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11. Genetic variation within a stick-insect species associated with community-level traits.

Author

Sinclair-Waters, Marion, Zamorano, Laura S, Gompert, Zachariah, Parchman, Tom, Tyukmaeva, Venera, Hopkins, David P, and Nosil, Patrik

Subjects
PHASMIDA, GENETIC variation, GENOME-wide association studies, ECOSYSTEM dynamics, PHENOTYPIC plasticity
Abstract

Phenotypic variation within species can affect the ecological dynamics of populations and communities. Characterizing the genetic variation underlying such effects can help parse the roles of genetic evolution and plasticity in "eco-evolutionary dynamics" and inform how genetic variation may shape patterns of evolution. Here, we employ genome-wide association (GWA) methods in Timema cristinae stick insects and their co-occurring arthropod communities to identify genetic variation associated with community-level traits. Previous studies have shown that maladaptation (i.e. imperfect crypsis) of T. cristinae can reduce the abundance and species richness of other arthropods due to an increase in bird predation. Whether genetic variation that is independent of crypsis has similar effects is unknown and was tested here using genome-wide genotyping-by-sequencing data of stick insects, arthropod community information, and GWA mapping with Bayesian sparse linear mixed models. We find associations between genetic variation in stick insects and arthropod community traits. However, these associations disappear when host-plant traits are accounted for. We thus use path analysis to disentangle interrelationships among stick-insect genetic variation, host-plant traits, and community traits. This revealed that host-plant size has large effects on arthropod communities, while genetic variation in stick insects has a smaller, but still significant effect. Our findings demonstrate that (1) genetic variation in a species can be associated with community-level traits but that (2) interrelationships among multiple factors may need to be analyzed to disentangle whether such associations represent causal relationships. This work helps to build a framework for genomic studies of eco-evolutionary dynamics. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Keystone Genes

Author

Skovmand, Lotte H., Xu, Charles C.Y., Servedio, Maria R., Nosil, Patrik, Barrett, Rowan D.H., and Hendry, Andrew P.

Published
2018
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26. DNA methylation differences between stick insect ecotypes.

Author

de Carvalho, Clarissa F., Slate, Jon, Villoutreix, Romain, Soria‐Carrasco, Víctor, Riesch, Rüdiger, Feder, Jeffrey L., Gompert, Zachariah, and Nosil, Patrik

Subjects
DNA methylation, PHASMIDA, CPG nucleotides, GENETIC variation, HOST plants, PLANT DNA, CYTOSINE
Abstract

Epigenetic mechanisms, such as DNA methylation, can influence gene regulation and affect phenotypic variation, raising the possibility that they contribute to ecological adaptation. Beginning to address this issue requires high‐resolution sequencing studies of natural populations to pinpoint epigenetic regions of potential ecological and evolutionary significance. However, such studies are still relatively uncommon, especially in insects, and are mainly restricted to a few model organisms. Here, we characterize patterns of DNA methylation for natural populations of Timema cristinae adapted to two host plant species (i.e. ecotypes). By integrating results from sequencing of whole transcriptomes, genomes and methylomes, we investigate whether environmental, host and genetic differences of these stick insects are associated with methylation levels of cytosine nucleotides in the CpG context. We report an overall genome‐wide methylation level for T. cristinae of ~14%, with methylation being enriched in gene bodies and impoverished in repetitive elements. Genome‐wide DNA methylation variation was strongly positively correlated with genetic distance (relatedness), but also exhibited significant host‐plant effects. Using methylome‐environment association analysis, we pinpointed specific genomic regions that are differentially methylated between ecotypes, with these regions being enriched for genes with functions in membrane processes. The observed association between methylation variation and genetic relatedness, and with the ecologically important variable of host plant, suggests a potential role for epigenetic modification in T. cristinae adaptation. To substantiate such adaptive significance, future studies could test whether methylation can be transmitted across generations and the extent to which it responds to experimental manipulation in field and laboratory studies. [ABSTRACT FROM AUTHOR]

Published
2023
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31. A multivariate view of the speciation continuum

Author

Bolnick, Daniel I, primary, Hund, Amanda K, additional, Nosil, Patrik, additional, Peng, Foen, additional, Ravinet, Mark, additional, Stankowski, Sean, additional, Subramanian, Swapna, additional, Wolf, Jochen B W, additional, and Yukilevich, Roman, additional

Published
2022
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