TECHNICAL NOTE Anonymous nuclear markers for cetacean species A. R. Amaral Æ M. C. Silva Æ L. M. Mo ¨ller Æ L. B. Beheregaray Æ M. M. Coelho Received: 19 March 2009 / Accepted: 21 March 2009 / Published online: 2 April 2009 Ó Springer Science+Business Media B.V. 2009 Abstract Here we report the development and charac- terization of 17 anonymous nuclear markers for cetacean species. These markers were isolated from a genomic library built from a common dolphin (genus Delphinus), and tested across several families within Cetacea. An average of 1 SNP per 272 bp was found in 10 anonymous markers screened for polymorphism within the genus Delphinus (total of 6,537 bp sequenced). These markers represent a significant addition to the set of tools used in genetic studies of cetaceans where population and species boundaries have to be inferred in order to implement proper conservation strategies. Keywords SNPs Á Anonymous loci Á Common dolphins Á Delphinids Mitochondrial DNA (mtDNA) and microsatellites are amongst the most common classes of markers in ecological and conservation genetic studies (Beheregaray 2008). However, some caveats exist when mtDNA and microsat- ellite data are compared. The mtDNA genome evolves as a single unit, which yields a single gene tree, no matter how many base pairs or genes are sequenced. This warrants the need to use multiple nuclear sequence loci in studies where parameters such as effective population sizes and coales- cent times are to be estimated (Ballard and Whitlock 2004). Microsatellites, on the other hand, are very popular because of their high variability and power to resolve population structure. However, the mutation models associated with these markers are not well understood in some cases and are not comparable to the mutation model of single nucleotide substitutions per nucleotide of mtDNA genes (Takezaki and Nei 1996). Additionally, using microsatel- lite frequencies to infer the phylogeny as part of a phylogeographic study involves making a number of heroic assumptions involving clustering individuals into popula- tions for analysis, and rooting the resulting distance trees (Zink and Barrowclough 2008). Recently, with an increasing number of genome sequencing projects underway for model organisms, single nucleotide polymorphisms (SNPs) have become markers of choice for a number of studies due to several advantages compared to microsatellites (Brumfield et al. 2003; Morin et al. 2004). In non-model organisms, SNPs have been tra- ditionally obtained following two different approaches: a targeted gene approach in which primers can be designed from conserved regions of aligned sequences of at least two species in order to amplify a less conserved region [CATS, (Lyons et al. 1999)]; and an alternative approach where a genomic library is constructed with randomly sheared DNA and loci obtained by cloning sequencing (Rosenblum et al. 2007). This latter approach is more appealing for non-model organisms where hardly any sequence information exists. The Family Delphinidae is the largest and most diverse family within the Order Cetacea, with currently 37 species (Caballero et al. 2008). It is a group with a complex A. R. Amaral (&) Á M. C. Silva Á M. M. Coelho Centro de Biologia Ambiental, Departamento de Biologia Animal, Faculdade de Cie ˆncias da Universidade de Lisboa, Campo Grande, 1749-016 Lisbon, Portugal e-mail: aramaral@fc.ul.pt A. R. Amaral Á L. M. Mo ¨ller Á L. B. Beheregaray Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia L. M. Mo ¨ller Á L. B. Beheregaray School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia 123 Conserv Genet (2010) 11:1143–1146 DOI 10.1007/s10592-009-9903-3