@article{9100f8c668d64d969e8969daea970bab,
title = "Standing geographic variation in eclosion time and the genomics of host race formation in Rhagoletis pomonella fruit flies",
abstract = "Taxa harboring high levels of standing variation may be more likely to adapt to rapid environmental shifts and experience ecological speciation. Here, we characterize geographic and host-related differentiation for 10,241 single nucleotide polymorphisms in Rhagoletis pomonella fruit flies to infer whether standing genetic variation in adult eclosion time in the ancestral hawthorn (Crataegus spp.)-infesting host race, as opposed to new mutations, contributed substantially to its recent shift to earlier fruiting apple (Malus domestica). Allele frequency differences associated with early vs. late eclosion time within each host race were significantly related to geographic genetic variation and host race differentiation across four sites, arrayed from north to south along a 430-km transect, where the host races co-occur in sympatry in the Midwest United States. Host fruiting phenology is clinal, with both apple and hawthorn trees fruiting earlier in the North and later in the South. Thus, we expected alleles associated with earlier eclosion to be at higher frequencies in northern populations. This pattern was observed in the hawthorn race across all four populations; however, allele frequency patterns in the apple race were more complex. Despite the generally earlier eclosion timing of apple flies and corresponding apple fruiting phenology, alleles on chromosomes 2 and 3 associated with earlier emergence were paradoxically at lower frequency in the apple than hawthorn host race across all four sympatric sites. However, loci on chromosome 1 did show higher frequencies of early eclosion-associated alleles in the apple than hawthorn host race at the two southern sites, potentially accounting for their earlier eclosion phenotype. Thus, although extensive clinal genetic variation in the ancestral hawthorn race exists and contributed to the host shift to apple, further study is needed to resolve details of how this standing variation was selected to generate earlier eclosing apple fly populations in the North.",
keywords = "clinal variation, eclosion time, ecological speciation, host races, standing variation",
author = "Doellman, {Meredith M.} and Egan, {Scott P.} and Ragland, {Gregory J.} and Meyers, {Peter J.} and Hood, {Glen R.} and Powell, {Thomas H.Q.} and Peter Lazorchak and Hahn, {Daniel A.} and Berlocher, {Stewart H.} and Patrik Nosil and Feder, {Jeffrey L.}",
note = "Funding Information: We thank M.M. Glover, L.A. Miller, J.J. Smith, and C. Tait for their assistance and C. Smadja and two anonymous reviewers for useful comments for improving the manuscript. This work was supported by the Univ. Notre Dame Genomics and Bioinformatics Core Facility, the Univ. of Notre Dame Advanced Diagnostics & Therapeutics Initiative (SPE, JLF), the Univ. of Notre Dame Environmental Change Initiative (GJR, SPE, JLF), the Florida Agricultural Experiment Station (DAH), a Food and Agriculture Association/International Atomic Energy Agency Coordinated Research Project in Dormancy Management to Enable Mass‐rearing (DAH), a Rice Univ. Huxley FacultyFellowship(SPE),NationalScienceFoundationgrantstoGJR, SPE, DAH, and JLF (DEB‐1638951, DEB‐1638997, DEB‐1639005, and IOS‐1700773 and IOS‐1257298), and a US Dept. of Agriculture grant to JLF (NIFA 2015‐67013‐23289). PN was supported by a European Research Council Starter Grant (NatHisGen R/129639). PL was funded by National Science Foundation Research Experience for Undergraduates (IIS‐1560363). Funding Information: We thank M.M. Glover, L.A. Miller, J.J. Smith, and C. Tait for their assistance and C. Smadja and two anonymous reviewers for useful comments for improving the manuscript. This work was supported by the Univ. Notre Dame Genomics and Bioinformatics Core Facility, the Univ. of Notre Dame Advanced Diagnostics & Therapeutics Initiative (SPE, JLF), the Univ. of Notre Dame Environmental Change Initiative (GJR, SPE, JLF), the Florida Agricultural Experiment Station (DAH), a Food and Agriculture Association/International Atomic Energy Agency Coordinated Research Project in Dormancy Management to Enable Mass-rearing (DAH), a Rice Univ. Huxley Faculty Fellowship (SPE), National Science Foundation grants to GJR, SPE, DAH, and JLF (DEB-1638951, DEB-1638997, DEB-1639005, and IOS-1700773 and IOS-1257298), and a US Dept. of Agriculture grant to JLF (NIFA 2015-67013-23289). PN was supported by a European Research Council Starter Grant (NatHisGen R/129639). PL was funded by National Science Foundation Research Experience for Undergraduates (IIS-1560363). Publisher Copyright: {\textcopyright} 2018 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.",
year = "2019",
month = jan,
doi = "10.1002/ece3.4758",
language = "English (US)",
volume = "9",
pages = "393--409",
journal = "Ecology and Evolution",
issn = "2045-7758",
publisher = "John Wiley & Sons, Ltd.",
number = "1",
}