Using RAD seq for rec on structing phylogenies of highly diverged taxa:A test using the tribe Scandiceae(Apiaceae)  

作　　者：Marcin Piwczynski Paulina Trzeciak Madalina-Oana Popa Maciej Pabijan Jose Maria Corral Krzysztof Spalik Andrzej Grzywacz 

机构地区：[1]Department of Ecology and Biogeography,Nicolaus Copernicus University in Torun,Lwowska 1,Torun PL-87-100,Poland [2]Departme nt of Comparative An atomy,In stitute of Zoology and Biomedical Research,Jagiellonia n Un iversity,Gronostajowa 9,Krakow 30-387,Poland [3]Division of Biochemistry,Department Biologie,Universitat Erlangen-Nurnberg,Erlangen 91058,Germany [4]Institute of Evolutionary Biology,Faculty of Biology,University of Warsaw Biological and Chemical Research Centre,Zwirki i Wigury 4,Warszawa 02-089,Poland

出　　处：《Journal of Systematics and Evolution》2021年第1期58-72,共15页植物分类学报（英文版）

摘　　要：The angiosperm Apiaceae tribe Scandiceae includes four major clades-subtribes Daucinae,Ferulinae,Torilidinae,and Scandicinae-that originated ca.20 Mya.Although all four subtribes are highly supported in molecular analyses,and morphological data indicate a sister relationship between Daucinae and Torilidinae,their branching order has not been resolved using standard Sanger multilocus data.Therefore,in this study,we test the utility of genomic RAD seq data in resolving deep phylogenetic relaUonships(up to 20 Mya)in Apiaceae subfamily Apioideae,with special emphasis on tribe Scandiceae using 12 representative species.We used two bioinformatic pipelines,pyRAD and RADIS(based on STACKS),to assemble RAD seq data and we tested the in fluence of various com bin ations of parameters on the robust ness of the inferred tree topologies.Although differe nt data processi ng approaches produced alignments with various amounts of missing data,they converged to two well-supported topologies,irrespec廿ve of the phylogenetic method applied.Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups,thus con firming the relationship inferred from morphology.We con elude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae.We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.

关 键 词：nrDNA ITS PDNA pyRAD RADIS STACKS UMBELLIFERAE 

分 类 号：Q948[生物学—植物学]