Archaeological and Anthropological Sciences
Mitochondrial DNA haplotypes ofDevensian hyaenas from Creswell Crags, England
SUPPLEMENTARY MATERIAL
Danae R. Dodge1, Abigail S. Bouwman2,*, Paul B. Pettitt1 and Terence A. Brown2
11Department of Archaeology, University of Sheffield, Northgate House, West Street, Sheffield S1 4ET, UK;2 Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, UK
* Current address: ZentrumfürEvolutionäreMedizin, Universität Zürich,Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
Corresponding author: Terry Brown: e-mail
Fig. S1 Photographs of the teeth used in this study.
Sample HY1 Creswell Crags Sample HY2 Creswell Crags
Sample HY3 Creswell Crags Sample HY4 Creswell Crags
Sample HY5 Creswell Crags Sample HY6 Kent’s Cavern
Sample HY7 Kent’s Cavern
Fig. S2 Complete alignment of DNA sequences. Sequences AJ809318–DQ157555 have previously been published (Hofreiteret al. 2004; Rohlandet al. 2005). The clade designation of each of these sequences is given. HY1CC09–HY5CC09 were obtained in this study. In these sequences, dashes indicate unsequenced regions and nucleotides that were read manually from the electrophoretograms are shown in lower case. Differences from the clade A1 sequences are highlighted.
....|....| ....|....| ....|....| ....|....|
10 20 30 40
AJ809318 A1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809319 A1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809320 A1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809321 A1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809322 A1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809323 A1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809324 A2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809325 A2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809326 A2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809327 A2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
DQ157554 A2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809331 B1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809332 B1 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809328 B2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809329 B2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
AJ809330 B2 TTATCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
DQ157555 D TTGTCAACAA ATCATTCATT GACCTCCCCA CCCCATCCAA
HY1CC09 ~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HY2CC09 TTATCAACAA ATCATTCATT GACCTCCCCa CCCCATCCAA
HY3CC09 TTATCAACAA ATCATTCATT GACCTCCCCaCCCTATCcaA
HY5CC09 ~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
....|....| ....|....| ....|....| ....|....|
50 60 70 80
AJ809318 A1 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809319 A1 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809320 A1 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809321 A1 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809322 A1 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809323 A1 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809324 A2 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809325 A2 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809326 A2 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809327 A2 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
DQ157554 A2 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
AJ809331 B1 CATCTCAGCA TGATGAAATT TCGGGTCACT ATTAGGAATC
AJ809332 B1 CATCTCAGCA TGATGAAATT TCGGGTCACT ATTAGGAATC
AJ809328 B2 CATCTCAGCA TGATGAAATT TCGGGTCACT ATTAGGAATC
AJ809329 B2 CATCTCAGCA TGATGAAATT TCGGGTCACT ATTAGGAATC
AJ809330 B2 CATCTCAGCA TGATGAAATT TCGGGTCACT ATTAGGAATC
DQ157555 D CATCTCAGCA TGATGAAACT TCGGATCACT ACTAGGAATC
HY1CC09 ~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~TC
HY2CC09 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATc
HY3CC09 CATCTCAGCA TGATGAAATT TCGGGTCACT ACTAGGAATC
HY5CC09 ~~~~~~~~~~ ~~~~~~~~~~~~~~~~~~~~ ~~~~~~~~TC
....|....| ....|....| ....|....| ....|....|
90 100 110 120
AJ809318 A1 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809319 A1 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809320 A1 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809321 A1 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809322 A1 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809323 A1 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809324 A2 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809325 A2 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809326 A2 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809327 A2 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
DQ157554 A2 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
AJ809331 B1 TGCTTAATCT TACAAATCCT GACAGGCTTA TTCCTAGCCA
AJ809332 B1 TGCTTAATCT TACAAATCCT GACAGGCTTA TTCCTAGCCA
AJ809328 B2 TGCTTAATCT TACAAATCCT GACAGGCTTA TTCCTAGCCA
AJ809329 B2 TGCTTAATCT TACAAATCCT GACAGGCTTA TTCCTAGCCA
AJ809330 B2 TGCTTAATCT TACAAATCCT GACAGGCTTA TTCCTAGCCA
DQ157555 D TGCTTAATCT TACAAATCCT GACAGGCCTA TTCCTGGCCA
HY1CC09 TGCTTAGT-T TACAAATCCT GACAGGCCTA TTCCTAGCCA
HY2CC09 tgcttAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
HY3CC09 TGCTTAGTCT TACAAATCCT GACAGGCCTA TTCCTAGCCA
HY5CC09 TGCTTANNNT TACAAATCCT GACAGGCCTA TTCCTAGCCA
....|....| ....|....| ....|....| ....|....|
