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Mehta D, Scandola S, Kennedy C, Lummer C, Gallo MCR, Grubb LE, Tan M, Scarpella E, Uhrig RG. Twilight length alters growth and flowering time in Arabidopsis via LHY/ CCA1. SCIENCE ADVANCES 2024; 10:eadl3199. [PMID: 38941453 PMCID: PMC11212724 DOI: 10.1126/sciadv.adl3199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/28/2024] [Indexed: 06/30/2024]
Abstract
Decades of research have uncovered how plants respond to two environmental variables that change across latitudes and over seasons: photoperiod and temperature. However, a third such variable, twilight length, has so far gone unstudied. Here, using controlled growth setups, we show that the duration of twilight affects growth and flowering time via the LHY/CCA1 clock genes in the model plant Arabidopsis. Using a series of progressively truncated no-twilight photoperiods, we also found that plants are more sensitive to twilight length compared to equivalent changes in solely photoperiods. Transcriptome and proteome analyses showed that twilight length affects reactive oxygen species metabolism, photosynthesis, and carbon metabolism. Genetic analyses suggested a twilight sensing pathway from the photoreceptors PHY E, PHY B, PHY D, and CRY2 through LHY/CCA1 to flowering modulation through the GI-FT pathway. Overall, our findings call for more nuanced models of day-length perception in plants and posit that twilight is an important determinant of plant growth and development.
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Affiliation(s)
- Devang Mehta
- Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
- Leuven Plant Institute, KU Leuven, B-3001 Leuven, Belgium
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Sabine Scandola
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Curtis Kennedy
- Department of Computing Science, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Christina Lummer
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | | | - Lauren E. Grubb
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Enrico Scarpella
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - R. Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2E9, Canada
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2
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Bison NN, Michaletz ST. Variation in leaf carbon economics, energy balance, and heat tolerance traits highlights differing timescales of adaptation and acclimation. THE NEW PHYTOLOGIST 2024. [PMID: 38532535 DOI: 10.1111/nph.19702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
Multivariate leaf trait correlations are hypothesized to originate from natural selection on carbon economics traits that control lifetime leaf carbon gain, and energy balance traits governing leaf temperatures, physiological rates, and heat injury. However, it is unclear whether macroevolution of leaf traits primarily reflects selection for lifetime carbon gain or energy balance, and whether photosynthetic heat tolerance is coordinated along these axes. To evaluate these hypotheses, we measured carbon economics, energy balance, and photosynthetic heat tolerance traits for 177 species (157 families) in a common garden that minimizes co-variation of taxa and climate. We observed wide variation in carbon economics, energy balance, and heat tolerance traits. Carbon economics and energy balance (but not heat tolerance) traits were phylogenetically structured, suggesting macroevolution of leaf mass per area and leaf dry matter content reflects selection on carbon gain rather than energy balance. Carbon economics and energy balance traits varied along a common axis orthogonal to heat tolerance traits. Our results highlight a fundamental mismatch in the timescales over which morphological and heat tolerance traits respond to environmental variation. Whereas carbon economics and energy balance traits are constrained by species' evolutionary histories, photosynthetic heat tolerance traits are not and can acclimate readily to leaf microclimates.
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Affiliation(s)
- Nicole N Bison
- Department of Botany, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Sean T Michaletz
- Department of Botany, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Biodiversity Research Centre, The University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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3
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Williamson M, Gerhard D, Hulme PE, Millar A, Chapman H. High-performing plastic clones best explain the spread of yellow monkeyflower from lowland to higher elevation areas in New Zealand. J Evol Biol 2023; 36:1455-1470. [PMID: 37731241 DOI: 10.1111/jeb.14218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 08/19/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
The relative contribution of adaptation and phenotypic plasticity can vary between core and edge populations, with implications for invasive success. We investigated the spread of the invasive yellow monkeyflower, Erythranthe gutatta in New Zealand, where it is spreading from lowland agricultural land into high-elevation conservation areas. We investigated the extent of phenotypic variation among clones from across the South Island, looked for adaptation and compared degrees of plasticity among lowland core versus montane range-edge populations. We grew 34 clones and measured their vegetative and floral traits in two common gardens, one in the core range at 9 m a.s.l. and one near the range-edge at 560 m a.s.l. Observed trait variation was explained by a combination of genotypic diversity (as identified through common gardens) and high phenotypic plasticity. We found a subtle signature of local adaptation to lowland habitats but all clones were plastic and able to survive and reproduce in both gardens. In the range-edge garden, above-ground biomass was on average almost double and stolon length almost half that of the same clone in the core garden. Clones from low-elevation sites showed higher plasticity on average than those from higher elevation sites. The highest performing clones in the core garden were also top performers in the range-edge garden. These results suggest some highly fit general-purpose genotypes, possibly pre-adapted to New Zealand montane conditions, best explains the spread of E. gutatta from lowland to higher elevation areas.
