[OANNES Foro] Pinniped phylogenetic relationships inferred using AFLP markers

[Mario Cabrejos]

Heredity (2009) 103, 168-177
published online 11 March 2009
doi:10.1038/hdy.2009.25

Pinniped phylogenetic relationships inferred using AFLP markers
K K Dasmahapatra1, J I Hoffman2 and W Amos2
1Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, London, UK 
2Department of Zoology, University of Cambridge, Cambridge, UK
Correspondence: Dr KK Dasmahapatra E-mail: k.dasmahapatra en ucl.ac.uk
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.

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