10.5061/DRYAD.FFBG79CST
Foster, Charles
0000-0002-6700-3746
University of Sydney
Van Dyke, James
La Trobe University
Thompson, Michael
University of Sydney
Smith, Nicholas
0000-0001-7841-9184
University of Queensland
Simpfendorfer, Colin
James Cook University
Murphy, Christopher
University of Sydney
Whittington, Camilla
0000-0001-5765-9699
University of Sydney
Different genes are recruited during convergent evolution of pregnancy and
the placenta
Dryad
dataset
2020
Evolutionary biology
Australian Research Council
https://ror.org/05mmh0f86
DP180103370
2022-06-10T00:00:00Z
2022-06-10T00:00:00Z
en
https://doi.org/10.1093/molbev/msac077
https://doi.org/10.5281/zenodo.6629815
https://doi.org/10.5281/zenodo.6629817
547993981 bytes
8
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
The repeated evolution of the same traits in distantly related groups
(convergent evolution) raises a key question in evolutionary biology: do
the same genes underpin convergent phenotypes? Here, we explore one such
trait, viviparity (live birth), which, qualitative studies suggest, may
indeed have evolved via genetic convergence. There are 150 independent
origins of live birth in vertebrates, providing a uniquely powerful system
to test the mechanisms underpinning convergence in morphology, physiology,
and/or gene recruitment during pregnancy. We compared transcriptomic data
from eight vertebrates (lizards, mammals, sharks) that gestate embryos
within the uterus. Since many previous studies detected qualitative
similarities in gene use during independent origins of pregnancy, we
expected to find significant overlap in gene use in viviparous taxa.
However, we found no more overlap in uterine gene expression associated
with viviparity than we would expect by chance alone. Each viviparous
lineage exhibits the same core set of uterine physiological functions.
Yet, contrary to prevailing assumptions about this trait, we find that
none of the same genes are differentially expressed in all viviparous
lineages, or even in all viviparous amniote lineages. Therefore, across
distantly related vertebrates, different genes have been recruited to
support the morphological and physiological changes required for
successful pregnancy. We conclude that redundancies in gene function have
enabled the repeated evolution of viviparity through recruitment of
different genes from genomic “toolboxes”, which are uniquely constrained
by the ancestries of each lineage.
These files are the Supplementary Materials for our manuscript submission:
"Different genes are recruited during convergent evolution of
pregnancy and the placenta". Briefly, transcriptomes (both de novo
and pre-existing) from eight vertebrates (lizards, mammals, shark) were
compared to determine gene-expression changes during pregnancy. We found
that, despite broad physiological and morphological convergence, there was
next to no convergence in gene recruitment during pregnancy. A more
in-depth explanation of methods can be found within the Supplementary
Methods.
This upload to Dryad contains all files supplementary to our submission to
PNAS. There are: 3 supplementary figures (.pdf) 13 supplementary tables
(.pdf; .xlsx) A "Supplementary Materials" document (.docx) with
supplementary figure captions This upload also contains: All de novo
transcriptome assemblies The raw counts for each sample from each species
The code necessary to replicate the DE and GO analysis results (and
associated accessory metadata files) The code for overlap analyses, and
associated metadata files