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Affiliation(s)
- Michelle Williamson
- Institute of Environmental Science and Research ESR Christchurch, Christchurch, New Zealand
| | - Daniel Gerhard
- School of Mathematics and Statistics, University of Canterbury, Christchurch, New Zealand
| | - Philip E Hulme
- Department of Pest Management and Conservation, Lincoln University, Lincoln, New Zealand
- Bioprotection Aotearoa, Lincoln University, Lincoln, New Zealand
| | - Aaron Millar
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Hazel Chapman
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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4
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McDonald LM, Scharnagl A, Turcu AK, Patterson CM, Kooyers NJ. Demographic consequences of an extreme heat wave are mitigated by spatial heterogeneity in an annual monkeyflower. Ecol Evol 2023; 13:e10397. [PMID: 37575594 PMCID: PMC10412438 DOI: 10.1002/ece3.10397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023] Open
Abstract
Heat waves are becoming more frequent and intense with climate change, but the demographic and evolutionary consequences of heat waves are rarely investigated in herbaceous plant species. We examine the consequences of a short but extreme heat wave in Oregon populations of the common yellow monkeyflower (Mimulus guttatus) by leveraging a common garden experiment planted with range-wide populations and observational studies of 11 local populations. In the common garden, 89% of seedlings died during the heat wave including >96% of seedlings from geographically local populations. Some populations from hotter and drier environments had higher fitness, however, others from comparable environments performed poorly. Observational studies of local natural populations drastically differed in the consequences of the heat wave-one population was completely extirpated and nearly half had a >50% decrease in fitness. However, a few populations had greater fitness during the heat wave year. Differences in mortality corresponded to the impact of the heat wave on soil moisture-retention of soil moisture throughout the heat wave led to greater survivorship. Our results suggest that not all populations experience the same intensity or degree of mortality during extreme events and such heterogeneity could be important for genetic rescue or to facilitate the distribution of adaptive variants throughout the region.
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Affiliation(s)
| | - Anna Scharnagl
- Department of BiologyUniversity of LouisianaLafayetteLouisianaUSA
- Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Andrea K. Turcu
- Department of BiologyUniversity of LouisianaLafayetteLouisianaUSA
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5
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van Katwijk MM, van Tussenbroek BI. Facultative Annual Life Cycles in Seagrasses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2002. [PMID: 37653920 PMCID: PMC10223934 DOI: 10.3390/plants12102002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Plant species usually have either annual or perennial life cycles, but facultative annual species have annual or perennial populations depending on their environment. In terrestrial angiosperms, facultative annual species are rare, with wild rice being one of the few examples. Our review shows that in marine angiosperms (seagrasses) facultative annual species are more common: six (of 63) seagrass species are facultative annual. It concerns Zostera marina, Z. japonica, Halophila decipiens, H. beccarii, Ruppia maritima, and R. spiralis. The annual populations generally produce five times more seeds than their conspecific perennial populations. Facultative annual seagrass species occur worldwide. Populations of seagrasses are commonly perennial, but the facultative annual species had annual populations when exposed to desiccation, anoxia-related factors, shading, or heat stress. A system-wide 'experiment' (closure of two out of three connected estuaries for large-scale coastal protection works) showed that the initial annual Z. marina population could shift to a perennial life cycle within 5 years, depending on environmental circumstances. We discuss potential mechanisms and implications for plant culture. Further exploration of flexible life histories in plant species, and seagrasses in particular, may aid in answering questions about trade-offs between vegetative and sexual reproduction, and preprogrammed senescence.
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Affiliation(s)
- Marieke M. van Katwijk
- Department of Environmental Science, Radboud Institute of Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525AJ Nijmegen, The Netherlands
| | - Brigitta I. van Tussenbroek
- Institute of Ocean Sciences and Limnology, Universidad Nacional Autónoma de México, Puerto Morelos 77580, Mexico;
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6
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Hjertaas AC, Preston JC, Kainulainen K, Humphreys AM, Fjellheim S. Convergent evolution of the annual life history syndrome from perennial ancestors. FRONTIERS IN PLANT SCIENCE 2023; 13:1048656. [PMID: 36684797 PMCID: PMC9846227 DOI: 10.3389/fpls.2022.1048656] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.
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Affiliation(s)
- Ane C. Hjertaas
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Jill C. Preston
- Department of Plant Biology, The University of Vermont, Burlington, VT, United States
| | - Kent Kainulainen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Aelys M. Humphreys
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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7
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Abstract
We organized this special issue to highlight new work and review recent advances at the cutting edge of 'wild quantitative genomics'. In this editorial, we will present some history of wild quantitative genetic and genomic studies, before discussing the main themes in the papers published in this special issue and highlighting the future outlook of this dynamic field.
