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New Tassie devil research published – Genetic diversity must be conserved

In 2013, researcher Dr Anna Brüniche-Olsen was awarded a Dr. Eric Guiler Tasmanian Devil Research Grant worth $35,000. This Grant was made possible through public donations received through the Save the Tasmanian Devil Appeal. Last week Anna, along with other contributors, published some of the findings which she summarized for us below:

"In our newest publication in we investigate whether there is evidence for devil facial tumor disease (DFTD) associated selection in the genome of Tasmanian devils.

This Page/Figure-1-Tas-Devil-Appeal.jpgSince DFTD’s emergence in the mid 1990s the disease has spread to most of the Tasmanian devil’s geographic range, causing extensive population decline. Tasmanian devil populations have responded to DFTD with behavioural changes, e.g., females reducing their dispersal distance, increased migration from DFTD-free populations to DFTD-affected populations, and devils breeding at a younger age. However, it was unclear to what extent the devils have responded genetically to the spread of DFTD.

Diseases with a high mortality—like DFTD—are expected to enforce a strong selection pressure on a population. Selection leaves ‘footprints’ in the DNA, and by sequencing genomes from devils before and after a population is infected with DFTD, we can detect any DNA ‘footprints’ that DFTD might have left. An earlier study of devil populations from the East cCast of Tasmania sampled in 2005–2007 indicated that devils showed some selective changes to DFTD. We were interested in investigating this further, expanding the study with respect to geographic area, timeframe across which selection may have operated, and extent of the genome surveyed.

Using 1,500 genetic markers scattered across the Tasmanian devil genome we investigated potential selection pressures associated with DFTD spread. We collected tissue samples from 527 Tasmanian devil from populations across Tasmania in 1999, 2004, 2009 and 2013 (see in PdF attached below). This time-series made it possible for us to trace changes in frequency of variants at each of the 1,500 genetic markers over a 15 years period. In this way we could determine if there was a consistent pattern of change in the DNA in populations across the island with respect to the arrival of DFTD in the populations.

Our results showed that there was no consistent selection pattern associated with the spread of DFTD. We detected multiple genetic markers to be under putative selection with respect to the arrival of DFTD at individual populations, but the markers were either not the same across the multiple DFTD affected populations, or the direction of selection for the individual markers was not the consistent. For some populations variants at a given marker increased in frequency, while it decreased in other populations. If DFTD enforced a strong selection pressure on the devil genome, we would have expected that this selection ‘footprint’ would be the same across all populations affected by DFTD and not random as we observed.

Given that DFTD exerts such high mortality on devils, what might explain the lack of a consistent selection response in the devil genome? There is generally two forces changing frequencies of variants of at DNA markers: ‘selection’ and ‘genetic drift’. The later is not associated with a direct adaptive change, but is rather a change in marker variant frequency occurring at random. In large populations ‘selection’ more readily drives the change in DNA, while in small populations ‘genetic drift’ dominates. As the Tasmanian devil population has low genetic diversity—which is equivalent to it being a small population in genetic terms—lack consistent genetic changes among populations with respect to DFTD is most likely the product of ‘genetic drift’.

This research is part of a bigger picture. We previously documented how Tasmanian devils lost genetic diversity 5,000–3,000 years ago, coinciding with a time of unstable climate, and have been living with low genetic diversity for thousands of years (see Brüniche-Olsen et al. 2014 and Appeal news 6/11/2014). This low genetic diversity leaves little room for selection to operate efficiently. Genetic diversity is what makes a population able to evolve and adapt to changes in its environment or respond to novel diseases. Thus, a species that has low genetic diversity is more prone to extinction. It is therefore essential that conservation measures aiming at conserving genetic diversity be implemented to limit further loss of genetic diversity in the Tasmanian devil and conserve the species for generations to come."

To read the full scientific publication, please visit: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147875

Figure 1 (above right): Sampling design - The individual population are indicated with circles. Grey circles correspond to healthy devil populations and black circles represent populations where DFTD is present. The grey areas correspond to the DFTD front at the time of sampling: 1999, 2004, 2009 and 2013.

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Photograph above: Sub-adult devil at Arthur River, photo by Georgina Andersen