Monday, November 19, 2012

Midden barcoding

For most of us midden is an expression for an old dump for domestic waste. Archaeologists use it to describe any kind of feature containing waste products relating to everyday human life. 

In the animal kingdom, ground burrows are also known as middens although they are primarily used for food storage. A midden may also be a regularly used toilet area or dunghill, created by many mammals, such as the hyrax, and also serving as a territorial marker..

In the case of some 30 000 year old American and Australian middens, the animals urinated and defecated on their nests during the course of habitation, and organic material such as plant and animal tissue, bone, hair and eggshell gathered from the local surroundings, became cemented together into a hard, impermeable mixture.

With the advent of affordable and accessible high-throughput sequencing and methods to extract ancient DNA it is now possible to genetically screen a wide range of complex modern and ancient substrates, with an unprecedented depth of sequence coverage. Recently studies have attempted the isolation of DNA from samples – including fossil rodent middens – collected in cool and dry environments but so far not from hot and dry regions. Cool and frozen environments were considered more suitable to long-term DNA preservation. However, an international team of researchers has now managed to isolate DNA from 30 000 year old faeces matter to ascertain which plants and animals existed at that time in a couple of hot and dry regions in Australia and South Africa. 

Using several genetic markers and next generation sequencing they discovered a range of plant and animals, some of which are now locally extinct, such as the common brushtail possum found in one midden in the Cavenagh Range in Western Australia. The group found flora and fauna that had previously gone undetected in different types of studies, such as a range of previously indistinguishable dry zone grasses.

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