Ancient DNA: Methods and Protocols (48 page)

Cytosine deamination ........................................................9 0

DNAse .......................................................5 7, 113, 135, 182

DNAstar ...................................................................... 3 1, 89

D

DNeasy .............................................................3 1, 34, 73, 74

Dodecyl trimethyl ammonium bromide

Deamination .............................................2 , 53, 90, 145, 164

(DTAB) .................................................................72

Decontamination .................................................................8

DTT.
See
Dithiothreitol (DTT)

Deletion ......................................................5 5, 192, 206, 225

Duplicates ................................................1 51, 220–222, 225

Demultiplex ..............................................2 01, 202, 209, 224

Dynabeads ................................................1 61, 182, 187, 191

Depurination .......................................................................2

Desiccated ............................................................. 3 4, 73, 76

E

Detergent ................................. 1 7, 23, 34, 43, 61, 68, 72, 74

EDTA.
See
Ethylenediaminetetraacetic acid (EDTA)

Direct multiplex sequencing (DMPS) ..................... 171–175

Eggshell ........................................................6 5–69, 123, 132

Dithiothreitol (DTT) ................................14, 16–18, 23, 29, Endonuclease ................................................................... 1 45

34, 39, 43–45, 47, 58, 59, 61, 66–68, 74, 95

EndoVIII ......................................................................... 1 52

DMPS .
See
Direct multiplex sequencing (DMPS)

Enrichment. ..................................... 1 24, 150, 174, 177–195, DNA

201, 206, 212, 214, 215

amplifiable ................................................2 2, 81, 98, 106

EtBr .
See
Ethidium bromide (EtBr)

authentic ................................................................ 4 , 190

Ethanol . ............................................. 8 , 9, 14, 15, 23, 27, 39, bacterial ................................................................. 8 , 174

40, 44, 46, 47, 60, 66, 67, 72, 73, 75, 82, 84, 95, 98,

contaminating .................................... 3 , 4, 22, 55, 61, 65, 114, 116, 160

103, 107, 108, 177, 181, 190, 193, 213

Ethidium bromide (EtBr) ...................................32, 53, 105, crosslinks ............................................................... 2 , 112

113, 115, 118, 135, 138, 140

degradation .......................................................... 4 3, 131

Ethylenediaminetetraacetic acid

denaturation ........................................1 05, 137, 173, 185

(EDTA) ..................................... 9, 14, 23, 31, 34, 39, double-stranded ......................... 1 22, 126, 131, 148, 151, 44, 66, 67, 73, 74, 82, 95, 97, 113, 114, 116, 135,

152, 156, 167, 183

147, 160, 161, 182, 183

endogenous .................................. 3 , 9, 22, 106, 174, 179, Eurasian ................................................................... 1 90, 194

181, 193, 198, 213, 216, 217, 220, 225

Europe . .................................................................... 1 72, 194

exogenous ..................................................3 , 55, 65, 174, 177, 213

F

fecal ................................................................. 3 9, 51, 55

fragmentation ............................. 3 1, 81, 82, 91, 108, 184

False-positive ................................................................... 2 06

genomic ......................................... 6 , 133, 144, 152, 178, FastDNA ...........................................................................5 8

181, 190, 191

FastPrep ................................................................. 5 9, 60, 62

mitochondrial ......................................3 0, 101, 112, 181, Feather ......................................................................... 4 3, 45

189–195

Feces ...................................................................... 3 7, 38, 41

modification .................................... 2 , 13, 48, 72, 77, 82, Forensic ........................................................... 1 34, 175, 229

144, 145, 178

Formalin

nuclear ..............................................2 9–35, 94, 108, 132

fixed ....................................................................... 8 1–85

overhangs ........................................................... 1 46, 147

Fossil

quantitation ........................................................... 6 , 123

fossilization ..................................................................2 1

single-stranded ...................................................... 2 , 125

fossilized ......................................................................9 0

DNA damage

Freeze-thaw ............................................9 , 19, 130, 131, 169

DNA crosslinks .............................................................2

G

hydrolytic damage ..........................................................2

miscoding lesions ........................................... 2 , 123, 145

GenBank ............................................... 3 1, 52, 89, 105, 107, oxidative damage ...........................................................8

108, 192, 232

post mortem .............................................................. 1 12

Genome ............................... 9 , 108, 134, 143, 144, 171–175, DNA extraction

177–179, 190, 198–200, 209, 212–214, 218,

extraction from eggshells .............................................6 5

223–225

extraction from formalin-fixed material ................. 8 1–85

Gigabase .......................................................................... 1 97

extraction from keratin .......................................... 4 3–48

Glyptodont ........................................................................8 8

ANCIENT DNA: METHODS AND PROTOCOLS 245

Index

Ground sloth .....................................................................3 7

Megabase ..................................................1 78, 179, 190, 225

Guanidinium isothiocyanate (GuSCN)

sized ....................................................1 78, 179, 190, 225

L2 buffer ......................................................................3 9

MegaBLAST .................................................................. 2 25

