Ancient DNA: Methods and Protocols (49 page)

BOOK: Ancient DNA: Methods and Protocols
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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

Document Outline

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