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Mol Biol Evol. 2016 Sep;33(9):2257-72. doi: 10.1093/molbev/msw093. Epub 2016 May 9.

Genomic Profiles of Diversification and Genotype-Phenotype Association in Island Nematode Lineages.

Author information

1
CSIRO Land & Water, Black Mountain Laboratories, Canberra, ACT, Australia School of BioSciences, University of Melbourne, Melbourne, VIC, Australia Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany ang.mcgaughran@gmail.com.
2
Department for Evolutionary Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
3
Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, Tübingen, Germany Zentrum Für Bioinformatik, Eberhard Karls Universität, Tübingen, Germany Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
4
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
5
Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems, Tübingen, Germany.

Abstract

Understanding how new species form requires investigation of evolutionary forces that cause phenotypic and genotypic changes among populations. However, the mechanisms underlying speciation vary and little is known about whether genomes diversify in the same ways in parallel at the incipient scale. We address this using the nematode, Pristionchus pacificus, which resides at an interesting point on the speciation continuum (distinct evolutionary lineages without reproductive isolation), and inhabits heterogeneous environments subject to divergent environmental pressures. Using whole genome re-sequencing of 264 strains, we estimate FST to identify outlier regions of extraordinary differentiation (∼1.725 Mb of the 172.5 Mb genome). We find evidence for shared divergent genomic regions occurring at a higher frequency than expected by chance among populations of the same evolutionary lineage. We use allele frequency spectra to find that, among lineages, 53% of divergent regions are consistent with adaptive selection, whereas 24% and 23% of such regions suggest background selection and restricted gene flow, respectively. In contrast, among populations from the same lineage, similar proportions (34-48%) of divergent regions correspond to adaptive selection and restricted gene flow, whereas 13-22% suggest background selection. Because speciation often involves phenotypic and genomic divergence, we also evaluate phenotypic variation, focusing on pH tolerance, which we find is diverging in a manner corresponding to environmental differences among populations. Taking a genome-wide association approach, we functionally validate a significant genotype-phenotype association for this trait. Our results are consistent with P. pacificus undergoing heterogeneous genotypic and phenotypic diversification related to both evolutionary and environmental processes.

KEYWORDS:

FST; differentiation; diversification; evolution; genome-wide association study; incipient speciation.

PMID:
27189551
DOI:
10.1093/molbev/msw093
[Indexed for MEDLINE]

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