RT Journal Article
T1 Assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors in a RAD‐seq phylogeny of Carex section Schoenoxiphium
A1 Villaverde, Tamara
A1 Maguilla Salado, Enrique
A1 Luceño Garcés, Modesto
A1 Hipp, Andrew L.
K1 Cyperaceae
K1 Divergence time estimation
K1 Next-generation sequencing
K1 Node ages
K1 Sedges
AB Restriction site‐associated DNA sequencing (RAD‐seq) and related methods have become relatively common approaches to resolve species‐level phylogeny. It is not clear, however, whether RAD‐seq data matrices are well suited to relaxed clock inference of divergence times, given the size of the matrices and the abundance of missing data. We investigated the sensitivity of Bayesian relaxed clock estimates of divergence times to alternative analytical decisions on an empirical RAD‐seq phylogenetic matrix. We explored the relative contribution of secondary calibration strategies, amount of missing data, and the data partition analyzed to overall variance in divergence times inferred using BEAST MCMC analyses of Carex section Schoenoxiphium (Cyperaceae)—a recent radiation for which we have nearly complete species sampling of RAD‐seq data. The crown node for Schoenoxiphium was estimated to be 15.22 (9.56–21.18) Ma using a single calibration point and low missing data, 11.93 (8.07–16.03) Ma using multiple calibration points and low missing data, and 8.34 (5.41–11.22)using multiple calibrations but high missing data. We found that using matrices with more than half of the individuals with missing data inferred younger mean ages for all nodes. Moreover, we have found that our molecular clock estimates are sensitive to the positions of the calibration(s) in our phylogenetic tree (using matrices with low missing data), especially when only a single calibration was applied to estimate divergence times. These results argue for sensitivity analyses and caution in interpreting divergence time estimates from RAD‐seq data.
PB Institute of Botany, Chinese Academy of Sciences
YR 2020
FD 2020-12-28
LK https://hdl.handle.net/10433/25448
UL https://hdl.handle.net/10433/25448
LA en
NO Journal of Systematics and Evolution, 59, 4: 687-697.
NO Universidad Pablo de Olavide. Departamento de Biología Molecular e Ingeniería Bioquímica
DS RIO
RD Apr 22, 2026