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Open Access Research article

One misdated sequence of rabbit hemorrhagic disease virus prevents accurate estimation of its nucleotide substitution rate

Allison L Hicks and Siobain Duffy*

Author Affiliations

Department of Ecology, Evolution, and Natural Resources, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, 14 College Farm Rd, New Brunswick, NJ, 08901, USA

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BMC Evolutionary Biology 2012, 12:74  doi:10.1186/1471-2148-12-74

Published: 30 May 2012

Additional files

Additional file 1:

MCC tree produced from the complete RHDV + RCV VP60 dataset (without AY269825). Node bars represent the 95% HPDs for the node ages. The dashed line indicates the 1984 emergence of RHD in China.

Format: TIFF Size: 338KB Download file

Open Data

Additional file 2:

MCC tree produced from the complete RHDV + RCV RdRp dataset. Node bars represent the 95% HPDs for the node ages. The dashed line indicates the 1984 emergence of RHD in China.

Format: TIFF Size: 527KB Download file

Open Data

Additional file 3:

RHDV nucleotide substitution rates estimated from the tip-date randomization control analyses. Mean substitution rates are shown with 95% HPD intervals for the VP60 dataset with AY269825 (65 taxa, left), the VP60 dataset without AY269825 (64 taxa, middle), and the RdRp dataset (31 taxa, right). For each group, the leftmost value is the estimated substitution rate from the actual dataset, while the following 10 values are those from the tip-date randomized datasets.

Format: TIFF Size: 616KB Download file

Open Data

Additional file 4:

RHDV nucleotide substitution rates estimated from the RdRp jackknife datasets. Mean substitution rates are shown with 95% HPD intervals for each of the 30 datasets of 15 random taxa.

Format: TIFF Size: 452KB Download file

Open Data

Additional file 5:

RHDV nucleotide substitution rates estimated from the RdRp “n-1” jackknife datasets. Mean substitution rates are shown with 95% HPD intervals for each of the 31 datasets. Each rate estimate is identified on the x-axis by the GenBank accession number and year of isolation of the taxon removed from its corresponding dataset.

Format: TIFF Size: 812KB Download file

Open Data

Additional file 6:

RHDV VP60 and RdRp Tip-Date Randomized Datasets. Taxa are listed with the random dates assigned to them for each of the 10 tip-date randomized datasets for the full VP60, with and without AY269825, and the RdRp genes.

Format: XLSX Size: 58KB Download file

Open Data

Additional file 7:

RHDV taxa included in the VP60 and RdRp random jackknife control analyses. Bolded taxa indicate those used in each of the 50 VP60 and 30 RdRp random jackknife datasets.

Format: XLSX Size: 70KB Download file

Open Data