A to Z Protocol for Sequencing Human mtDNA Genomes

Updates for:

  Clarke, A. C., Prost, S., Stanton, J.-A. L., White, W. T. J., Kaplan, M. E., Matisoo-Smith, E. A., and The Genographic Consortium. 2014. From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes. BMC Genomics 15: Article 68.

are available here.

Amplified Fragment Length Polymorphism (AFLP)

Due to hosting problems, material from The Allan Wilson Centre AFLP Page is now located here.

Lab Protocols

Below are lab protocols that you may find useful. I have done my best to ensure these protocols are as robust and accurate as possible but they should be treated as a guide only. If you have any queries, or suggestions for improvement, please e-mail me. I would appreciate your feedback.

If using these protocols, a brief attribution note and a link to my website would be appreciated, e.g., “Based on the AFLP protocol by Andrew Clarke & Heidi Meudt, http://www.clarkeresearch.org/.”


AFLP Protocol

This protocol is for generating fluorescently-labelled AFLPs (Amplified Fragment Length Polymorphisms).

Also check out the Allan Wilson Centre AFLP Page for other AFLP resources.

  PDF Version 4

TAIL PCR Protocol

Thermal Asymmetric Interlaced (TAIL) PCR is used to amplify, from genomic DNA, flanking regions from regions of known sequence.

In molecular ecology and evolution flanking regions are obtained to:

1. Improve the efficiency of sequence characterised amplified (SCAR) marker development by capturing polymorphisms in regions flanking SCAR markers,
2. Lengthen PCR markers so that more sequence data (more informative characters) are obtained,
3. Allow PCR primers to be designed in more conserved regions so that amplification across taxa is more reliable.

For more information see Clarke et al. (2006).

  PDF Version 2


Please feel free to make use of the following high resolution maps.

For files marked ‘ * ’ the white areas are transparent (i.e., in PowerPoint the background colour of the slide will show through). This is useful if you want to change the colour of the ocean, etc.


The Pacific Ocean

If using these maps, I would ask you to include a brief attribution note, e.g., “Map by Andrew Clarke” or, if the map is modified, “Base map by Andrew Clarke”. If there is room for my affiliation and/or a link to my website, that would be great, e.g., “Map by Andrew Clarke, University of Warwick, http://www.clarkeresearch.org/.”

Oceania Oceania
[TIFF] (164 kB) [TIFF] (151 kB)
[GIF]* (146 kB) [GIF]* (129 kB)

The World — Pacific-Centred

Created using Online Map Creation

World Map
[PostScript]* (160 kB)
[JPEG] (1 MB)
[TIFF] (10 MB)