Phylogenomics of Gesneriaceae using targeted capture of nuclear genes.

Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the limited number of informative characters provided by this type of data. To overcome this limitation, we developed here a Gesneriaceae-specific gene capture kit targeting 830 single-copy loci (776,754 bp in total), including 279 genes from the Universal Angiosperms-353 kit. With an average of 557,600 reads and 87.8% gene recovery, our target capture was successful across the family Gesneriaceae and also in other families of Lamiales. From our bait set, we selected the most informative 418 loci to resolve phylogenetic relationships across the entire Gesneriaceae family using maximum likelihood and coalescent-based methods. Upon testing the phylogenetic performance of our baits on 78 taxa representing 20 out of 24 subtribes within the family, we showed that our data provided high support for the phylogenetic relationships among the major lineages, and were able to provide high resolution within more recent radiations. Overall, the molecular resources we developed here open new perspectives for the study of Gesneriaceae phylogeny at different taxonomical levels and the identification of the factors underlying the diversification of this plant group

A molecular phylogeny of Southeast Asian Cyrtandra (Gesneriaceae) supports an emerging paradigm for Malesian plant biogeography

The islands of Southeast Asia comprise one of the most geologically and biogeographically complex areas in the world and are a centre of exceptional floristic diversity, harbouring 45,000 species of flowering plants. Cyrtandra, with over 800 species of herbs and shrubs, is the largest genus in the family Gesneriaceae and is one of the most emblematic and species-rich genera of the Malesian rainforest understorey. The high number of species and tendency to narrow endemism make Cyrtandra an ideal genus for examining biogeographic patterns. We sampled 128 Cyrtandra taxa from key localities across Southeast Asia to evaluate the geo-temporal patterns and evolutionary dynamics of this clade. One nuclear and four chloroplast regions were used for phylogenetic reconstruction, molecular dating, and ancestral range estimation. Results from the dating analysis suggest that the great diversity of Cyrtandra seen in the Malesian region results from a recent radiation, with most speciation taking place in the last five million years. Borneo was recovered as the most likely ancestral range of the genus, with the current distribution of species resulting from a west to east migration across Malesia that corresponds with island emergence and mountain building. Lastly, our investigation into the biogeographic history of the genus indicates high levels of floristic exchange between the islands on the Sunda shelf and the important role of the Philippines as a stepping stone to Wallacea and New Guinea. These patterns underlie much of the plant diversity in the region and form an emerging paradigm in Southeast Asian plant biogeography

Biogeographic history of the pantropical family Gesneriaceae with a focus on the Indian plate and diversification through the Old World

The Gesneriaceae consists of around 150 genera and c. 3750 species with a predominantly tropical and subtropical distribution across all continents. Although previous studies have proposed an American origin of Gesneriaceae, the biogeographic history of this pantropical plant family is still unclear, particularly in the Old World. To address this, we assembled the most comprehensively sampled matrix of Gesneriaceae with 143 Gesneriaceae genera and 355 species, including key samples from Sri Lanka analysed here for the first time. We generated molecular phylogenies based on four plastid gene regions (ndhF, matK, rps16 and trnL-F), obtained fossil-calibrated trees, and reconstructed ancestral areas and dispersal routes using Bayesian methods. Our results confirm the origin for the family in the Early Palaeocene (67. Ma) in the region of present-day Central America & Andean South America, and that diversity in the Old World originated from a long-distance dispersal event from South America around 59 Ma, most likely to the Indian plate, which was an island at the time. This lineage then dispersed to Malesia and later East Asia, which would ultimately become a major centre of diversity and source of many dispersals to other regions. Our results thus highlight the Indian plate as a likely key player in the early diversification of Old World Gesneriaceae, even though it is now more diverse elsewhere, and hence offer novel insights into this plant family’s dispersal routes and areas of diversification in the Old World

La colocación familiar de Cyrtandromoea

Cyrtandromoea is a genus consisting of about 12 species of perennial caulescent herbs with a distribution in China, India, Myanmar, Thailand, and western Malesia. The genus has previously been associated with either Gesneriaceae or the tribe Mimuleae in Phrymaceae (in former Scrophulariaceae) with morphology in favor of the latter and molecular plastid ndhF data the former. We addressed the placement of this genus by assembling a four gene dataset (matK, ndhF, rps16, and trnL-F) comprising 270 ingroup samples representing 270 species and 51 families of the core asterids, including all families of Lamiales currently recognized. These included 111 species representing 66 genera of Gesneriaceae. We used maximum parsimony, maximum likelihood, and Bayesian inference analyses to reconstruct phylogenies that showed Cyrtandromoea to be placed in Phrymaceae. A fine-scale analysis focusing on Phrymaceae using ITS and trnL-F and 79 samples revealed that Cyrtandromoea is most closely related to a clade of genera in Phrymaceae that included Mimulus s. s. A combination of morphological synapomorphies such as cymose inflorescences, 5-angled toothed calyx, flowers with bilocular ovary with axile placentation with numerous small seeds with endosperm, and loculicidal dehiscing capsule support this placement. Our results strongly support the placement of Cyrtandromoea in Phrymaceae

Tangled history of a multigene family: The evolution of <i>ISOPENTENYLTRANSFERASE</i> genes

<div><p><i>ISOPENTENYLTRANSFERASE</i> (<i>IPT</i>) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPT^Pfam) and Pfam IPPT (IPPT^Pfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPT^Pfam domain was only found in few bacteria lineages, whereas IPPT^Pfam is common except in Archaea and <i>Mycoplasma</i> bacteria. The bacterial IPPT^Pfam domain <i>miaA</i> genes were shown as ancestral of eukaryotic IPPT^Pfam domain genes. Plant <i>IPT</i>s diversified into class I, class II tRNA-<i>IPT</i>s, and Adenosine-phosphate <i>IPT</i>s; the class I tRNA-<i>IPT</i>s appeared to represent direct successors of <i>miaA</i> genes were found in all plant genomes, whereas class II tRNA-<i>IPT</i>s originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate <i>IPT</i>s were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that <i>IPT</i> genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.</p></div