DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Supplementary Information

NICOLAS J. RAWLENCE1, JAMIE R. WOOD2, KYLE N. ARMSTRONG1 and ALAN COOPER1,*

1 Australian Centre for Ancient DNA (ACAD), School of Earth and Environmental Sciences, University of Adelaide, South Australia, 5005.

2 Landcare Research, PO Box 40, Lincoln, New Zealand.

* Corresponding author

Correspondence:

Sequences have been deposited in Genbank (accession numbers GQ253937-GQ253945) or Table S3 if less than 50 bp in length.

Table S1 Moa and emu feather specimens included in this study. Sequence refers to the partial mtDNA control region fragment amplified using primers reported in Cooper et al. (2001); Bunce et al. (2003) and Wood et al. (2008) (Table S1).

Genus / Species / Museum No.1 / Rockshelter / Sequence / Sub-sample / Genbank No.2
Megalapteryx / didinus / OM Av10793.1 / Roxburgh Gorge B / CR262-294 / Calamus / Table S3
Megalapteryx / didinus / OM Av10791.1 / Roxburgh Gorge C / CR262-419 / GQ253937
Megalapteryx / didinus / A 06.49.20.1 / Sawers / CR262-419 / GQ253938
Megalapteryx / didinus / A 06.49.20.2 / Sawers / CR262-419 / GQ253939
Dinornis / robustus / OM Av10793.2 / Roxburgh Gorge B / CR262-419 / GQ253940
Euryapteryx / gravis / A 06.49.20.3 / Sawers / CR185-419 / GQ253941
Pachyornis / elephantopus / A 06.49.18 / Sawers / CR262-294 / Table S3
? / ? / OM Av10797 / Cainmuir Gully B / n/a / n/a
? / ? / OM Av10791.2 / Roxburgh Gorge C / n/a / n/a
? / ? / ACAD7148 / Sawers / n/a / Rachis, barbs / n/a
Dinornis / robustus / ACAD7149 / Sawers / CR262-294 / Table S3
Pachyornis / elephantopus / ACAD7150 / Sawers / CR262-294 / Table S3
Euryapteryx / gravis / ACAD7151 / Sawers / CR262-294 / Table S3
? / ? / ACAD7152 / Sawers / n/a / n/a
? / ? / ACAD7153 / Sawers / n/a / n/a
? / ? / ACAD7154 / Sawers / n/a / n/a
Euryapteryx / gravis / ACAD7155 / Sawers / CR262-419 / GQ253942
? / ? / ACAD7158 / Sawers / n/a / n/a
? / ? / ACAD7159 / Sawers / n/a / n/a
Dromaius / novaehollandiae / ACAD4885-893 / Adelaide / 12SE-12SH2 / Calamus, proximal rachis, distal rachis, barbs / GQ253943
Dromaius / novaehollandiae / ACAD4891-953 / Adelaide / 12SE-12SH2 / GQ253944
Dromaius / novaehollandiae / ACAD4897-49013 / Adelaide / 12SE-12SH2 / GQ253945

1OM: OtagoMuseum; A: AlexandraMuseum; ACAD: Australian Centre for Ancient DNA.

2 Sequences less than 50 bp can be found in Table S3 (not accepted by Genbank).

3 ACAD number refers to DNA extracts from each feather.

Table S2Primer sequences used in this study.

Primer / Sequences (5`-3`) / Reference
CR185F / GTACATTCCCTGCATTGGCTC / Cooper et al. 2001; Bunce et al. 2003
CR204F / AGATTTATARCTCGGACA / Wood et al. 2008
CR262F / GCGAAGACTGACTAGAAGC / Cooper et al. 2001; Bunce et al. 2003
CR294R / GCGAGATTTGAACAGTACG / Cooper et al. 2001; Bunce et al. 2003
CR419R / GGGTTGCTGATTTCTCGTGA / Cooper et al. 2001; Bunce et al. 2003
12SE / CCCACCTAGAGGAGCCTGTTC / Cooper et al. 2001
12SH2 / CCTTGACCTGTCTTGTTAGC / Cooper et al. 2001

Table S3 Mitochondrial DNA control region sequences less than 50 bp in lengthfrom sub-fossil moa feathers.

Museum number / Sequence
OM Av10793.1 / CTATAACCCGGACATGCCCTTTACC
A 06.49.18 / TTATAGCTCGAACATAACTCTTACC
ACAD7149 / ATAGATTTATAGCTCGGACATAATCTTAACC
ACAD7150 / ATAGATTTATAGCTCGAACATAACTYTTACC
ACAD7151 / ATAGATTTATAGCTCGGACATACACTCTACC

Supplementary References

Bunce, M., Worthy, T.H., Ford, T., Hoppitt, W., Willerslev, E., Drummond, A. & Cooper, A. 2003 Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis. Nature 425, 172-175.

Cooper, A., Fox-Lalueza, C., Anderson, A., Rambaut, A., Austin, J. & Ward, R. 2001 Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature409, 704-707.

Wood, J.R., Rawlence, N.J., Rogers, G.M., Austin, J.J., Worthy, T.H. & Cooper, A. 2008 Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes). Quat. Sci. Rev. 27, 2593-2602.

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