Growth Genes Are Implicated in the Evolutionary Divergence of Sympatric Piscivorous and Insectivorous Rainbow Trout (Oncorhynchus Mykiss) Jared A
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Grummer et al. BMC Ecol Evo (2021) 21:63 BMC Ecology and Evolution https://doi.org/10.1186/s12862-021-01795-9 RESEARCH Open Access Growth genes are implicated in the evolutionary divergence of sympatric piscivorous and insectivorous rainbow trout (Oncorhynchus mykiss) Jared A. Grummer1*, Michael C. Whitlock1, Patricia M. Schulte1 and Eric B. Taylor1,2 Abstract Background: Identifying ecologically signifcant phenotypic traits and the genomic mechanisms that underly them are crucial steps in understanding traits associated with population divergence. We used genome-wide data to identify genomic regions associated with key traits that distinguish two ecomorphs of rainbow trout (Oncorhyn- chus mykiss)—insectivores and piscivores—that coexist for the non-breeding portion of the year in Kootenay Lake, southeastern British Columbia. “Gerrards” are large-bodied, rapidly growing piscivores with high metabolic rates that spawn north of Kootenay Lake in the Lardeau River, in contrast to the insectivorous populations that are on average smaller in body size, with lower growth and metabolic rates, mainly forage on aquatic insects, and spawn in tributaries immediately surrounding Kootenay Lake. We used pool-seq data representing ~ 60% of the genome and 80 fsh per population to assess the level of genomic divergence between ecomorphs and to identify and interrogate loci that may play functional or selective roles in their divergence. Results: Genomic divergence was high between sympatric insectivores and piscivores ( FST 0.188), and in fact = higher than between insectivorous populations from Kootenay Lake and the Blackwater River ( FST 0.159) that are = > 500 km apart. A window-based FST analysis did not reveal “islands” of genomic diferentiation; however, the window with highest FST estimate did include a gene associated with insulin secretion. Although we explored the use of the “Local score” approach to identify genomic outlier regions, this method was ultimately not used because simula- tions revealed a high false discovery rate (~ 20%). Gene ontology (GO) analysis identifed several growth processes as enriched in genes occurring in the ~ 200 most divergent genomic windows, indicating many loci of small efect involved in growth and growth-related metabolic processes are associated with the divergence of these ecomorphs. Conclusion: Our results reveal a high degree of genomic diferentiation between piscivorous and insectivorous populations and indicate that the large body piscivorous phenotype is likely not due to one or a few loci of large efect. Rather, the piscivore phenotype may be controlled by several loci of small efect, thus highlighting the power of whole-genome resequencing in identifying genomic regions underlying population-level phenotypic divergences. Keywords: Genome scan, Small-efect loci, FST, GO analysis, Rainbow trout, Ecomorph Background *Correspondence: [email protected] Understanding the divergence of populations and the 1 Department of Zoology and Biodiversity Research Centre, University mechanisms responsible for it are important for the felds of British Columbia, 6270 University Blvd., Vancouver, BC V6T 1Z4, Canada of speciation, macroevolution, ecology, and conservation Full list of author information is available at the end of the article © The Author(s) 2021. 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The Creative Commons Public Domain Dedication waiver (http:// creat iveco mmons. org/ publi cdoma in/ zero/1. 0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Grummer et al. BMC Ecol Evo (2021) 21:63 Page 2 of 13 [1]. In many cases, population-level divergences are Identifying the genomic regions underlying divergent associated with character displacement and phenotypic ecological forms can provide insights into the genomic divergence of sympatric forms, such as in threespine architecture of population divergence. Here, we address sticklebacks (e.g., [2]) or Nicaraguan crater lake cich- this question in two ecomorphs of rainbow trout (Onco- lids (e.g., [3]). Recent advancements in sequencing tech- rhynchus mykiss) in Kootenay Lake of southeastern Brit- nologies have enabled investigations into the genomics ish Columbia. Rainbow trout in this lake provide an