Assessing the sensitivity of divergence time estimates to locus sampling, calibration points, and model priors in a RAD-seq phylogeny of Carex section Schoenoxiphium  

作　　者：Tamara Villaverde Enrique Maguilla Modesto Luceno Andrew L.Hipp 

机构地区：[1]The Morton Arboretum,4100 Illinois Route 53,Lisle,IL,USA [2]Universidad Pablo de Olavide,ctra.de Utrera kmi Seville 41013,Spain [3]Universidad de Sevilla,Reina Mercedes sn,Seville 41012,Spain [4]The Field Museum,1400 S Lake Shore Dr,Chicago,IL 60605,USA

出　　处：《Journal of Systematics and Evolution》2021年第4期687-697,共11页植物分类学报（英文版）

基　　金：supported by the Spanish Ministry of Science and Technology[CGL2012-38744,CGL2016-77401-P];the Spanish Ministry of Education,Culture and Sport(FPU fellowship AP2012-2189);U.S.National Science Foundation(Award 1255901 to ALH).TV is supported by grant UAL18-RNM-B082-B-E(UAL/CECEU/FEDER).

摘　　要：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.

关 键 词：CYPERACEAE divergence time estimation next-generation sequencing node ages SEDGES 

分 类 号：Q94[生物学—植物学]