Microevolutionary selection dynamics acting on immune genes of the green‐veined white butterfly, <i>Pieris napi</i>

Keehnen, Naomi; Hill, Jason; Nylin, Sören; Wheat, Christopher W.

doi:10.1111/mec.14722

Cited by 12 publications

(14 citation statements)

References 105 publications

(153 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We also defined outliers as those SNPs with anF ST above a thresholds corresponding to the 99.5 th percentile (e.g. Fabian et al, 2012;Keehnen, Hill, Nylin, & Wheat, 2018) of the genome-wide F ST distribution. A threshold of the 97.5 th percentile was used forF ST based on 5 kb windows (e.g.…”

Section: Identifying Potential Outliersmentioning

confidence: 99%

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

Saha¹,

Andersson²,

Kurland³

et al. 2021

Preprint

View full text Add to dashboard Cite

The sympatric existence of genetically distinct populations of the same species remains a puzzle in ecology. Coexisting salmonid fish populations are known from over 100 freshwater lakes. Most studies of sympatric populations have used limited numbers of genetic markers making it unclear if genetic divergence involves only certain parts of the genome. We return to the first reported case of salmonid sympatry, initially detected through contrasting homozygosity at a single allozyme locus (lactate dehydrogenase, LDH-A1) in brown trout in the small Lakes Bunnersjöarna, central Sweden. We use DNA from samples collected in the 1970s and a 96 SNP fluidigm array to verify the existence of the coexisting demes. We then apply whole-genome resequencing of pooled DNA to explore genome-wide diversity within and between these demes; strong genetic divergence is observed with genome-wide FST=0.13. Nucleotide diversity is estimated to 0.0013 in Deme I but only 0.0005 in Deme II. Individual whole-genome resequencing of two individuals per deme suggests considerably higher inbreeding in Deme II vs. Deme I. Comparing with similar data from other lakes we find that the genome-wide divergence between the demes is similar to that between reproductively isolated populations. We located two genes for LDH-A and found divergence between the demes in a regulatory section of one of the genes, but we could not find a perfect fit between allozyme and sequence data. Our data demonstrate genome-wide divergence governed by genetic drift and diversifying selection, confirming reproductive isolation between the sympatric demes.

show abstract

Section: Identifying Potential Outliersmentioning

confidence: 99%

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

Saha¹,

Andersson²,

Kurland³

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…The approach leverages the power of Pool‐seq to subsample the genome to obtain high‐resolution genomic insights quickly and at a reasonable cost (Neethiraj, Hornett, Hill, & Wheat, ). This pipeline has been utilized for elucidating the genomics underlying phenotypic differences between populations of several butterfly species (Keehnen, Hill, Nylin, & Wheat, ; Pruisscher, Nylin, Gotthard, & Wheat, ; Woronik & Wheat, ).…”

Section: Introductionmentioning

confidence: 99%

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

Kurland

Wheat

Celorio‐Mancera

et al. 2019

Ecology and Evolution

Self Cite

View full text Add to dashboard Cite

Developing genomic insights is challenging in nonmodel species for which resources are often scarce and prohibitively costly. Here, we explore the potential of a recently established approach using Pool‐seq data to generate a de novo genome assembly for mining exons, upon which Pool‐seq data are used to estimate population divergence and diversity. We do this for two pairs of sympatric populations of brown trout (Salmo trutta): one naturally sympatric set of populations and another pair of populations introduced to a common environment. We validate our approach by comparing the results to those from markers previously used to describe the populations (allozymes and individual‐based single nucleotide polymorphisms [SNPs]) and from mapping the Pool‐seq data to a reference genome of the closely related Atlantic salmon (Salmo salar). We find that genomic differentiation (FST) between the two introduced populations exceeds that of the naturally sympatric populations (FST = 0.13 and 0.03 between the introduced and the naturally sympatric populations, respectively), in concordance with estimates from the previously used SNPs. The same level of population divergence is found for the two genome assemblies, but estimates of average nucleotide diversity differ (trueπ¯ ≈ 0.002 and trueπ¯ ≈ 0.001 when mapping to S. trutta and S. salar, respectively), although the relationships between population values are largely consistent. This discrepancy might be attributed to biases when mapping to a haploid condensed assembly made of highly fragmented read data compared to using a high‐quality reference assembly from a divergent species. We conclude that the Pool‐seq‐only approach can be suitable for detecting and quantifying genome‐wide population differentiation, and for comparing genomic diversity in populations of nonmodel species where reference genomes are lacking.

show abstract

“…For our population genomics analysis, we used two previously published [43] Poolseq datasets originating from the two populations used in this experiment. These two libraries were mapped against the genome using Next-Gen mapper v.04.10.…”

Section: Gene Scan and Population Geneticsmentioning

confidence: 99%

A Population Genomic Investigation of Immune Cell Diversity and Phagocytic Capacity in a Butterfly

Keehnen

Fors

Järver

et al. 2021

Genes

Self Cite

View full text Add to dashboard Cite

Insects rely on their innate immune system to successfully mediate complex interactions with their internal microbiota, as well as the microbes present in the environment. Given the variation in microbes across habitats, the challenges to respond to them are likely to result in local adaptations in the immune system. Here we focus upon phagocytosis, a mechanism by which pathogens and foreign particles are engulfed in order to be contained, killed, and processed. We investigated the phenotypic and genetic variation related to phagocytosis in two allopatric populations of the butterfly Pieris napi. Populations were found to differ in their hemocyte composition and overall phagocytic capability, driven by the increased phagocytic propensity of each cell type. Yet, genes annotated to phagocytosis showed no large genomic signal of divergence. However, a gene set enrichment analysis on significantly divergent genes identified loci involved in glutamine metabolism, which recently have been linked to immune cell differentiation in mammals. Together these results suggest that heritable variation in phagocytic capacity arises via a quantitative trait architecture with variation in genes affecting the activation and/or differentiation of phagocytic cells, suggesting them as potential candidate genes underlying these phenotypic differences.

show abstract

Microevolutionary selection dynamics acting on immune genes of the green‐veined white butterfly, Pieris napi

Cited by 12 publications

References 105 publications

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

A Population Genomic Investigation of Immune Cell Diversity and Phagocytic Capacity in a Butterfly

Contact Info

Product

Resources

About