Étienne Léveillé-Bourret

Resolving Rapid Radiations within Angiosperm Families Using Anchored Phylogenomics

Abstract. Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are still based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high‐copy numbers and universal polymerase chain reaction (PCR) primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant‐specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: Weak or unresolved backbone due to rapid radiations (≤10 million years) followed by long divergence, using the Cariceae‐Dulichieae‐Scirpeae (CDS, Cyperaceae) clade as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger‐sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence‐based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long‐branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS clade. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups.

Why are there so many sedges? Sumatroscirpeae, a missing piece in the evolutionary puzzle of the giant genus Carex (Cyperaceae)

For over a century, the origins and mechanisms underlying the diversification of the enormous temperate genus Carex (>2100 species; Cariceae, Cyperaceae) have remained largely speculative. Characteristics such as its diverse ecology, varied biogeography, and intriguing cytology have made Carex a powerful model for studying plant evolution, but its uncertain sister-group relationships hinder its use in studies that depend on accurate ancestral state estimates and biogeographic inferences. To identify the sister to Carex, we estimated the phylogeny of all genera in the Cariceae-Dulichieae-Scirpeae clade (CDS) using three plastid and two nuclear ribosomal markers. Ancestral state reconstructions of key characters were made, and a time-calibrated tree estimated. Carex is strongly supported as sister to the rare East Asian Sumatroscirpus, sole genus of a new tribe, Sumatroscirpeae trib. nov. Believed to be unique to Carex, the perigynium (prophyllar bract enclosing a flower) is in fact a synapomorphy shared with this small tribe (∼4 species) that appeared 36 Mya. We thus suggest the initial key innovation in the remarkable diversification of Carex is not the perigynium, but could be the release of mechanical constraints on perigynia through spikelet truncation, resulting in novel adaptive morphologies. Monoecy, chromosomal change, and rapid inflorescence development enabling phenological isolation may also be involved. The tiny tribe Sumatroscirpeae will provide unprecedented insights into the inflorescence homology, evolution, diversification, and biogeographic history of its sister-group Carex, one of the worlds most diverse plant lineages.

Testing Hybridization Hypotheses with Morphometry: The Case of Eastern American Arctic Species of Potentilla sect. Niveae (Rosaceae)

Abstract Asexual reproduction, polyploidy and hybridization are well-known sources of taxonomic complexity in angiosperms. All these processes are believed to occur in Potentilla sect. Niveae (Rosaceae). Although it has been assumed that hybridization is common in section Niveae, this hypothesis has not been tested and recent studies suggest that phenotypic plasticity may sometimes better explain morphological intermediates in nature. To clarify the role of hybridization in the evolution of section Niveae, we tested two hybridization hypotheses for its eastern American Arctic species. The first is a potential hybrid between Potentilla nivea and Potentilla arenosa, and the second between Potentilla arenosa and Potentilla vahliana sensu lato. Twenty-four quantitative and 12 qualitative morphological characters were scored on specimens sampled from a representative range of the parental species and putative hybrids in the American Arctic east of the 100th meridian. Multivariate analyses showed that these two classes of characters give a congruent signal and that species form separate groups. Morphological evidence appears to give support to the hybridization hypothesis both between Potentilla arenosa and Potentilla nivea and between Potentilla arenosa and Potentilla vahliana sensu lato, although other explanations may also be conceivable. We discuss potential implications for the taxonomy of Potentilla and the study of hybridization in apomictic groups.

Pollinator specialization imposes stronger evolutionary constraints on flower shape

Flowers show an unrivalled diversity as reproductive organs but the evolutionary forces underlying this diversity are still poorly understood. In animal-pollinated species, flower shape is fashioned by selection imposed by pollinators, which is expected to vary according to specific guilds of effective pollinators. Using the Antillean subtribe Gesneriinae (Gesneriaceae), we tested the hypothesis that the corolla shapes of specialists effectively pollinated by one functional type of pollinator have maintained more similar shapes through time due to stronger selection constraints than those of species effectively pollinated by more than one functional type of pollinator. Using geometric morphometrics, we show that corolla shape can differentiate hummingbird specialists, bat specialists, and species with a mixed-pollination strategy (pollinated by hummingbirds, bats, and occasionally insects). Then, using evolutionary models, we show that the corolla shape of hummingbird specialists has been evolving under balancing selection, whereas a neutral model of evolution was favoured for mixed-pollination species. This suggests that the corolla shape of pollination specialists remains more similar over macro-evolutionary periods of time to remain fitted to their pollinators. In contrast, corollas of species with a mixed-pollination and thus more generalized strategy vary more, potentially because they experience effective pollination over a wider corolla shape space.Flowers show important structural variation as reproductive organs but the evolutionary forces underlying this diversity are still poorly understood. In animal-pollinated species, flower shape is strongly fashioned by selection imposed by pollinators, which is expected to vary according to guilds of effective pollinators. Using the Antillean subtribe Gesneriinae (Gesneriaceae), we tested the hypothesis that pollination specialists pollinated by one functional type of pollinator have maintained more similar corolla shapes through time due to stronger selection constraints compared to species with more generalist pollination strategies. Using geometric morphometrics and evolutionary models, we showed that the corolla of hummingbird specialists, bat specialists, and species with a mixed-pollination strategy (pollinated by hummingbirds and bats; thus a more generalist strategy) have distinct shapes and that these shapes have evolved under evolutionary constraints. However, we did not find support for smaller disparity in corolla shape for hummingbird specialists compared to more generalist species. This could be because the corolla shape of more generalist species in subtribe Gesneriinae, which has evolved multiple times, is finely adapted to be effectively pollinated by both bats and hummingbirds. These results suggest that pollination generalization is not necessarily associated with relaxed selection constraints.

