Biology Faculty Articles

Title

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

Document Type

Article

Publication Date

12-2004

Publication Title

Molecular Biology and Evolution

Keywords

ZFY, SMCY UBE1Y, SINE, Evolution, Felidae, Y chromosome

ISSN

0737-4038

Volume

21

Issue/No.

12

First Page

2299

Last Page

2309

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 nonrecombining region of the Y chromosome (NRY). Genomic segments from single-copy X-Y homologs SMCY, UBE1Y, and ZFY (3,604 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 Myr 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.

Comments

©2004 Society for Molecular Biology and Evolution

Additional Comments

National Cancer Institute contract #: N01-CO-12400; GenBank accession #s: AY219653-219681, AY518597-AY518631, AY518632-AY518667

ORCID ID

0000-0001-7353-8301

ResearcherID

N-1726-2015

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