775 largely single-copy nuclear genes identified in this study should prove useful in future studies of orchid evolution.

The butterfly plant arms-race escalated by gene and genome duplications.

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.

Elucidating steroid alkaloid biosynthesis in Veratrum californicum: production of verazine in Sf9 cells.

Steroid alkaloids have been shown to elicit a wide range of pharmacological effects that include anticancer and antifungal activities. Understanding the biosynthesis of these molecules is essential to bioengineering for sustainable production. Herein, we investigate the biosynthetic pathway to cyclopamine, a steroid alkaloid that shows promising antineoplastic activities. Supply of cyclopamine is limited, as the current source is solely derived from wild collection of the plant Veratrum californicum. To elucidate the early stages of the pathway to cyclopamine, we interrogated a V. californicum RNA-seq dataset using the cyclopamine accumulation profile as a predefined model for gene expression with the pattern-matching algorithm Haystack. Refactoring candidate genes in Sf9 insect cells led to discovery of four enzymes that catalyze the first six steps in steroid alkaloid biosynthesis to produce verazine, a predicted precursor to cyclopamine. Three of the enzymes are cytochromes P450 while the fourth is a γ-aminobutyrate transaminase; together they produce verazine from cholesterol.

Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations.

Understanding the environmental parameters that drive adaptation among populations is important in predicting how species may respond to global climatic changes and how gene pools might be managed to conserve adaptive genetic diversity. Here, we used Bayesian FST outlier tests and allele-climate association analyses to reveal two Eucalyptus EST-SSR loci as strong candidates for diversifying selection in natural populations of a southwestern Australian forest tree, Eucalyptus gomphocephala (Myrtaceae). The Eucalyptus homolog of a CONSTANS-like gene was an FST outlier, and allelic variation showed significant latitudinal clinal associations with annual and winter solar radiation, potential evaporation, summer precipitation and aridity. A second FST outlier locus, homologous to quinone oxidoreductase, was significantly associated with measures of temperature range, high summer temperature and summer solar radiation, with important implications for predicting the effect of temperature on natural populations in the context of climate change. We complemented these data with investigations into neutral population genetic structure and diversity throughout the species range. This study provides an investigation into selection signatures at gene-homologous EST-SSRs in natural Eucalyptus populations, and contributes to our understanding of the relationship between climate and adaptive genetic variation, informing the conservation of both putatively neutral and adaptive components of genetic diversity.

Development and testing of new gene-homologous EST-SSRs for Eucalyptus gomphocephala (Myrtaceae).

PREMISE OF THE STUDY: New microsatellite (simple sequence repeat [SSR]) primers were developed from Eucalyptus expressed sequence tags (ESTs) and optimized for genetic studies of the southwestern Australian tree E. gomphocephala, which is severely impacted by tree health decline and habitat fragmentation. • METHODS AND RESULTS: A total of 133 gene-homologous EST-SSR primer pairs were designed for Eucalyptus, and 44 were screened in E. gomphocephala. Of these, 17 produced reliable amplification products and 11 were polymorphic. Between two and 13 alleles were observed per locus, and observed heterozygosities ranged from 0.172 to 0.867. All 17 EST-SSRs that amplified E. gomphocephala cross-amplified to at least one of E. marginata, E. camaldulensis, and E. victrix. • CONCLUSIONS: This set of EST-SSR primer pairs will be valuable tools for future population genetic studies of E. gomphocephala and other eucalypts, particularly for studying gene-linked variation and informing seed-sourcing strategies for ecological restoration.

Do rewardless orchids show a positive relationship between phenotypic diversity and reproductive success?

Among rewardless orchids, pollinator sampling behavior has been suggested to drive a positive relationship between population phenotypic variability and absolute reproductive success, and hence population fitness. We tested this hypothesis by constructing experimental arrays using the rewardless orchid Dactylorhiza sambucina, which is dimorphic for corolla color. We found no evidence that polymorphic arrays had higher mean reproductive success than monomorphic arrays for pollinia removal, pollen deposition, or fruit set. For pollinia removal, monomorphic yellow arrays had significantly greater reproductive success, and monomorphic red the least. A tendency for yellow arrays to have higher pollen deposition was also found. We argue that differential population fitness was most likely to reflect differential numbers of pollinators attracted to arrays, through preferential long-distance attraction to arrays with yellow inflorescences. Correlative studies of absolute reproductive success in 52 populations of D. sambucina supported our experimental results. To our knowledge this is the first study to suggest that attraction of a greater number of pollinators to rewardless orchids may be of greater functional importance to population fitness, and thus ecology and conservation, than are the behavioral sequences of individual pollinators.

