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Detecting population structure of Paleosuchus trigonatus (Alligatoridae: Caimaninae) through microsatellites markers developed by next generation sequencing
We isolated and characterized 10 new microsatellites loci for
Paleosuchus trigonatus
using ION TORRENT Sequencing Technology. We tested the transferability of these loci to three related species of the subfamily Caimaninae, and used these bi-parental markers to test population structure and genetic diversity of two populations of
P. trigonatus
impacted by hydroelectric dam construction on the Madeira (N = 16) and Xingu (N = 16) rivers. We also investigated the transferability of these markers to three related species:
Paleosuchus palpebrosus
(N = 5),
Caiman crocodilus
(N = 6) and
Melanosuchus niger
(N = 6). The genetic diversity of
P. trigonatus
was low in both the Madeira (
He
: 0.535 ± 0.148) and Xingu (
He
: 0.381 ± 0.222) populations, but the loci were sufficiently polymorphic to be used in system of mating and kinship studies in
P. trigonatus
. DAPC analysis with our set of microsatellites loci was able to separate the four species of Caimaninae studied and to detect a shallow genetic structure between Madeira and Xingu populations of
P. trigonatus
. AMOVA and STRUCTURE analyses using
locprior
model corroborate this shallow genetic structure. These novel molecular markers will be also useful in conservation genetics and phylogeographic studies of
P. trigonatus
, since they improve our ability to monitor the putative effects of dams on the loss of genetic diversity and allow us to investigate population dynamics and microevolutionary processes that occurred in the species.