Read Ancient DNA: Methods and Protocols Online
Authors: Beth Shapiro
171–175, 225
Quantification ................................... 3 8, 121, 123, 126, 128, PCR negative controls ............................... 1 14, 136–139
147, 149–151, 153, 174, 186, 187, 190–192, 198
post- .......................................................4, 5, 7, 138, 139
pre- .......................................................................... 5, 31
R
quantitative PCR (qPCR) .........................38, 62, 65, 69, Rabbit serum albumin (RSA) ........... 8, 32, 89, 113, 135–137
121–132, 147, 149–151, 153, 158–160, 164, 167,
RAxML .............................................................................3 2
173, 174, 181, 186, 190, 193
Replication ......................................... 3 , 5, 18, 105, 139, 178
real time ................................................8 2, 121–132, 160
Reproducibility .................................................... 5 , 126, 152
second step ......................................................... 1 35–140
RNA ..... ....................................................1 22, 180, 181, 212
singleplex ................................................... 1 34, 137, 139
RNAse. ........................................................................ 7 4, 77
two-step ..................................................... 1 28, 134, 171
RSA.
See
Rabbit serum albumin (RSA)
PEC .
See
Primer extension capture (PEC)
PEG.
See
Polyethylene glycol (PEG)
S
Permafrost
preserved DNA ............................................... 9 , 21, 111
Sample preparation ................... 7 –9, 14, 15, 24–25, 103, 144
Phenol
Sample storage ................................................... 7 –9, 81, 118
-chloroform ................................... 1 3–19, 52, 73, 76, 82, SDS.
See
Sodium dodecyl sulphate (SDS)
83, 87
Sediment ..................................................................... 2 1, 37
Phylogenetic analysis ..........................3 2, 105, 212, 229–239
DNA .........................................................5 7–62, 72, 123
Phylogeny ............................................................ 3 0, 33, 230
Sensitivity ..................................... 3 , 129, 130, 133, 175, 225
Phylogeographic .........................................9 3, 107, 190, 229
Sequencing ....................................... 454 , 157, 168, 175, 181
Phylogeography ....................................................... 1 94–195
coverage ...................................... 1 78, 179, 193, 198, 200
Phytolith ............................................................................7 2
DNA-sequencing ............... 1 44, 150, 153, 175, 197–226
Pipeline ............................................. 1 68, 206, 212, 222, 224
error .................................... 1 94, 201, 206, 208, 211, 220
Pleistocene ........................................................... 8 7–91, 108
genomic ...................... 1 23, 143, 144, 155, 190, 192, 193
Pollen ... ..............................................................................7 2
library ........................................ 1 44, 150, 153, 155, 172, Polyethylene glycol (PEG) ........................18, 152, 159, 161, 173, 186, 204
162, 166, 182, 184
multiplex ............................................................ 2 02, 209
Polymerase
paired-end ..........................................1 98, 201, 206–211
Bst- ......................146, 149, 152, 160, 163, 166, 182, 184
platform ..................................... 1 34, 145, 156, 157, 172, T4- ............................................................ 146, 162, 165
178, 179, 182, 198–200, 212, 224
Polynucleotide kinase ..............................1 45, 148, 159, 162, Sanger- ....................................... 138, 143, 155, 171, 230
165, 182, 184
shotgun ...................................................... 1 56, 177, 197
Preamplified ................................................................... 1 73
Silica
Precipitation .............................................. 4 4, 58, 60, 73, 82, based .................... 3 8, 43, 69, 73, 89, 94, 96, 98, 105, 172
84, 98, 116
Siliconized tubes ...........................................2 6, 99, 163, 169
precipitated ..................................... 4 2, 47, 48, 61, 83, 85
Sloth .... .................................................................. 3 7, 51–55
Preservation conditions ............................................. 3 , 9, 72
Sodium dodecyl sulphate (SDS) ........................... 14, 16–18, Primer
43, 44, 47, 61, 68, 74, 82
dimer .................................... 3 2, 118, 131, 140, 167, 173
Sodium hypochlorite ............................................. 8 , 14, 103
extension .............................................1 50, 156, 179, 180
Soil ............................................................. 2 2, 37, 57–62, 72
Primer3 .................................................................... 103, 172
Solexa .............................................. 1 23, 134, 143, 145, 156, Primer extension capture
157, 159, 163, 165
(PEC) ...........................................150, 156, 179–181
SOLiD ..................................... 1 23, 143, 181, 187, 223, 224
Protein 2 ......................................... 14, 17, 38, 46, 60, 61, 73, Sonicator ................................................................. 1 82, 184
76, 81– 83, 223, 233
Spin-columns ............................................ 4 6, 47, 58, 61, 66, Proteinase K ........................................ 1 4, 16–18, 23, 25, 26, 145, 148–150, 161, 162, 165
31, 34, 43–45, 47, 58, 59, 61, 66–68, 73, 74
SPRI beads .............................................................. 1 83, 187
ANCIENT DNA: METHODS AND PROTOCOLS 247
Index
Streptavidin .............................................1 52, 161, 163, 168, Transversion .............................................................. 9 0, 238
181, 182, 186, 187
Trimming .................................................1 98, 204, 206–211
Subfossil .................................................................... 3 8, 190
trimmed ..................................................... 2 05, 209, 224
Subsampling .......................................................... 2 9, 88, 89
Tris
Substitution ....................................... 9 0, 108, 201, 213, 214, -HCl ....................... 1 4, 23, 39, 44, 58, 59, 61, 73, 82, 95, 225, 232, 233, 238
147, 160, 161
SYBR
Tris-acetate-EDTA (TAE) .......................113, 115, 135, 138
Green ..........................................1 22, 124, 126, 128–130
Tris-borate-EDTA (TBE) .............................. 115, 135, 138
Tris-EDTA (TE) ......................39, 40, 44, 47, 52, 72, 73, 75, T
76, 82, 84, 89, 95, 97, 98, 103, 104, 113, 135, 147,
TAE.
See
Tris-acetate-EDTA (TAE)
150, 151, 153, 160–163, 165–167, 182, 186, 187
Tag(s) ... .................................................................... 155, 199
Triton-X100 ......................................................................95
Tagging .................................................................... 1 72, 200
Tween-20 .................................... 39, 40, 147, 153, 160–163, Taq
165–168, 182, 183
AmpliTaq .................................. 1 12, 114, 118, 124, 126, U
130, 135–137, 139, 146, 149, 152, 160, 164, 168, 173
AmpliTaq Gold ......................... 1 12, 114, 118, 124, 126, Uracil
130, 135–137, 139, 146, 149, 152, 160, 164, 168, 173
DNA-glycosylase (UDG) .......................2, 112, 145, 152
Hifi Taq ..................................................................... 1 14
N-glycosylase (UNG) ................................ 112, 125, 130
High Fidelity Taq ...................................3 2, 89, 112, 114
UV irradiation ........................................................... 8 , 9, 14
Target
enrichment ................................................ 1 50, 177–188
V
specific ....................................................................... 1 90
Vivaflow ............................................................................9 7
TBE.
See
Tris-borate-EDTA (TBE)
Vivaspi . .................................................................. 6 6, 67, 69
TE.
See
Tris-EDTA (TE)
TempNet ......................................................................... 1 05
W
TOPO-TA cloning ...............................5 3, 89, 114, 116, 118
Transition ..................................... 2 , 8, 53, 55, 112, 145, 238
Waterlogged ............................................................... 7 1, 72