Ancient DNA: Methods and Protocols (47 page)

9. It is diffi cult to determine the appropriate settings for the MCMC analysis in advance. Generally, the aim is to draw a suffi cient number of samples in the smallest number of steps, but to draw them infrequently enough so that successive samples are reasonably independent of each other. The default settings in BEAUti include a total sampling period of 10,000,000 steps, with samples drawn every 1,000 steps. For analyses involving large data sets or parameter-rich models, the length of the MCMC should be increased, perhaps to 50,000,000 or more

steps. The sampling frequency should be reduced correspondingly so that the sizes of the output fi les remain manageable.

Suffi cient sampling can be gauged by the ESS for each parameter, as computed in
Tracer
. ESS values can be raised by increasing the number of samples drawn from the MCMC (by increasing the total number of steps and/or decreasing the interval between successive samples), but will be reduced by autocorrelation between successive samples.

10. For very large data sets, some of the programs will encounter memory problems. This is indicated by the Java error message “OutOfMemoryError.” Step-by-step instructions on how to

increase memory allocation are available on the offi cial
BEAST

site (http://beast.bio.ed.ac.uk/).

Acknowledgments

SYWH is supported by the Australian Research Council and by a start-up grant from the University of Sydney. Beth Shapiro provided helpful comments.

240

S.Y.W. Ho

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sdfsdf

INDEX

A

Bleach .. ...................................8 , 9, 14, 15, 44, 45, 47, 52, 66, 67, 75, 77, 103

Abasic site ........................................................................ 1 47

Blocking lesion ............................................................ 3 , 145

Adaptor (or adapter)

Bone ......................................... 3 , 5, 8–10, 15, 18, 21, 22, 24, artifacts ..............................................1 53, 198, 204–206, 29, 31, 34, 37, 41, 43, 65, 87–90, 94–97, 102, 123,

209, 212, 215

127, 132, 134, 171, 172, 190

double_multiplex ............................................... 2 04, 205

Bottle gourd ........................................................... 7 3, 76, 77

ligation ......................................... 6 9, 151, 152, 156, 157, Bovine serum albumin (BSA) ..............................8, 112, 124, 161–162, 166, 169

126, 135–137

PCR ............................................ 1 50, 165, 172, 173, 181

Bst polymerase .......................... 1 46, 149, 152, 163, 166, 184

Aerosols ................................................1 4, 66, 114, 124, 131

Burn-in .................................................................... 2 35, 236

Africa ... .....................................................1 02, 103, 107, 175

Agarose. ..............................5 3, 105, 113, 115, 116, 127, 131, C

135, 138, 184, 190, 193

Carrier DNA ..............................................6 , 8, 10, 117, 139

Alignment ................................. 5 4, 194, 206, 209, 212–214, Cetyl trimethyl ammonium bromide

216–221, 224, 225, 230–233

(CTAB) ..................................................... 72–75, 77

Aliquot .................................1 9, 24, 39–41, 95, 96, 112, 118, Chaotropic

123, 124, 127, 130, 149

non- ....................................................................... 97, 98

Amino acid racemization .....................................................5

Chimpanzee ............................................................ 1 01–109

Amplicon ................................. 1 21, 122, 124, 128–131, 164, Chitinous ..................................................................... 4 3, 45

167, 178, 181, 186

Chloroform .......................................... 1 3–19, 44, 46, 48, 52, Archaeological ....................................................... 6 9, 71, 72

58–60, 72–74, 76, 77, 82–84, 87

Arthropod .............................................................. 4 5, 94, 98

Cleanroom ....................................................... 1 44, 147, 152

Artifact ............................................ 1 12, 153, 157, 164, 181, Clonal sequence ............................................................... 1 07

198, 201, 204–206, 209, 212, 215, 223, 224

Cloning .............................................. 2 , 5, 6, 53, 89, 90, 105, Authentication

111–118, 128, 171, 193

authentic DNA .............................................. 4 , 123, 190

ClustalW ........................................................................ 1 05

authenticity ............................... 5 , 90, 105, 112, 145, 194

Color-space ..................................................................... 2 23

B

Columns ...................................2 2–27, 31, 34, 44, 46, 47, 58, 61, 66–69, 98, 139, 145, 148–150, 161, 162, 165,

Barcode

184, 186, 187, 201, 202, 219, 233

barcoded ............. 1 34, 144, 155–170, 172–174, 190, 200

Concentrator(s) ..................................................... 15, 16, 48

barcoding ................................... 1 38, 155–157, 165, 168, Contaminant(s) ....................................... 3–9, 18, 19, 27, 45, 172, 173, 200, 201

55, 62, 88, 89, 99, 106, 112, 117, 118, 178, 198, 213,

Base-modifications .......................................2 , 144, 145, 178

217–220

Bayesian .......................................... 3 2, 33, 35, 230–235, 238

Contamination

BEAST ................................................................... 2 29–239

contaminated .....................................3 –5, 7–10, 22, 118, BioEdit .............................................................. 5 3, 105, 192

139, 140, 217

Biotin.. ...................................... 1 58, 159, 180, 181, 183, 185

criteria for authenticity ..................................................5

dUTP .................................................1 82, 185, 187, 191

cross-contamination ............................ 5 , 14, 59, 98, 106, Biotinylated ...................... 1 56, 158, 159, 180–184, 187, 191

109, 127, 136, 152, 157, 187

BlastSearch ...................................................................... 1 05

Coprolite ..................................................................... 3 7, 73

Beth Shapiro and Michael Hofreiter (eds.),
Ancient DNA: Methods and Protocols
, Methods in Molecular Biology, vol. 840, DOI 10.1007/978-1-61779-516-9, © Springer Science+Business Media, LLC 2012

243

244 ANCIENT DNA: METHODS AND PROTOCOLS

Index

Covaris ............................................................................ 1 82

extraction from paleofeces ............................... 3 7–42, 51

Criteria of authenticity ........................................................5

extraction via silica columns ........................................3 4

CTAB .
See
Cetyl trimethyl ammonium bromide (CTAB) phenol-chloroform extraction .................... 1 3–19, 73, 87