High-throughput DNA sequencing techniques enable time- and cost-effective sequencing of large portions of the genome. Instead of sequencing and annotating whole genomes, many phylogenetic studies focus sequencing effort on large sets of pre-selected loci, which further reduces costs and bioinformatic challenges while increasing coverage. One common approach that enriches loci before sequencing is often referred to as target sequence capture. This technique has been shown to be applicable to phylogenetic studies of greatly varying evolutionary depth. Moreover, it has proven to produce powerful, large multi-locus DNA sequence datasets suitable for phylogenetic analyses. However, target capture requires careful considerations, which may greatly affect the success of experiments. Here we provide a simple flowchart for designing phylogenomic target capture experiments. We discuss necessary decisions from the identification of target loci to the final bioinformatic processing of sequence data. We outline challenges and solutions related to the taxonomic scope, sample quality, and available genomic resources of target capture projects. We hope this review will serve as a useful roadmap for designing and carrying out successful phylogenetic target capture studies.

Department of Anthropology National Museum of Natural History Smithsonian Institution Washington DC United States

Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden

Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden

Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden Institute of Entomology Biology Centre of the Czech Academy of Sciences České Budějovice Czechia

Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden Gothenburg Global Biodiversity Centre Gothenburg Sweden Royal Botanic Gardens Kew Richmond Surrey United Kingdom

Department of Biological and Environmental Sciences University of Gothenburg Gothenburg Sweden INRAE Centre Nouvelle Aquitaine Poitiers Lusignan France

Gothenburg Global Biodiversity Centre Gothenburg Sweden Programa de Pós Graduação em Genética Conservação e Biologia Evolutiva PPG GCBEv Instituto Nacional de Pesquisas da Amazônia INPA Campus 2 Manaus Brazil Coordenação de Zoologia Museu Paraense Emílio Goeldi Belém Brazil

Natural History Museum University of Oslo Oslo Norway

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