Experimental investigation of the effect of spatial aggregation on reproductive success in a rewardless orchid.

Plant reproductive success within a patch may depend on plant aggregation through pollinator attraction. For rewardless plants that lack rewards for pollinators, reproductive success may rely strongly on the learning abilities of pollinators. These abilities depend on relative co-flowering rewarding and rewardless plant species spatial distributions. We investigated the effect of aggregation on the reproductive success of a rewardless orchid by setting up 16 arrays in a factorial design with two levels of intraspecific aggregation for both a rewardless orchid and a rewarding co-flowering species. Our results show that increasing aggregation of both species negatively influenced the reproductive success of the rewardless plants. To our knowledge, this is the first experimental study demonstrating negative effects of aggregation on reproductive success of a rewardless species due both to its own spatial aggregation and that of a co-flowering rewarding species. We argue that pollinator learning behaviour is the key driver behind this result.

Pollinator limitation and inbreeding depression in orchid species with and without nectar rewards.

Many orchids produce no nectar rewards. Foraging pollinators should visit more flowers per inflorescence in species with nectar, which could increase geitonogamous self-fertilization. If a history of selfing decreases genetic load, then nectar-producing orchids should harbour lower inbreeding depression than nectarless species. Here, I tested this hypothesis by quantifying inbreeding depression and pollinator limitation in populations of three closely related orchid species, one of which provides nectar. I also compared inbreeding depression for nectarless and nectar-producing species of orchids using published studies. All field populations expressed pollinator limitation, but the nectar-providing species was intermediate to the two nectarless species. All populations expressed inbreeding depression, and levels increased in later life-history stages. There was no tendency for nectarless species to express higher inbreeding depression either in experiments or published studies. Nectarless orchids may not express higher levels of inbreeding depression because pollinators fail to visit more flowers in nectar-bearing species, because such visitations do not result in greater selfing, and/or because higher selfing may be ineffective in purging the mutations that cause load.

Epiphytism and pollinator specialization: drivers for orchid diversity?

Epiphytes are a characteristic component of tropical rainforests. Out of the 25,000 orchid species currently known to science, more than 70% live in tree canopies. Understanding when and how these orchids diversified is vital to understanding the history of epiphytic biomes. We investigated whether orchids managed to radiate so explosively owing to their predominantly epiphytic habit and/or their specialized pollinator systems by testing these hypotheses from a statistical and phylogenetic standpoint. For the first approach, species numbers of 100 randomly chosen epiphytic and terrestrial genera were compared. Furthermore, the mean number of pollinators per orchid species within the five subfamilies was calculated and correlated with their time of diversification and species richness. In the second approach, molecular epiphytic orchid phylogenies were screened for clades with specific suites of epiphytic adaptations. Epiphytic genera were found to be significantly richer in species than terrestrial genera both for orchids and non-orchids. No evidence was found for a positive association between pollinator specialization and orchid species richness. Repeated associations between a small body size, short life cycle and specialized clinging roots of twig epiphytes in Bulbophyllinae and Oncidiinae were discovered. The development of twig epiphytism in the first group seems repeatedly correlated with speciation bursts.

The evolution of empty flowers revisited.

The evolution of plants that provide no form of reward for their pollinators is puzzling because they receive low numbers of pollinator visits and so have low reproductive success. To predict the evolutionary dynamics of empty morphs within a plant population, we modeled different foraging strategies that pollinators could use to avoid them. We predicted that the optimal strategy was to visit empty inflorescences randomly when these were infrequent but to use strategies such as visiting fewer flowers per inflorescence to avoid wasting time on them. As the frequencies of empty inflorescences increased, discriminating directly against empty morphs was more likely to be an optimal strategy than was avoiding the species altogether and switching to an alternative one. An experimental test of this model using artificial inflorescences showed that bumblebees used a variety of strategies to minimize time wasted on empty inflorescences. They showed weak discrimination against empty inflorescences but switched to an alternative type of inflorescence as the frequency of empty inflorescences increased. We predicted that empty morphs would be at a visitation rate disadvantage even when at low frequencies in a plant population. Differences in outcrossing rates, or male function, may explain how rewardlessness spreads in a plant population.