130 140 150 160
AJ809318 A1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809319 A1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809320 A1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809321 A1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809322 A1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809323 A1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809324 A2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809325 A2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809326 A2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809327 A2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
DQ157554 A2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809331 B1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809332 B1 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809328 B2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809329 B2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
AJ809330 B2 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
DQ157555 D TACACTACAC ATCAGACACA ATAACCGCCT TCTCATCAGT
HY1CC09 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
HY2CC09 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
HY3CC09 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCAGT
HY5CC09 TACACTACAC ATCAGACACA ACAACCGCCT TCTCATCNNT
....|....| ....|....| ....|....| ....|....|
170 180 190 200
AJ809318 A1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809319 A1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809320 A1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809321 A1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809322 A1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809323 A1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809324 A2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809325 A2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809326 A2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809327 A2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
DQ157554 A2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809331 B1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809332 B1 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809328 B2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809329 B2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
AJ809330 B2 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
DQ157555 D GACCCATATC TGCCGAGACG TTAACTACGG CTGAATCATC
HY1CC09 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATCATC
HY2CC09 GACCCACATC TGCCGAGACG TTAACTACGG CTGAATcatC
HY3CC09 GACCCACATC T~~~~~~~~~ ~~~~~~~~~~ ~~~~~-----
HY5CC09 GACCNACATC TGTCGAGACG TTAACTACGG CTGAATCaTC
....|....| ....|....| ....|....| ....|....|
210 220 230 240
AJ809318 A1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809319 A1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809320 A1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809321 A1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809322 A1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809323 A1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809324 A2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809325 A2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809326 A2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809327 A2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
DQ157554 A2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809331 B1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809332 B1 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809328 B2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809329 B2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
AJ809330 B2 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
DQ157555 D CGATATACAC ACGCCAACGG GGCCTCTATA TTCTTCATCT
HY1CC09 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
HY2CC09 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
HY3CC09 ------
HY5CC09 CGATACATAC ACGCCAACGG AGCTTCCATA TTCTTCATCT
....|....| ....|....| ....|....| ....|....|
250 260 270 280
AJ809318 A1 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809319 A1 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809320 A1 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809321 A1 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809322 A1 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809323 A1 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809324 A2 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809325 A2 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809326 A2 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809327 A2 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
DQ157554 A2 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
AJ809331 B1 GTCTATATAT ACATATCGGC CGAGGAATAT ACTACGGATC
AJ809332 B1 GTCTATATAT ACATATCGGC CGAGGAATAT ACTACGGATC
AJ809328 B2 GTCTATATAT ACATATCGGC CGAGGAATAT ACTACGGATC
AJ809329 B2 GTCTATATAT ACATATCGGC CGAGGAATAT ACTACGGATC
AJ809330 B2 GTCTATATAT ACATATCGGC CGAGGAATAT ACTACGGATC
DQ157555 D GTCTATATAT ACATATCGGC CGAGGAATAT ACTACGGATC
HY1CC09 GTCTATATAT ACACATCGG......
HY2CC09 GTCTATATAT ACACATCGGC CGAGGAATAT ACTACGGATC
HY3CC09 -----TATAT ACACATCGGC CGAGGAATAT ACTACGGATT
HY5CC09 GTCTATATAT ACACATCGG......
