Multifactorial processes underlie parallel opsin loss in neotropical bats
- University of California, Los Angeles, United States
- Queen Mary University of London, United Kingdom
- Stony Brook University, United States
- University of Illinois, United States
- Harvard University, United States
- University of California, Merced, United States
Abstract
The loss of previously adaptive traits is typically linked to relaxation in selection, yet the molecular steps leading to such repeated losses are rarely known. Molecular studies of loss have tended to focus on gene sequences alone, but overlooking other aspects of protein expression might underestimate phenotypic diversity. Insights based almost solely on opsin gene evolution, for instance, have made mammalian color vision a textbook example of phenotypic loss. We address this gap by investigating retention and loss of opsin genes, transcripts and proteins across ecologically diverse noctilionoid bats. We find multiple, independent losses of short-wave sensitive opsins. Mismatches between putatively functional DNA sequences, mRNA transcripts, and proteins implicate transcriptional and post-transcriptional processes in the ongoing loss of S-opsins in some noctilionoid bats. Our results provide a snapshot of evolution in progress during phenotypic trait loss, and suggest vertebrate visual phenotypes cannot always be predicted from genotypes alone.
Data availability
Sequencing data have been deposited in GenBank in the Nucleotide Database. The accession numbers are as follows: RHO: MK209460 - MK209505; OPN1LW: MK209506 - MK209551; OPN1SW: MK209552 - MK209592. The GenBank numbers for the OPN1SW PCR sequences are MK248618 - MK248630. Gene alignments are available via Dryad (http://dx.doi.org/10.5061/dryad.456569k).
-
Gene alignment data from Multifactorial processes underlie parallel opsin loss in neotropical batsDryad Digital Repository, doi:10.5061/dryad.456569k.
Article and author information
Author details
Funding
National Science Foundation (1442142)
- Kalina TJ Davies
- Laurel R Yohe
- Stephen J Rossiter
National Science Foundation (1442314)
- Alexa Sadier
- Kun Yun
- Karen E Sears
National Science Foundation (1442278)
- Paul Donat
- Brandon P Hedrick
- Elizabeth R Dumont
European Research Council (310482)
- Kalina TJ Davies
- Stephen J Rossiter
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols 14199 at UIUC and 2017-093 at UCLA. Every effort was made to minimize suffering.
Copyright
© 2018, Sadier et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 2,852
- views
-
- 365
- downloads
-
- 42
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Multifactorial processes underlie parallel opsin loss in neotropical bats
eLife 7:e37412.
https://doi.org/10.7554/eLife.37412
Further reading
-
- Evolutionary Biology
Cichlid fishes inhabiting the East African Great Lakes, Victoria, Malawi, and Tanganyika, are textbook examples of parallel evolution, as they have acquired similar traits independently in each of the three lakes during the process of adaptive radiation. In particular, ‘hypertrophied lip’ has been highlighted as a prominent example of parallel evolution. However, the underlying molecular mechanisms remain poorly understood. In this study, we conducted an integrated comparative analysis between the hypertrophied and normal lips of cichlids across three lakes based on histology, proteomics, and transcriptomics. Histological and proteomic analyses revealed that the hypertrophied lips were characterized by enlargement of the proteoglycan-rich layer, in which versican and periostin proteins were abundant. Transcriptome analysis revealed that the expression of extracellular matrix-related genes, including collagens, glycoproteins, and proteoglycans, was higher in hypertrophied lips, regardless of their phylogenetic relationships. In addition, the genes in Wnt signaling pathway, which is involved in promoting proteoglycan expression, was highly expressed in both the juvenile and adult stages of hypertrophied lips. Our comprehensive analyses showed that hypertrophied lips of the three different phylogenetic origins can be explained by similar proteomic and transcriptomic profiles, which may provide important clues into the molecular mechanisms underlying phenotypic parallelisms in East African cichlids.
-
- Evolutionary Biology
Mammalian gut microbiomes are highly dynamic communities that shape and are shaped by host aging, including age-related changes to host immunity, metabolism, and behavior. As such, gut microbial composition may provide valuable information on host biological age. Here, we test this idea by creating a microbiome-based age predictor using 13,563 gut microbial profiles from 479 wild baboons collected over 14 years. The resulting ‘microbiome clock’ predicts host chronological age. Deviations from the clock’s predictions are linked to some demographic and socio-environmental factors that predict baboon health and survival: animals who appear old-for-age tend to be male, sampled in the dry season (for females), and have high social status (both sexes). However, an individual’s ‘microbiome age’ does not predict the attainment of developmental milestones or lifespan. Hence, in our host population, gut microbiome age largely reflects current, as opposed to past, social and environmental conditions, and does not predict the pace of host development or host mortality risk. We add to a growing understanding of how age is reflected in different host phenotypes and what forces modify biological age in primates.
