Data from: Phylogeographic and demographic patterns reveal congruent histories in seven Amazonian white-sand ecosystems birds

Aim: As the most biodiverse region of the world, the drivers of genetic
diversity in Amazonia are still poorly understood. It has been debated
that species on distinct ecosystems will show unique biogeographic
histories tied to their habitats which in turn help understand landscape
climatic history in Amazonia. We studied bird species associated with
patchy Amazonian white-sand ecosystems (WSE) to evaluate the occurrence of
shared patterns and its relationship to species habitat preferences and
Amazonian environmental and landscape history. Location: Northern South
America; Amazonia. Taxon: Passerine birds. Methods: We sequenced
Ultra-conserved Elements (UCEs) from 177 samples of seven bird species
associated with WSE that have overlapping ranges. We used the SNP matrices
and sequence data to estimate genetic structure patterns and migration
surfaces using ‘conStruct’ and eems, perform model-selection to obtain the
most probable demographic histories on ‘PipeMaster’, and implement
analyses of shared demography with ecoevolity. Results: Shallow genetic
structure patterns varied among species with the Amazon river being the
only barrier shared among them. Population structure dates to no more than
450,000 years ago. We identified 17 geographically structured populations
from which nine showed signals of population size changes and eight of
these occur in Northern Amazonia. Population expansion was inferred at two
distinct times: ~100,000 years ago and ~50,000 years ago. The timing of
co-expanding populations is consistent with differences in habitat
preference, as species that prefer dense scrubby to forested vegetation
expanded more recently compared to species that prefer open vegetation.
Main conclusions: We show that WSE species responded in concert to past
environmental and landscape changes. Past population expansions were
likely driven by the genesis of new WSE patches and a return to wetter
conditions after glacial periods. Pleistocene climatic cycles affected the
distribution and dynamics of open vegetation habitats in Amazonia,
especially in the Northern region, driving genetic diversity and
demographic patterns of its associated biota.