Data from: Genetic diversity loss in a biodiversity hotspot: ancient DNA quantifies genetic decline and former connectivity in a critically endangered marsupial.

The extent of genetic diversity loss and former connectivity between
fragmented populations are often unknown factors when studying endangered
species. While genetic techniques are commonly applied in extant
populations to assess temporal and spatial demographic changes, it is no
substitute for directly measuring past diversity using ancient DNA (aDNA).
We analysed both mitochondrial DNA (mtDNA) and nuclear microsatellite loci
from 64 historical fossil and skin samples of the critically endangered
Western Australian woylie (Bettongia penicillata ogilbyi), and compared
them with 231 (n=152 for mtDNA) modern samples. In modern woylie
populations 15 mitochondrial control region (CR) haplotypes were
identified. Interestingly, mtDNA CR data from only 29 historical samples
demonstrated 15 previously unknown haplotypes and detected an extinct
divergent clade. Through modelling, we estimated the loss of CR mtDNA
diversity to be between 46% and 91% and estimated this to have occurred in
the past 2000-4000 years in association with a dramatic population
decline. Additionally, we obtained near-complete 11-loci microsatellite
profiles from 21 historical samples. In agreement with the mtDNA data, a
number of ‘new’ microsatellite alleles was only detected in the historical
populations despite extensive modern sampling, indicating a nuclear
genetic diversity loss greater than 20%. Calculations of genetic diversity
(heterozygosity and allelic rarefaction) showed that these were
significantly higher in the past and that there was a high degree of gene
flow across the woylie's historical range. These findings have an
immediate impact on how the extant populations are managed and we
recommend the implementation of an assisted migration program to prevent
further loss of genetic diversity. Our study demonstrates the value of
integrating aDNA data into current-day conservation strategies.