The potential for floral mimicry in rewardless orchids: an experimental study.

More than one-third of orchid species do not provide their pollinators with either pollen or nectar rewards. Floral mimicry could explain the maintenance of these rewardless orchid species, but most rewardless orchids do not appear to have a rewarding plant that they mimic specifically. We tested the hypothesis that floral mimicry can occur through similarity based on corolla colour alone, using naive bumble-bees foraging on arrays of plants with one rewarding model species, and one rewardless putative mimic species (Dactylorhiza sambucina) which had two colour morphs. We found that when bees were inexperienced, they visited both rewardless morphs randomly. However, after bees had gained experience with the rewarding model, and it was removed from the experiment, bees resampled preferentially the rewardless morph most similar to it in corolla colour. This is the first clear evidence, to our knowledge, that pollinators could select for floral mimicry. We suggest that floral mimicry can be a selective force acting on rewardless orchids, but only under some ecological conditions. In particular, we argue that selection on early-flowering rewardless orchids that receive visits from a large pool of naive pollinators will be weakly influenced by mimicry.

The consequences of rewardlessness in orchids: reward-supplementation experiments with Anacamptis morio (Orchidaceae).

Pollinators are expected to respond to low reward availability in an inflorescence by visiting fewer flowers before departure, thus potentially causing reduced visitation, but also reduced geitonogamous selfing. I tested this hypothesis using Anacamptis morio, an orchid that does not reward its pollinators. Supplementation of inflorescences with artificial nectar did not result in an increase in fruit set on supplemented inflorescences compared to control inflorescences and tended to reduce pollinia removal. Supplementation resulted in reduced fruit quality, but there was no evidence that this was as a result of inbreeding depression. Behavioral experiments showed that pollinating bumble bees, as predicted, visited more flowers on supplemented inflorescences. Bumble bees also deposited more self-pollen on supplemented inflorescences, but this was marginally significant. Bumble bee queens removed significantly more pollinia from control inflorescences, while Bombus terrestris and B. lucorum workers did not. I conclude that while pollinators behaved as predicted, there was weak evidence that pollinia removal, pollen deposition, and fruit set followed the predictions of the hypothesis. I argue that this was probably because some pollinators were more efficient at removing and depositing pollen on control inflorescences, while others were not.

NEGATIVE FREQUENCY-DEPENDENT SELECTION BY POLLINATORS ON ARTIFICIAL FLOWERS WITHOUT REWARDS.

Many species of nonmodel deceptively pollinated orchids are polymorphic for corolla color. These species are pollinated by naive insects searching for nectar, and are not mimics. It has been suggested that the foraging behavior of insect pollinators during the avoidance learning process results in these stable corolla color polymorphisms; for this to occur pollinators must induce negative frequency-dependent selection on corolla color. Therefore the hypothesis that pollinator behavior results in a preference for rare color morphs of deceptive species was tested experimentally. Bumblebees (Bombus terrestris) foraged in the laboratory on arrays of artificial flowers with different corolla color morphs. Morphs were varied in frequency, and bumblebee preferences were recorded on arrays where morphs did and did not contain sucrose solution rewards. Bumblebees preferred the most common color morph when flowers contained sucrose solution rewards, but overvisited rare morphs when sampling flowers that contained no rewards. Bumblebees also tended to move between unlike color morphs when these were unrewarding, suggesting that a probabilistic sampling strategy was adopted. Thus experiments demonstrated that pollinator behavior could result in a selective advantage for rare color morphs of plant species that are pollinated by deception without mimicry, which would induce negative frequency-dependent selection on corolla color. The observed pollinator behavior could allow stable corolla color polymorphisms to be maintained by selection in nonmodel deceptively pollinated species.