Greater pollination generalization is not associated with reduced constraints on corolla shape in Antillean plants: POLLINATION GENERALIZATION AND COROLLA SHAPE

Flowers show important structural variation as reproductive organs but the evolutionary forces underlying this diversity are still poorly understood. In animal‐pollinated species, flower shape is strongly fashioned by selection imposed by pollinators, which is expected to vary according to guilds of effective pollinators. Using the Antillean subtribe Gesneriinae (Gesneriaceae), we tested the hypothesis that pollination specialists pollinated by one functional type of pollinator have maintained more similar corolla shapes through time due to more constant and stronger selection constraints compared to species with more generalist pollination strategies. Using geometric morphometrics and evolutionary models, we showed that the corolla of hummingbird specialists, bat specialists, and species with a mixed‐pollination strategy (pollinated by hummingbirds and bats; thus a more generalist strategy) have distinct shapes and that these shapes have evolved under evolutionary constraints. However, we did not find support for greater disparity in corolla shape of more generalist species. This could be because the corolla shape of more generalist species in subtribe Gesneriinae, which has evolved multiple times, is finely adapted to be effectively pollinated by both bats and hummingbirds. These results suggest that ecological generalization is not necessarily associated with relaxed selection constraints.

Phylogeny and Systematics of Cyperaceae, the Evolution and Importance of Embryo Morphology

Despite recent advances in molecular phylogenetic studies, deep evolutionary relationships in Cyperaceae are still not entirely resolved. Reduction of floral morphology and complex inflorescences pose difficulties to unravel relationships based on morphology alone. One of the most phylogenetically informative structures in Cyperaceae are the embryos. The utility of embryo characters and types in Cyperaceae systematics is reviewed in a molecular phylogenetic context using a DNA supermatrix incorporating sequences from five plastid (matK, ndhF, rbcL, rps16, trnL-F) and two nuclear ribosomal (ETS, ITS) regions. The phylogenetic hypothesis presented includes the most extensive sampling of the family to date. Fourteen qualitative morphological embryo characters were coded, ancestral state reconstructions were performed, and the embryo of each sampled genus was classified in a typological system based on key morphological features. Embryo morphology provides a valuable source of independent data for Cyperaceae systematics that can be used to place species with unknown affinities, when molecular data is not available, or when results of analyses are inconclusive or conflicting. Integrating embryo data will remain critical for future higher level studies of Cyperaceae evolution and classification.

Resolving Rapid Radiations Within Families Using Anchored Phylogenomics

Despite the promise that molecular data would provide a seemingly unlimited source of independent characters, many plant phylogenetic studies are based on only two regions, the plastid genome and nuclear ribosomal DNA (nrDNA). Their popularity can be explained by high copy numbers and universal PCR primers that make their sequences easily amplified and converted into parallel datasets. Unfortunately, their utility is limited by linked loci and limited characters resulting in low confidence in the accuracy of phylogenetic estimates, especially when rapid radiations occur. In another contribution on anchored phylogenomics in angiosperms, we presented flowering plant-specific anchored enrichment probes for hundreds of conserved nuclear genes and demonstrated their use at the level of all angiosperms. In this contribution, we focus on a common problem in phylogenetic reconstructions below the family level: weak or unresolved backbone due to rapid radiations (≤ 10 million years) followed by long divergence, using the Cariceae-Dulichieae-Scirpeae clade (CDS, Cyperaceae) as a test case. By comparing our nuclear matrix of 461 genes to a typical Sanger-sequence dataset consisting of a few plastid genes (matK, ndhF) and an nrDNA marker (ETS), we demonstrate that our nuclear data is fully compatible with the Sanger dataset and resolves short backbone internodes with high support in both concatenated and coalescence-based analyses. In addition, we show that nuclear gene tree incongruence is inversely proportional to phylogenetic information content, indicating that incongruence is mostly due to gene tree estimation error. This suggests that large numbers of conserved nuclear loci could produce more accurate trees than sampling rapidly evolving regions prone to saturation and long-branch attraction. The robust phylogenetic estimates obtained here, and high congruence with previous morphological and molecular analyses, are strong evidence for a complete tribal revision of CDS. The anchored hybrid enrichment probes used in this study should be similarly effective in other flowering plant groups. [Carex, coalescent based species tree, flowering plants, low-copy nuclear genes, low-level phylogenetics, universal hybrid enrichment probes]