Received: 14 October 2016 | Revised: 5 March 2017 | Accepted: 3 April 2017 DOI: 10.1111/1755-0998.12681 RESOURCE ARTICLE Squamate Conserved Loci (SqCL): A unified set of conserved loci for phylogenomics and population genetics of squamate reptiles Sonal Singhal1 | Maggie Grundler1 | Guarino Colli2 | Daniel L. Rabosky1 1Museum of Zoology and Department of Ecology and Evolutionary Biology, Abstract University of Michigan, Ann Arbor, MI, USA The identification of conserved loci across genomes, along with advances in target 2Departamento de Zoologia, Universidade capture methods and high-throughput sequencing, has helped spur a phylogenomics de Brasılia, Brasılia, Brazil revolution by enabling researchers to gather large numbers of homologous loci Correspondence across clades of interest with minimal upfront investment in locus design. Target Sonal Singhal, Museum of Zoology and Department of Ecology and Evolutionary capture for vertebrate animals is currently dominated by two approaches—anchored Biology, University of Michigan, Ann Arbor, hybrid enrichment (AHE) and ultraconserved elements (UCE)—and both approaches MI, USA. Email:
[email protected] have proven useful for addressing questions in phylogenomics, phylogeography and population genomics. However, these two sets of loci have minimal overlap with Funding information Conselho Nacional do Desenvolvimento each other; moreover, they do not include many traditional loci that that have been Cientıfico e Tecnologico – CNPq; used for phylogenetics. Here, we combine across UCE, AHE and traditional phyloge- Coordenacß~ao de Apoio a Formacßao~ de Pessoal de Nıvel Superior – CAPES; netic gene locus sets to generate the Squamate Conserved Loci set, a single inte- Fundacßao~ de Apoio a Pesquisa do Distrito grated probe set that can generate high-quality and highly complete data across all Federal – FAPDF; Directorate for Biological Sciences, Grant/Award Number: DBI three loci types.