L6 buffer ................................................................ 3 9–41

Megafauna .........................................................................3 7

Guidelines ....................................................4 –6, 47, 83, 129

Melanin ....................................................................... 4 7, 48

Mercaptoethanol .......................................5 8, 59, 73, 74, 76

H

MgCl .. .................................... 104, 113, 114, 117, 124, 126, 2

Hair

135–137, 160, 164, 168, 173, 183, 185

shafts ..........................................................5 1, 52, 54, 55

MgSO .................................................32, 89, 113, 114, 135

4

Haplotype ........................................................ 1 06–108, 225

Microsatellite ........................................................... 1 02, 132

Hominid ...................................................................... 1 , 134

Minelute ..................................................1 47–150, 160–162, Homo

165, 183–187

Homopolymer ......................................................... 2 22, 224

Miscoding lesions .........................................2 , 123, 133, 145

HPLC............................... ...................... 2 3, 58, 59, 95, 103, Misincorporation ................................................... 2 , 90, 225

104, 130, 186

Moa ..... ...................................................................... 6 5, 127

Hybridization capture

MobiCol ............................................................................2 3

bait ............................................................. 1 78–181, 191

Modeltest .................................................................. 3 2, 238

in-solution ......................................................... 1 79–181

Molecular weight cut off

microarray .................................................................. 1 80

(MWCO) ................................. 18, 48, 62, 66, 67, 69

Mortar........................................................ 2 3, 24, 66, 68, 77

I

MrBayes ............................................................................3 2

Multiplex .........................................1 33–140, 155–175, 198, IBIS....................................................................... .. 1 91, 212

200–205, 209, 224, 225

Illumina ................................... 1 23, 143, 145, 156, 157, 159, Museum

163, 181, 187, 190–192, 197–199, 201, 206, 208,

specimens ................................. 3 0, 93–99, 102, 105, 106, 223, 224

108, 109, 220

Index .... ............................................1 92, 201–204, 212–215, stored ................................................................... 2 9, 106

218, 223, 224

MWCO.
See
Molecular weight cut off (MWCO)

Inhibition .............................2 7, 38, 62, 69, 72, 76, 112, 123, 124, 127–129, 131

N

Inhibitors ..................................1 8, 34, 38, 42, 66, 69, 72, 99, 112, 118, 123, 127

Neandertal/Neanderthal .......................................... 1 78, 217

coextracted ............................................................... 1 12

Network ....................................................1 05, 107, 108, 199

Isopropanol .................................... 4 3, 44, 46, 48, 60, 72–74, Next generation sequencing (NGS) ..............3, 14, 143–153, 82, 83, 85, 98

155, 156, 169, 177

NimbleGen ...................................................... 1 79, 180, 186

K

Nondestructive ........................................... 9 3–99, 101–109

N-phenacylthiazone bromide (PTB) .......................2, 14, 17, Keratin ......................................................................... 4 3–48

37–39, 41, 58, 59, 61, 72–77, 112

Keratinous ............................................................. 4 3, 45, 51

Nuclease ............................................... 2 , 7, 57, 61, 144, 145

Nucleic acid ...................1 3, 14, 18, 41, 77, 82, 124, 223, 229

L

Nucleotide ........................................ 1 05, 108, 124, 126, 130, Laboratory setup ........................................................... 1 –10

157, 182, 198, 199, 201, 222–224, 233, 238

Laminar flow hood ...................................................... 7 , 138

O

Library construction ........................................................ 1 44

Ligase .................................................1 46, 148, 152, 159, Oligo.... ..................................... 1 25, 151, 157–161, 182, 183

162, 166, 168, 169, 182, 184, 187

blocking ..................................................................... 1 85

Ligation ..................................... 6 9, 145, 148, 151, 152, 156, Oligonucleotide. .............................. 1 24–126, 129, 130, 151, 157, 161, 162, 166, 168, 169, 181, 184

156, 179, 182, 183, 186, 187, 204

M

P

Maize ... ........................................................................ 7 2, 73

Paleofeces ........................................................ 3 7–42, 51–55

Mammoth .........................................................3 7, 134, 175, Parameter .................................. 3 2, 192, 199, 209, 214, 219, 230, 232

230, 233, 234, 236, 237, 239

Mega4 . ............................................................................. 192

Passenger pigeon ......................................................... 2 9–35

246 ANCIENT DNA: METHODS AND PROTOCOLS

Index

PCR

PTB.
See
N-phenacylthiazone bromide (PTB)

emulsion-(em) ........................................................... 169

Purification ....... 2 2–24, 26, 42–48, 66–68, 72, 76, 82, 94–99, first step ............................................................. 1 36–139

105, 123, 130, 135, 138, 145, 147, 149

hot-start ..............................................1 12, 114, 115, 137

jumping ........................................ 2 , 5, 55, 157, 181, 201

Q

long-range ......................................................... 1 81–184

Qiaquick ...................................................4 4, 46, 48, 68, 105

multiplex PCR ...................................1 33–140, 156, 165, Quagga .......................................................................... 1 , 93