10.5061/DRYAD.XKSN02VBW
Xue, Alexander T.
0000-0003-1521-6448
Cold Spring Harbor Laboratory
Hickerson, Mike
,
Data from: Comparative phylogeographic inference with genome-wide data
from aggregated population-pairs
Dryad
dataset
2020
Evolutionary genomics
National Science Foundation
https://ror.org/021nxhr62
DEB-1253710, DEB-1343578, DEB-1457232
National Institute of General Medical Sciences
https://ror.org/04q48ey07
1R15GM096267-01
FAPESP
BIOTA, 2013/50297-0
2020-02-10T00:00:00Z
2020-02-10T00:00:00Z
en
241407 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Comparing divergences across multiple sister population-pairs has been a
focus in phylogeography since its inception. Initial approaches utilized
organelle genetic data and involved qualitative comparisons of
phylogenetic patterns to evaluate hypotheses of shared and variable
evolutionary responses. This endeavor has progressed with coalescent
model-based statistical techniques and advances in next-generation
sequencing, yet there remains a need for methods that can exploit
aggregated genomic-scale data within a unified analytical framework. To
this end, we introduce the aggregate joint site frequency spectrum (ajSFS)
by validating its use within a hierarchical Bayesian framework through
several in silico experiments. Subsequently, we applied our method against
two published restriction site associated DNA marker datasets consisting
of eight local replicates of a lamprey species-pair and six co-distributed
passerine taxon-pairs respectively, with the aim of inferring variability
in co-divergence and co-migration histories. We found that the lamprey
population-pairs exhibited temporal synchrony in both co-divergence and
collective secondary contact times, yet an idiosyncratic pattern in
secondary migration intensities. In contrast, the bird population-pairs
displayed thoroughly asynchronous co-divergence histories. Our results
demonstrate that the ajSFS can be exploited for complex and flexible
co-demographic inference, opening up new possibilities for comparative
phylogeography and population genomic studies.
Simulated datasets via Multi-DICE and fastsimcoal2