DOI: 10.5061/dryad.00000001g
title: Foraging shifts and visual preadaptation in ecologically diverse bats

description: 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.
description: 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 &lt;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 &gt;50 % gaps and
 sequences &lt;50 codons were removed using a Perl script which kept
 codons intact. Alignments were retained if they contained &gt;100
 codons and at least six species, with at least one of these being a focal
 species (i.e. a noctilionoid).
description: 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.