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Yardeni, Gil [1], de la Harpe, Marylaure [2], Barfuss, Michael [3], Till, Walter [1], Crego, Clara Groot [1], Rivera, Norma [4], Viruel, Juan [5], Paris, Margot [6], Hess, Jaqueline [7], Kroemer, Thorsten [8], Lexer, Christian [1], Paun, Ovidiu [9], LeRoy, Thibault [1].

Custom-made or universal? The use of target capture to bridge macro- and microevolutionary processes in tillandsioid bromeliads (Tillandsia spp), a Neotropical rapid radiation.

The study of rapid radiations calls for integrative approaches, bridging phylogenetics and population genetics to uncover the genomic substrate of diversification at different time scales. Target capture approaches emerged as an important tool to study evolutionary radiations in non-model taxa, enabling researchers to retrieve large data sets with few genomic resources. While developing taxon-specific target capture kits requires sustained effort, universal kits are readily available but may offer comparatively shallower insights, especially at short evolutionary timescales. The species-rich and ecologically diverse Bromeliaceae family provides an excellent system for studying the drivers and constraints of rapid, adaptive radiations. We focus on Tillandsia, a young subgenus (~6 Mya), yet the largest and most diverse within bromeliads with over 600 species, extensive geographical ranges and a variety of key adaptations such as epiphytism and divergent photosynthetic and pollination syndromes. We present a taxon-specific target sequence capture set for bromeliads, designed to address a wide range of evolutionary hypotheses and to assess the dynamics of adaptive and neutral variation by targeting 1,776 coding regions, including also genes putatively involved in several key traits. We compare our bait set to the 'universal' Angiosperms353 probe set, examining their power to resolve phylogenomic relationships using concatenation and species tree methods, estimate population genetic statistics and infer admixture in  Tillandsia subgenus Tillandisa. The taxon-specific set results in high enrichment success across the entire family, yet both kits offer abundant information. The taxon-specific set outperforms the universal set with respect to gene tree concordance and inferred population structure, and provides reliable data for inference of admixture and population structure. Importantly, the performance of both kits is comparable for phylogenomic analysis, highlighting the vast potential of universal kits in research at different evolutionary scales. We further discuss methodological aspects and limitations of the approach.

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1 - University of Vienna, Department of Botany and Biodiversity Research, Rennweg 14, Vienna, 1030, Austria
2 - University of Zürich, Department of Geography / RSL, Winterthurerstrasse 190, Zürich, 8057, Switzerland
3 - University Of Vienna, Botany And Biodiversity Research, Rennweg 14, Vienna, 9, 1030, Austria
4 - Max Planck Institute for Evolutionary Biology, Department of Microbial Population Biology, August-Thienemann-Str. 2, Plön, 06120, Germany
5 - Royal Botanic Gardens, Kew , Conservation Genetics, Richmond, Surrey TW9 3AE, London, UK
6 - University of Fribourg, Department of Biology, Chemin du Musée 10, Fribourg, 1700, Switzerland
7 - Helmholtz Centre for Environmental Research, Halle (Saale), Germany
8 - Universidad Veracruzana, , Centro de Investigaciones Tropicales, José María Morelos 44-46, Xalapa, Veracruz, Mexico
9 - University Of Vienna , Department Of Botany And Biodiversity Research, Rennweg 14, Vienna, A-1030, Austria

targeted sequencing
target capture
evolutionary radiation
population genetic structure

Presentation Type: Oral Paper
Session: PHYLOIII, Phylogenomics III
Location: Virtual/Virtual
Date: Thursday, July 22nd, 2021
Time: 11:00 AM(EDT)
Number: PHYLOIII005
Abstract ID:592
Candidate for Awards:Margaret Menzel Award

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