Data from: Historical population size change and differentiation of relict populations of the endangered giant kangaroo rat

From a conservation management perspective it is important to understand
how genetic diversity is partitioned across a species’ range, including
(1) identification of evolutionarily distinct units versus those recently
isolated through anthropogenic activities and (2) the relative genetic
contributions among components of fragmented (meta)populations. To address
these questions, we investigated the phylogeography and metapopulation
structure among relict populations of the endangered giant kangaroo rat
(Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem.
This keystone species underwent a ~97% range reduction over the past
century, resulting in a current range that is highly fragmented, with two
dominant northern and southern populations occurring 150 km apart. We
sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear
microsatellites in >275 D. ingens to assess the evolutionary
relationship of these populations as well as the genetic structure within
the northern metapopulation. A Bayesian Skyline Plot indicated that the
species experienced a demographic expansion toward the end of the
Pleistocene, with a recent population decline. Northern and southern D.
ingens split 1,857–13,443 years ago, prior to the massive conversion of
the San Joaquin Valley to irrigated agriculture. We recommend that the
northern and southern populations of D. ingens be re-classified as
distinct population segments under the United States Endangered Species
Act. We also observed population structure and asymmetrical migration
within northern D. ingens where the Tumey Hills acted as a source
contributing gene flow to all peripheral populations. This emphasized the
importance of this location in the conservation of the metapopulation as a
whole.