0000000001323206
AUTHOR
Oscar Alejandro Pérez-escobar
Hundreds of nuclear and plastid loci yield novel insights into orchid relationships.
Pérez-Escobar, Oscar Alejandro, Dodsworth, Steven, Bogarín, Diego, Bellot, Sidonie, Balbuena, Juan A, Schley, Rowan J, Kikuchi, Izai A, Morris, Sarah K, Epitawalage, Niroshini, Cowan, Robyn, Maurin, Olivier, Zuntini, Alexandre, Arias, Tatiana, Serna-Sánchez, Alejandra, Gravendeel, Barbara, Torres Jimenez, Maria Fernanda, Nargar, Katharina, Chomicki, Guillaume, Chase, Mark W, Leitch, Ilia J, Forest, Félix, Baker, William J (2021): Hundreds of nuclear and plastid loci yield novel insights into orchid relationships. American journal of botany 108 (7): 1166-1180, DOI: http://doi.org/10.5281/zenodo.7778176
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 …
Hundreds of nuclear and plastid loci yield insights into orchid relationships
ABSTRACTPremise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test…
Random Tanglegram Partitions (Random TaPas): An Alexandrian Approach to the Cophylogenetic Gordian Knot
Abstract Symbiosis is a key driver of evolutionary novelty and ecological diversity, but our understanding of how macroevolutionary processes originate extant symbiotic associations is still very incomplete. Cophylogenetic tools are used to assess the congruence between the phylogenies of two groups of organisms related by extant associations. If phylogenetic congruence is higher than expected by chance, we conclude that there is cophylogenetic signal in the system under study. However, how to quantify cophylogenetic signal is still an open issue. We present a novel approach, Random Tanglegram Partitions (Random TaPas) that applies a given global-fit method to random partial tanglegrams of …
Data from: 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 …