10.5061/DRYAD.00000001G
Davies, Kalina T. J.
0000-0002-4258-4775
Queen Mary University of London
Yohe, Laurel R.
Stony Brook University
Almonte, Jesus
Independent Scientist
Sánchez, Miluska K. R.
Universidad Nacional de Piura
Rengifo, Edgardo M.
University of Sao Paulo
Dumont, Elizabeth R.
University of California, Merced
Sears, Karen E.
UCLA Health
Dávalos, Liliana M.
Stony Brook University
Rossiter, Stephen J.
Queen Mary University of London
Foraging shifts and visual preadaptation in ecologically diverse bats
Dryad
dataset
2020
Vision
Foraging
preadaptation
molecular adaptation
European Research Council
https://ror.org/0472cxd90
310482 EVOGENO
University of Michigan–Ann Arbor
https://ror.org/00jmfr291
ECR bridging fund
National Science Foundation
https://ror.org/021nxhr62
DEB-1442142
National Science Foundation
https://ror.org/021nxhr62
DEB-1442314
National Science Foundation
https://ror.org/021nxhr62
DEB-1701414
National Science Foundation
https://ror.org/021nxhr62
DBI-1812035
2020-05-21T00:00:00Z
2020-05-21T00:00:00Z
en
https://doi.org/10.1111/mec.15445
111228481 bytes
3
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Changes in behaviour may initiate shifts to new adaptive zones, with
physical adaptations for novel environments evolving later. While new
mutations are commonly considered engines of adaptive change, sensory
evolution enabling access to new resources might also arise from standing
genetic diversity, and even gene loss. We examine the relative
contribution of molecular adaptations, measured by positive and relaxed
selection, acting on eye expressed genes associated with shifts to new
adaptive zones in ecologically diverse bats from the superfamily
Noctilionoidea. Collectively, noctilionoids display remarkable ecological
breadth, from highly divergent echolocation to flight strategies linked to
specialized insectivory, the parallel evolution of diverse plant-based
diets (e.g., nectar, pollen, and fruit) from ancestral insectivory, and
–unusually for echolocating bats– often have large, well-developed eyes.
We report contrasting levels of positive selection in genes associated
with the development, maintenance, and scope of visual function, tracing
back to the origins of noctilionoids and Phyllostomidae (the bat family
with most dietary diversity), instead of during shifts to novel diets.
Generalized plant visiting was not associated with exceptional molecular
adaptation, and exploration of these novel niches took place in an
ancestral phyllostomid genetic background. In contrast, evidence for
positive selection in vision genes was found at subsequent shifts to
either nectarivory or frugivory. Thus, neotropical noctilionoids that use
visual cues for identifying food and roosts, as well as for orientation,
were effectively preadapted, with subsequent molecular adaptations in
nectar-feeding lineages and the Stenodermatinae subfamily of fig-eating
bats fine-tuning pre-existing visual adaptations for specialized purposes.
Multiple sequence alignments for protein-coding gene coding sequences in
bat species, including sequences from the Noctilionoidea superfamily and
out-group taxa. Genes were identified with best hit reciprocal blast
(blast+/2.2.29) using the longest representative sequences of human
proteins (Ensembl 86), applying an e-value cut-off <1e-6. Multiple
sequence alignments were generated with GUIDANCEv.2.02 using the
PRANKv.170427 algorithm, with 10 bootstrap replicates and codons enforced.
For 10 genes encoding proteins of ≥5000 amino acids, alignments were
constructed with MAFFTv.7.310 instead of PRANK, due to computational
limits of run-time. Low confidence sites (below default score of 0.93)
and/or low quality sequences (below default score of 0.6), were removed.
Genes for which low quality sequences were detected were re-aligned with
these removed. All alignments sites containing >50 % gaps and
sequences <50 codons were removed using a Perl script which kept
codons intact. Alignments were retained if they contained >100
codons and at least six species, with at least one of these being a focal
species (i.e. a noctilionoid).
Multiple sequence alignments (in fasta format) for protein-coding gene
coding sequences obtained from RNA-Seq data collected from bats
representing the Noctilionoidea superfamily and out-group taxa.