Abstract
Sequence capture of ultraconserved elements (UCEs) associated with massively parallel sequencing has become a common source of nuclear data for studies of animal systematics and phylogeography. However, mitochondrial and microsatellite variation are still commonly used in various kinds of molecular studies, and probably will complement genomic data in years to come. Here we show that besides providing abundant genomic data, UCE sequencing is an excellent source of both sequences for microsatellite loci design and complete mitochondrial genomes with high sequencing depth. Identification of dozens of microsatellite loci and assembly of complete mitogenomes is exemplified here using three species of Poospiza warbling finches from southern and southeastern Brazil. This strategy opens exciting opportunities to simultaneously analyze genome-wide nuclear datasets and traditionally used mtDNA and microsatellite markers in non-model amniotes at no additional cost.
Highlights
Mitochondrial DNA and microsatellites have been the markers of choice since the emergence of molecular data in studies of ecology and evolution [1,2]
Sequencing of mitochondrial DNA and isolation of microsatellites have relied for a long time on classic methods such as Sanger sequencing of amplicons [3], library enrichment [4] or cloning [5]
All specimens were housed at the ornithological collection of the Museu de Zoologia da Universidade de São Paulo (MZUSP), and tissue samples deposited at the Laboratório de Genética e Evolução de Aves da Universidade de São Paulo (LGEMA-USP, see Table 1)
Summary
Mitochondrial DNA and microsatellites have been the markers of choice since the emergence of molecular data in studies of ecology and evolution [1,2]. Sequencing of mitochondrial DNA and isolation of microsatellites have relied for a long time on classic methods such as Sanger sequencing of amplicons [3], library enrichment [4] or cloning [5]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. RAPiD Genomics provided support in the form of salaries for authors LGN and MFRR, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific roles of these authors are articulated in the ‘author contributions’ section
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