Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper... Show morePhylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip. Show less
Bogarin Chaves, D.G.; Fernandez, M.; Borkent, A.; Heemskerk, A.; Pupulin, F.; Ramirez, S.; ... ; Gravendeel, B. 2018
Pleurothallidinae (Epidendreae) are a megadiverse Neotropical orchid subtribe comprising > 5100 species, most of which are probably pollinated by Diptera. The role of pollinators as drivers of... Show morePleurothallidinae (Epidendreae) are a megadiverse Neotropical orchid subtribe comprising > 5100 species, most of which are probably pollinated by Diptera. The role of pollinators as drivers of species diversity is largely unknown because knowledge of pollination systems in Pleurothallidinae is still scarce. Here, we addressed the pollination of Trichosalpinx s.s. through study of floral anatomy, pollinator behaviour and floral traits shared with other angiosperms to elucidate its pollination mechanisms. We identified midge specimens with DNA bar-coding and morphology, documented pollination with video recordings, studied the anatomy of flowers by combining microscopy (light microscopy, scanning electron microscopy and transmission electron microscopy) and histochemistry and analysed floral scents with gas chromatography-mass spectrometry. We found that two Trichosalpinx spp. are pollinated exclusively by female biting midges of a Forcipomyia (Euprojoannisia) sp. (Ceratopogonidae). The midges land on the motile lip and appear to suck substances from its papillose surface. We detected secretion of carbohydrates and proteins on the lip and sepals, and thus, Trichosalpinx might stimulate a protein collection instinct in female biting midges. The well-developed mandibles and poorly developed laciniae of the pollinators indicate that they mainly feed on invertebrate hosts from which they draw haemolymph. Thus, Trichosalpinx flowers offer small quantities of proteins and carbohydrates that may act as flavour teases and together with the colour, fragrances, trichomes and movement of the lip, they probably form part of a complex deceptive system. Some other angiosperms that are also pollinated by biting midges possess similar dark purple flowers with ciliate ornamentation and use myophily, sapromyophily or kleptomyiophily as strategies to exploit different families of Diptera as pollinators. One Forcipomyia sp. (Euprojoannisia) is kleptoparasitic, suggesting that kleptomyiophily may have evolved in Trichosalpinx. The similar floral morphology among members of Trichosalpinx and some species of the closely related genera Anathallis and Lankesteriana suggests that they are also pollinated by biting midges. Show less
