Oscar Alejandro Pérez-Escobar

Rumbling Orchids: How To Assess Divergent Evolution Between Chloroplast Endosymbionts and the Nuclear Host

Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or outlier associations (i.e., linked pairs of operational terminal units in two phylogenies) among these data sets often provide valuable information on evolutionary processes such as chloroplast capture following hybridization, incomplete lineage sorting, and horizontal gene transfer. Statistical tools that to date have been used in cophylogenetic studies only also have the potential to test for the degree of topological congruence between organellar and nuclear data sets and reliably detect outlier associations. Two distance-based methods, namely ParaFit and Procrustean Approach to Cophylogeny (PACo), were used in conjunction to detect those outliers contributing to conflicting phylogenies independently derived from chloroplast and nuclear sequence data. We explored their efficiency of retrieving outlier associations, and the impact of input data (unit branch length and additive trees) between data sets, by using several simulation approaches. To test their performance using real data sets, we additionally inferred the phylogenetic relationships within Neotropical Catasetinae (Epidendroideae, Orchidaceae), which is a suitable group to investigate phylogenetic incongruence because of hybridization processes between some of its constituent species. A comparison between trees derived from chloroplast and nuclear sequence data reflected strong, well-supported incongruence within Catasetum, Cycnoches, and Mormodes. As a result, outliers among chloroplast and nuclear data sets, and in experimental simulations, were successfully detected by PACo when using patristic distance matrices obtained from phylograms, but not from unit branch length trees. The performance of ParaFit was overall inferior compared to PACo, using either phylograms or unit branch lengths as input data. Because workflows for applying cophylogenetic analyses are not standardized yet, we provide a pipeline for executing PACo and ParaFit as well as displaying outlier associations in plots and trees by using the software R. The pipeline renders a method to identify outliers with high reliability and to assess the combinability of the independently derived data sets by means of statistical analyses.

Geographical structure, narrow species ranges, and Cenozoic diversification in a pantropical clade of epiphyllous leafy liverworts.

Abstract The evolutionary history and classification of epiphyllous cryptogams are still poorly known. Leptolejeunea is a largely epiphyllous pantropical liverwort genus with about 25 species characterized by deeply bilobed underleaves, elliptic to narrowly obovate leaf lobes, the presence of ocelli, and vegetative reproduction by cladia. Sequences of three chloroplast regions (rbcL, trnL‐F, psbA) and the nuclear ribosomal ITS region were obtained for 66 accessions of Leptolejeunea and six outgroup species to explore the phylogeny, divergence times, and ancestral areas of this genus. The phylogeny was estimated using maximum‐likelihood and Bayesian inference approaches, and divergence times were estimated with a Bayesian relaxed clock method. Leptolejeunea likely originated in Asia or the Neotropics within a time interval from the Early Eocene to the Late Cretaceous (67.9 Ma, 95% highest posterior density [HPD]: 47.9–93.7). Diversification of the crown group initiated in the Eocene or early Oligocene (38.4 Ma, 95% HPD: 27.2–52.6). Most species clades were established in the Miocene. Leptolejeunea epiphylla and L. schiffneri originated in Asia and colonized African islands during the Plio‐Pleistocene. Accessions of supposedly pantropical species are placed in different main clades. Several monophyletic morphospecies exhibit considerable sequence variation related to a geographical pattern. The clear geographic structure of the Leptolejeunea crown group points to evolutionary processes including rare long‐distance dispersal and subsequent speciation. Leptolejeunea may have benefitted from the large‐scale distribution of humid tropical angiosperm forests in the Eocene.

Andean Mountain Building Did not Preclude Dispersal of Lowland Epiphytic Orchids in the Neotropics

The Andean uplift is one of the major orographic events in the New World and has impacted considerably the diversification of numerous Neotropical lineages. Despite its importance for biogeography, the specific role of mountain ranges as a dispersal barrier between South and Central American lowland plant lineages is still poorly understood. The swan orchids (Cycnoches) comprise ca 34 epiphytic species distributed in lowland and pre-montane forests of Central and South America. Here, we study the historical biogeography of Cycnoches to better understand the impact of the Andean uplift on the diversification of Neotropical lowland plant lineages. Using novel molecular sequences (five nuclear and plastid regions) and twelve biogeographic models, we infer that the most recent common ancestor of Cycnoches originated in Amazonia ca 5 Mya. The first colonization of Central America occurred from a direct migration event from Amazonia, and multiple bidirectional trans-Andean migrations between Amazonia and Central America took place subsequently. Notably, these rare biological exchanges occurred well after major mountain building periods. The Andes have limited plant migration, yet it has seldom allowed episodic gene exchange of lowland epiphyte lineages such as orchids with great potential for effortless dispersal because of the very light, anemochorous seeds.

Strong biogeographic signal in the phylogenetic relationships of Rochefortia Sw. (Ehretiaceae, Boraginales)

Dioecious and thorny Rochefortia Sw. is a poorly known though distinct element of the Ehretiaceae comprising woody plants restricted to the Caribbean and the adjacent American mainland. The approximately ten species display a great morphological variability and overlapping taxonomic boundaries, which makes it difficult to differentiate them (particularly in the Caribbean region). We investigated the phylogenetic relationships of Rochefortia using DNA sequence data from one nuclear locus (Internal Transcribed Spacer) and three chloroplast DNA loci (rps16, trnL–trnF, trnS–trnG). The monophyly of Rochefortia was confirmed, with a sister group relationship between an American mainland clade and a Caribbean clade. The latter segregates into three, morphologically rather variable lineages, distributed either in the Lesser Antilles or in the eastern Greater Antilles or in the western Greater Antilles. Thus, geographic occurrence rather than morphology is indicative of taxonomic delimitation in Rochefortia.

A phylogeny of Cephaloziaceae (Jungermanniopsida) based on nuclear and chloroplast DNA markers

Cephaloziaceae represent a subcosmopolitan lineage of largely terrestrial leafy liverworts with three-keeled perianths, a reduced seta, capsules with bistratose walls, filamentous sporelings, large, thin-walled cells, and vegetative distribution by gemmae. Here we present the most comprehensively sampled phylogeny available to date based on the nuclear ribosomal internal transcribed spacer region and the chloroplast markers trnL-trnF and rbcL of 184 accessions representing 41 of the 89 currently accepted species and four of the five currently accepted subfamilies. Alobielloideae are placed sister to the remainder of Cephaloziaceae. Odontoschismatoideae form a sister relationship with a clade consisting of Schiffnerioideae and Cephalozioideae. Cephalozioideae are subdivided in three genera, Fuscocephaloziopsis, Cephalozia, and Nowellia, the last two in a robust sister relationship. Most morphological species circumscriptions are supported by the molecular topologies but the Cephalozia bicuspidata complex and the Cephalozia hamatiloba complex require further study. A Neotropical clade of Odontoschisma originates from temperate ancestors. Odontoschisma yunnanense is described as new to science.