Eight anonymous nuclear loci for the squamate antbird ( Myrmeciza squamosa ), cross-amplifiable in other species of typi
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TECHNICAL NOTE
Eight anonymous nuclear loci for the squamate antbird (Myrmeciza squamosa), cross-amplifiable in other species of typical antbirds (Aves, Thamnophilidae) Fa´bio Raposo do Amaral • Scott V. Edwards Cristina Y. Miyaki
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Received: 30 January 2012 / Accepted: 8 February 2012 / Published online: 24 February 2012 Ó Springer Science+Business Media B.V. 2012
Abstract Typical antbirds (*209 species) represent a diverse radiation of Neotropical birds that includes many species of conservation concern. Here we present eight anonymous nuclear loci designed for the squamate antbird Myrmeciza squamosa, a species endemic to the Atlantic Forest of Brazil. We also show that those anonymous nuclear loci are amplifiable in a number of other typical antbird species from related genera (Myrmeciza, Percnostola, Gymnocichla, Myrmoborus, Pyriglena and Formicivora), including three threatened species (Myrmeciza ruficauda, Formicivora littoralis, and Pyriglena atra). Those markers will be useful not only to help management of threatened species of typical antbirds, but also to explore their evolutionary histories, both at intra and interspecific levels. Keywords Anonymous nuclear loci Typical antbirds Thamnophilidae Myrmeciza
F. R. do Amaral (&) C. Y. Miyaki Departamento de Gene´tica e Biologia Evolutiva, Universidade de Sa˜o Paulo, Rua do Mata˜o, 277, Cidade Universita´ria, Sa˜o Paulo, SP 05508-090, Brazil e-mail: [email protected] Present Address: F. R. do Amaral Departamento de Cieˆncias Biolo´gicas, Universidade Federal de Sa˜o Paulo, Campus Diadema. Rua Prof. Artur Riedel, 275, Jardim Eldorado, Diadema, SP 09972-270, Brazil S. V. Edwards Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138, USA
The Neotropical region is home of the typical antbirds, family Thamnophilidae, which contains approximately 209 species (Zimmer and Isler 2003). The Atlantic Forest (AF) harbours several endemic species of typical antbirds, including species of conservation concern (IUCN 2011). Anonymous nuclear loci (ANL) are single-copy nuclear markers, randomly obtained throughout the genome (Balakrishnan et al. 2010). Compared to commonly used introns, these markers may present higher variation (Lee and Edwards 2008), be less affected by selection, gene hitchhiking, and the negative impact of ascertainment bias in marker choice (Balakrishnan et al. 2010), what make them ideal sources of neutral variation. Eight ANLs were obtained from the squamate antbird following published protocols (Jennings and Edwards 2005; Lee and Edwards 2008). Genomic DNA from one vouchered specimen (LSUMZ B-16940) was extracted using the DNeasy kit (Qiagen, Inc) according to the manufacturer’s protocol. The resulting DNA was fragmented using a HydroShear DNA shearing device (Digilab Inc., Holliston, MA), using 20 fragmentation cycles and speed code 3. Blunt-end cloning was performed using a TOPO Shotgun Subcloning Kit (Invitrogen, Carlsbad, CA) using pUC19 vector and chemically competent Escherich
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