Genomic signatures of mitonuclear coevolution across populations of Tigriopus californicus
Felipe S. Barreto, Eric T. Watson, Thiago G. Lima, Christopher S. Willett, Suzanne Edmands, Weizhong Li & Ronald S. Burton
Nature Ecology & Evolution (2018)
Assembly and evolution of a copepod genome.
Abstract
The copepod Tigriopus californicus shows extensive population divergence and is becoming a model for understanding allopatric differentiation and the early stages of speciation. Here, we report a high-quality reference genome for one population (~190 megabases across 12 scaffolds, and ~15,500 protein-coding genes). Comparison with other arthropods reveals 2,526 genes presumed to be specific to T. californicus, with an apparent proliferation of genes involved in ion transport and receptor activity. Beyond the reference population, we report re-sequenced genomes of seven additional populations, spanning the continuum of reproductive isolation. Populations show extreme mitochondrial DNA divergence, with higher levels of amino acid differentiation than observed in other taxa. Across the nuclear genome, we find elevated protein evolutionary rates and positive selection in genes predicted to interact with mitochondrial DNA and the proteins and RNA it encodes in multiple pathways. Together, these results support the hypothesis that rapid mitochondrial evolution drives compensatory nuclear evolution within isolated populations, thereby providing a potentially important mechanism for causing intrinsic reproductive isolation.
Acknowledgements
This work was supported by US National Science Foundation grants (IOS1154321 to S.E.; IOS1155030 to R.S.B.; and IOS1155325 to C.S.W.) and Oregon State University faculty startup funds to F.S.B. The authors thank S. Morgan and R. J. Pereira for help with sample collection.
Author information
Affiliations
Department of Integrative Biology, Oregon State University, Corvallis, OR, USA
Felipe S. Barreto
Marine Biology Research Division, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
Felipe S. Barreto, Thiago G. Lima & Ronald S. Burton
Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
Eric T. Watson & Suzanne Edmands
Department of Biology, University of North Carolina, Chapel Hill, NC, USA
Thiago G. Lima & Christopher S. Willett
Center for Research in Biological Systems, University of California, San Diego, La Jolla, CA, USA
Weizhong Li
Contributions
F.S.B., E.T.W., T.G.L., C.S.W., S.E. and R.S.B. contributed to the design of the project, collection of biological samples, and sequence data acquisition. W.L. contributed to initial genome sequence assembly. F.S.B., E.T.W. and C.S.W. contributed to genome annotation. F.S.B., E.T.W., T.G.L. and C.S.W. contributed to computational and statistical analyses. F.S.B., E.T.W., T.G.L., C.S.W., S.E. and R.S.B. contributed to data interpretation and writing of the manuscript.
Competing interests
The authors declare no competing interests.
Corresponding author
Correspondence to Felipe S. Barreto.
FREE PDF GRATIS: Nature Ecology and Evolution, Sup. Info., Reporting Summary, Supplementary Data
