Long‐term balancing selection on chromosomal variants associated with crypsis in a stick insect

Abstract

How polymorphisms are maintained within populations over long periods of time remains debated, because genetic drift and various forms of selection are expected to reduce variation. Here, we study the genetic architecture and maintenance of phenotypic morphs that confer crypsis in Timema cristinae stick insects, combining phenotypic information and genotyping-by-sequencing data from 1,360 samples across 21 populations. We find two highly divergent chromosomal variants that span megabases of sequence and are associated with colour polymorphism. We show that these variants exhibit strongly reduced effective recombination, are geographically widespread and probably diverged millions of generations ago. We detect heterokaryotype excess and signs of balancing selection acting on these variants through the species' history. A third chromosomal variant in the same genomic region likely evolved more recently from one of the two colour variants and is associated with dorsal pattern polymorphism. Our results suggest that large-scale genetic variation associated with crypsis has been maintained for long periods of time by potentially complex processes of balancing selection.

Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

“…Kemppainen et al () recently released a tool for calculating linkage disequilibrium (LDna) that uses network analytical tools to visualize groups of linked loci across a genome. LDna has been used to reduce data dimensionality while searching for QTLs in model organisms (Li, Kemppainen, Rastas, & Merila, ) and can provide evidence of inversions and islands of genomic differentiation (Benestan et al, ; Lindtke et al, ; Ravinet et al, ). In this paper, we employ a similar approach to reduce dimensionality in our data while looking for cohorts of linked markers undergoing divergence or directional selection.…”

Karyotype-environment associations support a role for a chromosomal inversion in local adaptation in the seaweed flyCoelopa frigida

“…[16,20,21] or chromosomal rearrangements associated with ecotype divergence [22][23][24][25]. The pattern of inversion frequency distributions can be variable, ranging from fixation between distinct habitats [24,26], clinal modulation of intermediate frequencies [20] to widespread polymorphism in other cases [27][28][29]. The fate of an inversion depends on the selective mechanisms at play and on the genes trapped within the inversion.…”

Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders

“…; Lindtke et al. ), or if the phenotypes arose after the split via convergence (Renaut et al. ; Soria‐Carrasco et al.…”

“…However, we are unaware of an example of a plethodontid species with two morphotypes that each exhibit a set of distinct, consistently produced color pattern and skeletal traits. Furthermore, the presence of both morphotypes in two highly diverged lineages raises the question of whether phenotypic differences arose prior to the split between Pisgah and Nantahala and was then maintained through selective pressures (Pfennig et al 2010;Arnegard et al 2014;Lindtke et al 2017), or if the phenotypes arose after the split via convergence (Renaut et al 2014;Soria-Carrasco et al 2014;Bailey et al 2015). Both of these scenarios should produce a signature of genetic divergence that has thus far remained elusive, and acquisition of a dataset with high enough coverage of the genome to detect signatures of selection will remain a challenge for this group until sequencing technology makes its next leap forward.…”