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Ancient DNA of European pikas: Tables

TABLE 1. Details of the Ochotona samples analysed in this study. Asterisks indicate the specimens donated by A. Lissovsky (*) and N. Abramson (**). The absolute age of the specimens in years: 20,000 (1), 150 (2), 550 (3), 36 (4), 17,000 (5), 9915 ± 60 BP (OxA8073) after Ramsey et al. (2002) and Price (2003) (6).

No. Taxon (initial ID) Country Locality Age Reference
1* Ochotona pusilla Kazakhstan - Recent This paper
2* Ochotona pusilla Russia - Recent This paper
3** Ochotona pusilla Russia - Recent This paper
4** Ochotona pusilla Russia - Recent This paper
5 Ochotona spelaea Ukraine Novgorod-Siverskyi 1 Last Glacial Rekovets, 1985
6 Ochotona pusilla Ukraine Kozatske2 Late Holocene Pidoplichka, 1934
7 Ochotona pusilla Ukraine Raiky3 Late Holocene Pidoplichka, 1934
8 Ochotona pusilla Russia Orenburg4 Recent This paper
9 Ochotona pusilla Ukraine Mezhyrich5 Last Glacial Rekovets, 1985
10 Ochotona pusilla Ukraine Mezhyrich5 Last Glacial Rekovets, 1985
11 Ochotona sp. Belgium Rocher de Nevioux Last Glacial This paper
12 Ochotona sp. Belgium Rocher de Nevioux Last Glacial This paper
13 Ochotona sp. Belgium Rocher de Nevioux Last Glacial This paper
14 Ochotona sp. Belgium Rocher de Nevioux Last Glacial This paper
15 Ochotona sp. Belgium Rocher de Nevioux Last Glacial This paper
16 Ochotona sp. England Bridget Pot Younger Dryas This paper
17 Ochotona sp. England Bridget Pot Younger Dryas This paper
18 Ochotona sp. England Bridget Pot Younger Dryas This paper
19 Ochotona sp. England Bridget Pot Younger Dryas This paper
20 Ochotona sp. England Bridget Pot Younger Dryas This paper
21 Ochotona sp. England Merlin’s Cave6 Younger Dryas This paper
22 Ochotona sp. England Merlin’s Cave6 Younger Dryas This paper
23 Ochotona sp. England Merlin’s Cave6 Younger Dryas This paper
24 Ochotona sp. England Merlin’s Cave6 Younger Dryas This paper

 

 

 

 

TABLE 2. The list of specimens from GenBank used to compare the obtained results.

Species GenBank Species GenBank
Ochotona alpina AF273009 Ochotona princeps EU590921
Ochotona alpina DQ335517 Ochotona princeps EU590922
Ochotona alpina EF567055 Ochotona pusilla AY260744
Ochotona alpina HM346527 Ochotona pusilla HM366945
Ochotona alpina HM346529 Ochotona pusilla JX682567
Ochotona collaris EU549738 Ochotona pusilla JX682568
Ochotona collaris JQ624503 Ochotona roylei JX682573
Ochotona collaris JQ624508 Ochotona rutila JX682566
Ochotona collaris KP411020 Ochotona thibetana AF272986
Ochotona erythrotis AF272999 Ochotona thibetana KU359597
Ochotona forresti AF272998 Ochotona thibetana KU359598
Ochotona huangensis JN645147 Ochotona thibetana KU359599
Ochotona hyperborea AB053257 Ochotona thibetana KU359600
Ochotona hyperborea KR076818 Ochotona thomasi AF272987
Ochotona hyperborea KR076820 Ochotona thomasi KU359612
Ochotona hyperborea KR076821 Ochotona thomasi KU359613
Ochotona hyperborea KR076823 Ochotona thomasi KU359614
Ochotona koslowi AF272993 Ochotona thomasi KU359615
Ochotona macrotis AF273010 *Sequences added to root the tree:
Ochotona macrotis JQ670914 *Microtus pennsylvanicus KC473477
Ochotona macrotis JX682574 *Peromyscus boylii AF155387

 

 

TABLE 3. Primer pairs used to amplify the ancient mtDNA control-region sequence of the cytochrome b.

Primer name Primer sequences (5′-3′) Size (bp) Ta*, °C
Och1f AAACCACCCCCTAATAAAAA 143 50
Och1r GTATGGCTAGGAATAAGCC    
Och2f CCGCATGATGAAACTTCGGA 121 50
Och2r TGGGTGACTGATGAGAATGC    
Och3f TCCTAGCCATACACTACACA 121 50
Och3r AATATGGATGCGCCGTT    
Och4bf TAAACTACGGCTGAATTATCC 129 52
Och4br CCGATGTTTCATGTTTCTGAG    
Och5f CTATTCCTACACGTAGGCCG 141 50
Och5r GAAGGATATTTGTCCTCATGG    
Och6bf TAGCAACCGCCTTCATAGG 131 52
Och6br AGCCGCCTCAGATTCATTG    
Och7bf CCATGAGGACAAATATCCTTC 127 52
Och7br GTGAGGGTAGCTTTATCAACTG    
Recent specimen (ER008)
Och1f AAACCACCCCCTAATAAAAA 143 50
Och1r GTATGGCTAGGAATAAGCC    
Och2f CCGCATGATGAAACTTCGGA 121 50
Och2r TGGGTGACTGATGAGAATGC    
Och3f TCCTAGCCATACACTACACA 121 50
Och3r AATATGGATGCGCCGTT    
Och4f ACGGCTGAATTATCCGCTAC 115 50
Och4r CATGTTTCTGAGTAGGTGTA    
Och5f CTATTCCTACACGTAGGCCG 141 50
Och5r GAAGGATATTTGTCCTCATGG    
Och6f CCGCCTTCATAGGCTAC 121 50
Och6r CCTCAGATTCATTGGAC    
Och7f AACCGTAATTACCAACCTCC 113 50
Och7r AGGCAAAGAATCGAGTTAGG    

* Annealing temperature