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Bridging the micro and macroevolutionary levels in phylogenomics: Hyb-Seq solves relationships from populations to species and above

AuthorsTamara Villaverde; Lisa Pokorny; Sanna Olsson; Mario Rincón-Barrado; Matthew G. Johnsson; Elliot M. Gardner; Norman J. Wickett; Julià Molero; Ricarda Riina ; Sanmartín, Isabel
KeywordsEuphorbiaceae, Rand Flora
plastid skimming
target enrichment
Rand Flora
Issue DateJul-2018
CitationNew Phytologist
Abstract Reconstructing phylogenetic relationships at the micro- and macroevoutionary levels within the same tree is problematic because of the need to use different data types and analytical frameworks. We test the power of target enrichment to provide phylogenetic resolution based on DNA sequences from above-species to within-populations, using a large herbarium sampling and Euphorbia balsamifera (Euphorbiaceae) as a case-study.  Target enrichment with custom probes was combined with genome skimming (Hyb-Seq) to sequence 431 low-copy nuclear genes and partial plastome DNA. We used supermatrix, multispecies-coalescent approaches, and Bayesian dating to estimate phylogenetic relationships and divergence times.  Euphorbia balsamifera, with a disjunct Rand Flora-type distribution at opposite sides of Africa, comprises three well-supported subspecies: western Sahelian sepium is sister to eastern African-southern Arabian adenensis and Macaronesian-southwest Moroccan balsamifera. Lineage divergence times support Late Miocene to Pleistocene diversification and climate-driven vicariance to explain the Rand Flora pattern.  We show that probes designed using genomic resources from taxa not directly related to the focal group are effective in providing phylogenetic resolution at deep and shallow evolutionary levels. Low capture efficiency in herbarium samples increased the proportion of missing data but did not bias estimation of phylogenetic relationships or branch lengths
DescriptionData associated: Three folders: Bait_sequences. Draft_assemblies. Full_length_targets.
Appears in Collections:(RJB) Conjuntos de datos
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DIGITAL.zipZip Folder containing three subfolders with associated data: 1) Bait_sequences. 2) Draft_assemblies. 3) Full_Length_targets. Each subfolder includes a "ReadMe" file. 50,33 MBUnknownView/Open
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