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<DIV id=cite><I></I> </DIV>
<DIV><I>Heredity</I> (2009) <B>103,</B> 168–177</DIV>
<DIV>published online 11 March 2009</DIV>
<DIV>doi:10.1038/hdy.2009.25</DIV>
<DIV> </DIV>
<DIV id=atl><FONT size=4>Pinniped phylogenetic relationships inferred using AFLP
markers</FONT></DIV>
<DIV id=aug>K K Dasmahapatra<SUP><A title="affiliated with 1"
href="http://www.nature.com/hdy/journal/v103/n2/abs/hdy200925a.html#aff1">1</A></SUP>,
J I Hoffman<SUP><A title="affiliated with 2"
href="http://www.nature.com/hdy/journal/v103/n2/abs/hdy200925a.html#aff2">2</A></SUP>
and W Amos<SUP><A title="affiliated with 2"
href="http://www.nature.com/hdy/journal/v103/n2/abs/hdy200925a.html#aff2">2</A></SUP></DIV>
<DIV id=aff1><SUP>1</SUP>Galton Laboratory, Department of Biology, University
College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, London, UK
</DIV>
<DIV id=aff2><SUP>2</SUP>Department of Zoology, University of Cambridge,
Cambridge, UK</DIV>
<DIV class=caff>Correspondence: Dr KK Dasmahapatra E-mail: <A
href="mailto:k.dasmahapatra@ucl.ac.uk">k.dasmahapatra@ucl.ac.uk</A></DIV>
<DIV>
<P class=prdates><FONT size=3><STRONG>Abstract</STRONG></FONT></P>
<DIV id=abs>
<P class="abs lead">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 <IMG
style="BORDER-TOP-WIDTH: 0px; BORDER-LEFT-WIDTH: 0px; BORDER-BOTTOM-WIDTH: 0px; VERTICAL-ALIGN: baseline; BORDER-RIGHT-WIDTH: 0px"
alt=approx
src="http://www.nature.com/__chars/math/special/sim/black/med/base/glyph.gif">15
million years old. </P>
<P class="abs lead">Although supporting the existing ideas about pinniped
relationships, our data shed light on relationships within the hitherto
relatively unresolved <U>Phocine species group</U>, and provide further
supporting evidence for raising two subspecies of <I>Zalophus californianus</I>,
<I>Z. c. californianus</I> and <I>Z. c. wollebaeki</I>, to species level. </P>
<P class="abs lead">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.</P>
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