1. ¹Galton Laboratory, Department of Biology, University College London, London, UK
2. ²Department of Zoology, University of Cambridge, Cambridge, UK

Correspondence: Dr KK Dasmahapatra, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK. E-mail: k.dasmahapatra@ucl.ac.uk

Received 21 November 2008; Revised 9 February 2009; Accepted 10 February 2009; Published online 11 March 2009.

Abstract

Amplified fragment length polymorphisms (AFLPs) are widely used for phylogenetic reconstruction in plants but their use in animal taxa has been limited, and in mammals rare. In addition, their use has been largely limited to shallow relationships amongst species or subspecies. Here, we genotype 23 pinniped species for 310 AFLP markers and find a strong phylogenetic signal, with individuals coclustering within species, and overall a good agreement between our phylogeny and those constructed using mitochondrial DNA and nuclear sequences even at nodes 15 million years old. Although supporting the existing ideas about pinniped relationships, our data shed light on relationships within the hitherto relatively unresolved Phocine species group, and provide further supporting evidence for raising two subspecies of Zalophus californianus, Z. c. californianus and Z. c. wollebaeki, to species level. Plotting AFLP divergence time estimates against those based on both mtDNA and nuclear sequences we find strong linear relationships, suggesting that the different markers are evolving in a clocklike fashion. These data further emphasize the utility of AFLP markers as general tools for phylogenetic reconstruction.