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Open Access Highly Accessed Research article

Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

Zhuo Chen, Shixia Xu, Kaiya Zhou and Guang Yang*

Author Affiliations

Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210046, China

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BMC Evolutionary Biology 2011, 11:314  doi:10.1186/1471-2148-11-314

Published: 27 October 2011

Additional files

Additional file 1:

Electrophoretic gel patterns of PCR products for the SINE loci analyzed in this study. Bands indicating the presence of the SINE are shown by black arrowheads, whereas gray arrowheads show those that indicate SINE absence. Loci are assigned alphabetically from A to J according to the clade on the phylogenetic tree shown in Figure 4. The species are numbered as follows: 1, Striped dolphin; 2, Risso's dolphin; 3, Indo-Pacific bottlenose dolphin; 4, Common bottlenose dolphin; 5, Long-beaked common dolphin; 6, Chinese white dolphin; 7, Pantropical spotted dolphin; 8, Beluga; 9, Finless porpoise; 10, Yangtze River dolphin; 11, Ginkgo-toothed beaked whale; 12, Ganges River dolphin; 13, Pygmy sperm whale; 14, Omura's whale; 15, Common minke whale; 16, hippopotamus.

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Additional file 2:

Data matrix showing the character states for the loci isolated in the present study. 0 = absence, 1 = presence,? = missing. The descriptions of each locus and taxa analyzed in this study are shown in the boxes.

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Additional file 3:

Alignments of sequences for loci Stec35 (A) and the two different SINE insertions (B). Dots indicate nucleotides identical to the consensus sequence at the top. The name of the SINE family as well as the two different SINEs are indicated in a bold box. The line above the sequences represents the tRNA-related region of the SINE. Box A and Box B promoters for RNA Polymerase III are boxed and highlighted. Putative flanking direct repeats are underlined.

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Additional file 4:

Alignments of sequences for loci Turt164 (A) (including Band A and Band B) and the four SINE insertions amplified in the four species in this study (B). Dots indicate nucleotides identical to the consensus sequence at the top. The name of the SINE family as well as its subfamily is indicated in a bold box. The line above the sequences represents the tRNA-related region of the SINE. Box A and Box B promoters for RNA Polymerase III are boxed and highlighted. Putative flanking direct repeats are underlined.

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Additional file 5:

Primers used in this study.

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