underlying traits associated with phenotypic divergences example of divergence into co-existing insectivorous and in non-model systems. In some cases, few highly difer- piscivorous forms, which has repeatedly been observed entiated loci of large efect can be responsible for popu- in trout and char. For example, Arctic charr (Salvelinus lation-level phenotypic or behavioural divergence in spite alpinus) have repeatedly evolved sympatric forms of zoo- of the majority of genomic diferentiation being very low planktivores and piscivores on multiple continents [15, between populations as the result of either recent diver- 16], including Iceland’s Lake Tingvallavatn (e.g., [17]). gence and/or ongoing gene fow (e.g., Heliconius butter- Additionally, a large and piscivorous form of brown trout fies; [4, 5]). (“Ferox” trout; Salmo trutta) occurs throughout Ireland Determining the genetic architecture of a pheno- and Scotland [18, 19]. A variety of divergent life-history typic trait—whether the trait is controlled by few loci of patterns can be found in populations across the native large efect, many loci of small efect, or some combina- range of O. mykiss, including migration patterns (resident tion thereof—is important for understanding how traits vs. anadromous), habitat type (lake vs. stream), and diet respond to evolutionary processes including selection (piscivory vs. insectivory) [20]. Whereas genomic regions and migration [6]. In fshes, there are a few examples have been found that are associated with migration and of a small number of loci having an efect on pheno- habitat type [9, 21], little is known about the evolutionary typic divergence between sympatric forms. For instance, mechanisms promoting divergence of piscivorous and Jacobs et al. [7] identifed ~ 10 genomic outlier regions insectivorous O. mykiss populations. in brown trout (Salmo trutta) containing several genes Te rainbow trout ecomorphs in Kootenay Lake dif- involved in development, growth, and gene expression fer in a wide variety of ecological and life-history traits. and regulation that difer between piscivorous (fsh- Individuals of the large piscivorous form (often > 60 cm eating) and insectivorous populations. In Atlantic cod and 5 kg, but up to 12 kg) are locally known as “Gerrards” (Gadus morhua), a ~ 17 MB (megabase) region contain- and have an adult dietary specialization on Kokanee ing two chromosomal inversions is associated with pop- salmon—small, land-locked sockeye salmon (O. nerka)— ulation divergence based on migration phenotype [8]. and spawn near the abandoned town site Gerrard (thus Additionally, in Pacifc salmon (genus Oncorhynchus), the name “Gerrards”) on the Lardeau River that drains one small genomic region has been shown to control a into the north arm of Kootenay Lake [22, 23]. In con- vital phenotype for the natural history of two species— trast, the smaller form (typically ≤ 50 cm and ≤ 2 kg) is adult migration timing [9]. primarily insectivorous and made up of several popula- Teory predicts that the distribution of allelic efects tions that spawn in smaller tributaries that drain into on quantitative traits should be nearly exponential, where Kootenay Lake [23] (Fig. 1). Te piscivorous and insec- few loci have large efects and explain most of the vari- tivorous forms are sympatric in the lake for a majority of ance in traits, but many loci with smaller efects explain the year (e.g., non-breeding season) after spending their the remaining variation in the trait [10, 11]. Tis pat- frst 1–2 years separated as juveniles in their respective tern was seen for “age at maturity” in Atlantic salmon, streams. Piscivorous individuals have signifcantly larger where two genes of large efect and > 100 genes of small head and upper jaw sizes, likely due to their specializa- efect underly this trait [12]. Across taxa, several phe- tion on larger prey (Neufeld, BC Ministry of Forests, notypes are explained by many loci of small efect. For Lands, Natural Resource Operations and Rural Develop- instance, hundreds of genetic variants explain only ~ 10% ment, unpublished data). In addition to these morpho- of the phenotypic variation in human height [13]. And a logical diferences between ecomorphs, the piscivores genome-wide analysis of 50,000 SNPs (single nucleotide have signifcantly faster growth rates and higher stand- polymorphism) in the collared fycatcher (Ficedula albi- ard metabolic rates relative to those