RESEARCH

Historical biogeography of Cymbidieae. Branches color-coded according to ancestral estimated areas.
Historical biogeography of Cymbidieae. Branches color-coded according to ancestral estimated areas.

Pérez-Escobar et al. 2017 (New Phyt.)

Species richness and macroevoluionary dynamics of Cymbideae orchids in the Neotropics
Species richness and macroevoluionary dynamics of Cymbideae orchids in the Neotropics

Pérez-Escobar et al., 2017 (New Phyt.)

Maximum Likelihood phylogeny of the tribe Cymbidieae (5 markers - ~810 terminals).
Maximum Likelihood phylogeny of the tribe Cymbidieae (5 markers - ~810 terminals).

Pérez et al. 2017 (New Phyt.)

Historical biogeography of Cymbidieae. Branches color-coded according to ancestral estimated areas.
Historical biogeography of Cymbidieae. Branches color-coded according to ancestral estimated areas.

Pérez-Escobar et al. 2017 (New Phyt.)

Origin and diversification of Neotropical orchids

Orchids are one of the most prominent components of the Neotropical Flora, but their origin and diversification in the different biodiversity hotspots and ecosystems in the American Tropics remain poorly understood. In particular, the Andes, a premier biodiversity hotspot containing ca 15% of the world's plant species in just 1% of the earth's surface, is unclear how different biotic and abiotic variables have affected the pace at which Andean orchids diversified. This is mainly due to the lack of densely sampled, solid phylogenetic frameworks that have precluded research on these issues. To answer these questions, I am currently compiling phylogenies of assorted orchid lineages distributed mainly in the Andes and Central America using Sanger and next-generation sequencing methods. Using as a model group speciose Andean orchid lineages, we aim to trace in time and space their diversification, and to disentangle the contribution of main biotic (e.g. pollination syndromes, plant habits) and abiotic (e.g. Andean orogeny) diversification drivers. We are also interested in understanding how main geological events have affected migrations through time in the Neotropical region. Currently, we are building a phylogeny of the species-richest neotropical subtribe Pleurothallidinae using a target enrichment approach combined with genome skimming to resolve deep polytomies and provide support to nodes leading to rapid diversifications. An exciting paper derived from this project is available here, and was featured in the Kew Science blog (also available here). This project is supported by Prof. Alexandre Antonelli via a grant from the European Research Council. 

Changes in climatic niches and pollinators, and their corresponding morphological adaptations are recurrent across the evolutionary history of flowering plants. However, the genomic bases of those morpho-ecological transitions and their contribution to lineage diversifications are still poorly studied. To better understand the evolution of morphological novelty in plants and its link with lineage diversification, we are investigating changes in climatic envelopes and morphology through time in the orchid genus Dendrobium. This hyper-diverse clade of approximately 1500 species inhabits in a rich array of ecosystems in tropical Asia and Australasia, ranging from sea-level xerophytic forests to subalpine vegetation (>3000 m). The lineage is characterized by a remarkable diversity of vegetative and reproductive morphology, driven by repeated transitions contrasting morphological states. This system provides a unique opportunity to elucidate the role that duplication and loss of genes associated to plant development play in the evolution of morphological diversity and diversifications in plants. We are generating a well-resolved phylogenomic framework for Dendrobium, by combining newly sequenced skimmed-genomic data with GenBank sequences. Using a novel target enrichment approach optimized for complex gene families, we are sequencing genomic regions containing MADS-domain transcription factors for selected Dendrobium species spanning the entire morphological and climatic diversity of the lineage. 

Dendrobium mobile Lindl., a widely cultivated ornamental orchid
Dendrobium mobile Lindl., a widely cultivated ornamental orchid

O.Pérez (2015)

Maximum Likelihood phylogeny of MADS-box type II genes present in orchids
Maximum Likelihood phylogeny of MADS-box type II genes present in orchids

Multiple climatic niche transitions in Dendrobium orchids
Multiple climatic niche transitions in Dendrobium orchids

Figure 2 (Pérez-Escobar et al. in prep.)

Dendrobium mobile Lindl., a widely cultivated ornamental orchid
Dendrobium mobile Lindl., a widely cultivated ornamental orchid

O.Pérez (2015)

Uncorrected P-distance network of 333 concatenated nuclear genes - 160 terminals
Uncorrected P-distance network of 333 concatenated nuclear genes - 160 terminals

Pérez-Escobar et al. (in prep.)

Sampling_fraction_Epidendroids_PAFTOL_Fig2_OP.jpg
Sampling_fraction_Epidendroids_PAFTOL_Fig2_OP.jpg

Uncorrected P-distance network of 333 concatenated nuclear genes - 160 terminals
Uncorrected P-distance network of 333 concatenated nuclear genes - 160 terminals

Pérez-Escobar et al. (in prep.)

Building a family-wide orchid phylogeny using target enrichment and genome skimming

Using a combination of target enrichment and genome skimming approaches, this project aims to provide the first solid, genus-level phylogeny of one of the most speciose clades and spectacular diversifications among flowering plants: the orchid family. Perhaps equally important, it will also provide genomic data of several lineages for which DNA data is not available to date in public databases (i.e. ~40% of the genera). We aim to sample genome-wise ca. 50% of all current generic lineages, but will expand sampling in hyper-diverse clades (e.g. Bulbophyllum, Dendrobium, Epidendrum, Lepanthes). Orchid sampling makes part of the "Plant and Fungal Trees of Life" initiative developed at Kew gardens. This project is supported by the PAFTOL steering group, but additional funds top keep expanding the taxon sampling are always welcome!

Genome evolution of date palms and watermelon through archaeogenomics

In an effort to gain a better understanding of Gene Transcription Enhancers, I have recently begun to use a new technique to investigate the organization and functionality of the diverse parts of my experimental model. I am currently looking to expand this work by collaborating with other labs who have the facilities and prior experience to investigate this project further.

Maximum Likelhood tree inferred from whole plastid genomes of African and Asian Phoenix dactylifera
Maximum Likelhood tree inferred from whole plastid genomes of African and Asian Phoenix dactylifera

Pérez-Escobar et al. (submitted)

Population structure of modern Asian, African and ~2,000 ys old P. dacylifera populations derived fr
Population structure of modern Asian, African and ~2,000 ys old P. dacylifera populations derived fr

Pérez-Escobar et al. (submitted)

Maximum Likelhood tree inferred from whole plastid genomes of African and Asian Phoenix dactylifera
Maximum Likelhood tree inferred from whole plastid genomes of African and Asian Phoenix dactylifera

Pérez-Escobar et al. (submitted)