....|....| ....|....| ....|....| ....|....|
290 300 310 320
AJ809318 A1 TTATACACTC CCAGAGACAT GAAATATCGG AATCCTACTA
AJ809319 A1 TTATACACTC CCAGAGACAT GAAATATCGG AATCCTACTA
AJ809320 A1 TTATACACTC CCAGAGACAT GAAATATCGG AATCCTACTA
AJ809321 A1 TTATACACTC CCAGAGACAT GAAATATCGG AATCCTACTA
AJ809322 A1 TTATACACTC CCAGAGACAT GAAATATCGG AATCCTACTA
AJ809323 A1 TTATACACTC CCAGAGACAT GAAATATCGG AATCCTACTA
AJ809324 A2 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
AJ809325 A2 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
AJ809326 A2 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
AJ809327 A2 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
DQ157554 A2 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
AJ809331 B1 TTACACACTC CCAGAGACAT GAAACATCGG AGTCCTACTA
AJ809332 B1 TTACACACTC CCAGAGACAT GAAACATCGG AGTCCTACTA
AJ809328 B2 TTACACACTC CCAGAGACAT GAAACATCGG AGTCCTACTA
AJ809329 B2 TTACACACTC CCAGAGACAT GAAACATCGG AGTCCTACTA
AJ809330 B2 TTACACACTC CCAGAGACAT GAAACATCGG AGTCCTACTA
DQ157555 D TTACACACTC CCAGAGACAT GAAACATCGG AATCCTACTA
HY1CC09 ......
HY2CC09 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
HY3CC09 TTATACACTC CCAGAGACGT GAAATACCGG AATCCTACTA
HY5CC09 ......
....|....| ....|....| ....|....| ....|....|
330 340 350 360
AJ809318 A1 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809319 A1 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809320 A1 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809321 A1 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809322 A1 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809323 A1 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809324 A2 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809325 A2 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809326 A2 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809327 A2 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
DQ157554 A2 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
AJ809331 B1 CTATTCACAG TAATAGCTAC CGCATTTATG GGTTATGTCC
AJ809332 B1 CTATTCACAG TAATAGCTAC CGCATTTATG GGTTATGTCC
AJ809328 B2 CTATTCACAG TAATAGCTAC CGCATTTATG GGTTATGTCT
AJ809329 B2 CTATTCACAG TAATAGCTAC CGCATTTATG GGTTATGTCT
AJ809330 B2 CTATTCACAG TAATAGCTAC CGCATTTATG GGTTATGTCT
DQ157555 D TTATTCACAG TAATAGCTAC CGCATTCATG GGCTACGTTC
HY1CC09 ......
HY2CC09 CTaTtcacAGtAATAGCTAC CGCATTCATG GGTTATGTCC
HY3CC09 CTATTCACAG TAATAGCTAC CGCATTCATG GGTTATGTCC
HY5CC09 ......
....|....| ....|....| ....|....|
370 380 390
AJ809318 A1 TACCGT......
AJ809319 A1 TACCGT......
AJ809320 A1 TACCGT......
AJ809321 A1 TACCGT......
AJ809322 A1 TACCGT......
AJ809323 A1 TACCGT......
AJ809324 A2 TACCGT......
AJ809325 A2 TACCGT......
AJ809326 A2 TACCGT......
AJ809327 A2 TACCGT......
DQ157554 A2 TACCGT......
AJ809331 B1 TACCAT......
AJ809332 B1 TACCAT......
AJ809328 B2 TACCAT......
AJ809329 B2 TACCAT......
AJ809330 B2 TACCAT......
DQ157555 D TACCAT......
HY1CC09 ......
HY2CC09 TACCGT~~~~ ~~~~~~~~~~ ~~~~~~~~~~
HY3CC09 TACCGT......
HY5CC09 ......
Table S1 PCR primers
PCRPrimer sequences (5´3´)Expected amplicon size
1GAAAATCTCACCCACTCATTAAAA147 bp
GTATGGCTAGGAATAGACCTGTCAG
2GAAATTTCGGGTCACTATTAGGAA136 bp
CCGTAGTTTACGTCTCGGC
3CAACAACCGCCTTCTCATCAG146 bp
GTAAGATCCGTAGTATATTCCTCGG
4GAGCTTCCATATTCTTCATCTGTCTA171 bp
CACCTCAGAATGATATTTGGCCTC