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PremiseHerbarium specimens have been used to detect climate‐induced shifts in flowering time by using the day of year of collection (DOY) as a proxy for first or peak flowering date. Variation among herbarium sheets in their phenological status, however, undermines the assumption thatDOYaccurately represents any particular phenophase. Ignoring this variation can reduce the explanatory power of pheno‐climatic models (PCMs) designed to predict the effects of climate on flowering date. MethodsHere we present a protocol for the phenological scoring of imaged herbarium specimens using an ImageJ plugin, and we introduce a quantitative metric of a specimen's phenological status, the phenological index (PI), which we use inPCMs to control for phenological variation among specimens ofStreptanthus tortuosus(Brassicaceeae) when testing for the effects of climate onDOY. We demonstrate that includingPIas an independent variable improves model fit. ResultsIncludingPIinPCMs increased the modelR2relative toPCMs that excludedPI; regression coefficients for climatic parameters, however, remained constant. DiscussionOur protocol provides a simple, quantitative phenological metric for any observed plant. IncludingPIinPCMs increasesR2and enables predictions of theDOYof any phenophase under any specified climatic conditions.
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Extreme copy number variation at a tRNA ligase gene affecting phenology and fitness in yellow monkeyflowers
Abstract Copy number variation (CNV) is a major part of the genetic diversity segregating within populations, but remains poorly understood relative to single nucleotide variation. Here, we report on atRNAligase gene (Migut.N02091;RLG1a) exhibiting unprecedented, and fitness‐relevant,CNVwithin an annual population of the yellow monkeyflowerMimulus guttatus.RLG1a variation was associated with multiple traits in pooled population sequencing (PoolSeq) scans of phenotypic and phenological cohorts. Resequencing of inbred lines revealed intermediate‐frequency three‐copy variants ofRLG1a (trip+;5/35 = 14%), andtrip+lines exhibited elevatedRLG1a expression under multiple conditions.trip+carriers, in addition to being over‐represented in late‐flowering and large‐flowered PoolSeq populations, flowered later under stressful conditions in a greenhouse experiment (p < 0.05). In wild population samples, we discovered an additional rareRLG1a variant (high+) that carries 250–300 copies ofRLG1a totalling ~5.7 Mb (20–40% of a chromosome). In the progeny of ahigh+carrier, Mendelian segregation of diagnostic alleles andqPCR‐based copy counts indicate thathigh+is a single tandem array unlinked to the single‐copyRLG1a locus. In the wild,high+carriers had highest fitness in two particularly dry and/or hot years (2015 and 2017; bothp < 0.01), while single‐copy individuals were twice as fecund as eitherCNVtype in a lush year (2016:p < 0.005). Our results demonstrate fluctuating selection onCNVs affecting phenological traits in a wild population, suggest that planttRNAligases mediate stress‐responsive life‐history traits, and introduce a novel system for investigating the molecular mechanisms of gene amplification.
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- Award ID(s):
- 1736249
- PAR ID:
- 10081145
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Molecular Ecology
- Volume:
- 28
- Issue:
- 6
- ISSN:
- 0962-1083
- Page Range / eLocation ID:
- p. 1460-1475
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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