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MBE Advance Access published online on August 25, 2004
Molecular Biology and Evolution, doi:10.1093/molbev/msh241
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2004; all rights reserved
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Accepted August 23, 2004

Research Article

Phylogenetic Assessment of Introns and SINEs Within the Y-chromosome Using the Cat Family Felidae as a Species Tree

J. Pecon-Slattery 1*, A. J. Pearks Wilkerson 2, W. J. Murphy 2, S.J. O'Brien 1

1 National Cancer Institute-Frederick, Frederick MD 21702
2 Basic Research Program, SAIC-Frederick, Inc, NCI-Frederick, Frederick MD 21702

* To whom correspondence should be addressed. E-mail: Slattery{at}mail.ncifcrf.gov.


  Abstract

The cat family Felidae was used as a species tree to assess the phylogenetic performance of genes, and their embedded SINE elements, within the non-recombining region of the Y-chromosome (NRY). Genomic segments from single copy X-Y homologues SMCY, UBE1Y and ZFY (3604 bp) were amplified in 36 species of cat. These genes are located within the X-degenerate region of the NRY and are thought to be molecular "fossils" that ceased conventional recombination with the X-chromosome early within the placental mammal evolution. The pattern and tempo of evolution at these three genes is significant in light of the recent, rapid evolution of the family over approximately 12 MY and provides exceptional support for each of the eight recognized felid lineages as well as clear diagnostic substitutions identifying nearly all species. Bootstrap support and Bayesian posterior probabilities are uniformly high for defining each of the eight monophyletic lineages. Further, the preferential use of specific target site motifs facilitating SINE insertion is empirically supported by sequence analyses of SINEs embedded within the three genes. Target site insertion is thought to explain the contradiction between intron phylogeny and results of the SMCY SINE phylogeny that unites distantly related species. Overall, our data suggest X-degenerate genes within the NRY are singularly powerful markers and offer a valuable patrilineal perspective in species evolution.

Keywords: ZFY; SMCY UBE1Y; SINE; evolution; Felidae; Y-chromosome.
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