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Affiliation(s)
- Susan E Johnston
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, Edinburgh EH9 3FL, UK
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, 14627, NY, USA
| | - Emily B Josephs
- Department of Plant Biology and Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, 48824, MI, USA
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8
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Rotter MC, Christie K, Holeski LM. Climate and the biotic community structure plant resistance across biogeographic groups of yellow monkeyflower. Ecol Evol 2022; 12:e9520. [DOI: 10.1002/ece3.9520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Michael C. Rotter
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Department of Biology Utah Valley University Orem Utah USA
| | - Kyle Christie
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
- Department of Plant Biology Michigan State University East Lansing Michigan USA
| | - Liza M. Holeski
- Department of Biological Sciences Northern Arizona University Flagstaff Arizona USA
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9
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Kolis KM, Berg CS, Nelson TC, Fishman L. Population genomic consequences of life-history and mating system adaptation to a geothermal soil mosaic in yellow monkeyflowers. Evolution 2022; 76:765-781. [PMID: 35266558 DOI: 10.1111/evo.14469] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 01/13/2022] [Accepted: 01/26/2022] [Indexed: 01/21/2023]
Abstract
Local selection can promote phenotypic divergence despite gene flow across habitat mosaics, but adaptation itself may generate substantial barriers to genetic exchange. In plants, life-history, phenology, and mating system divergence have been proposed to promote genetic differentiation in sympatry. In this study, we investigate phenotypic and genetic variation in Mimulus guttatus (yellow monkeyflowers) across a geothermal soil mosaic in Yellowstone National Park (YNP). Plants from thermal annual and nonthermal perennial habitats were heritably differentiated for life-history and mating system traits, consistent with local adaptation to the ephemeral thermal-soil growing season. However, genome-wide genetic variation primarily clustered plants by geographic region, with little variation sorting by habitat. The one exception was an extreme thermal population also isolated by a 200 m geographical gap of no intermediate habitat. Individual inbreeding coefficients (FIS ) were higher (and predicted by trait variation) in annual plants and annual pairs showed greater isolation by distance at local (<1 km) scales. Finally, YNP adaptation does not reuse a widespread inversion that underlies M. guttatus life-history ecotypes range-wide, suggesting a novel genetic mechanism. Overall, this work suggests that life-history and mating system adaptation strong enough to shape individual mating patterns does not necessarily generate incipient speciation without geographical barriers.
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Affiliation(s)
- Kory M Kolis
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: O'Connor Center for the Rocky Mountain West, University of Montana, Missoula, MT, 59812
| | - Colette S Berg
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
| | - Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812.,Current Address: Embark Veterinary, Inc., Boston, Massachusetts, 02210
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812
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10
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Lu M, Fradera-Soler M, Forest F, Barraclough TG, Grace OM. Evidence linking life-form to a major shift in diversification rate in Crassula. AMERICAN JOURNAL OF BOTANY 2022; 109:272-290. [PMID: 34730230 DOI: 10.1002/ajb2.1797] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/29/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Plants have evolved different ecological strategies in response to environmental challenges, and a higher lability of such strategies is more common in plant groups that adapt to various niches. Crassula (Crassulaceae), occurring in varied mesic to xeric habitats, exhibits a remarkable diversity of life-forms. However, whether any particular life-form trait has shaped species diversification in Crassula has remained unexplored. This study aims to investigate diversification patterns within Crassula and identify potential links to its life-form evolution. METHODS A phylogenetic tree of 140 Crassula taxa was reconstructed using plastid and nuclear loci and dated based on the nuclear DNA information only. We reconstructed ancestral life-form characters to estimate the evolutionary trends of ecophysiological change, and subsequently estimated net diversification rates. Multiple diversification models were applied to examine the association between certain life-forms and net diversification rates. RESULTS Our findings confirm a radiation within Crassula in the last 10 million years. A configuration of net diversification rate shifts was detected, which coincides with the emergence of a speciose lineage during the late Miocene. The results of ancestral state reconstruction demonstrate a high lability of life-forms in Crassula, and the trait-dependent diversification analyses revealed that the increased diversification is strongly associated with a compact growth form. CONCLUSIONS Transitions between life-forms in Crassula seem to have driven adaptation and shaped diversification of this genus across various habitats. The diversification patterns we inferred are similar to those observed in other major succulent lineages, with the most-speciose clades originating in the late Miocene.
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Affiliation(s)
- Meng Lu
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK
| | - Marc Fradera-Soler
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Timothy G Barraclough
- Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Olwen M Grace
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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11
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Liu Z, Roesti M, Marques D, Hiltbrunner M, Saladin V, Peichel CL. Chromosomal fusions facilitate adaptation to divergent environments in threespine stickleback. Mol Biol Evol 2021; 39:6462204. [PMID: 34908155 PMCID: PMC8826639 DOI: 10.1093/molbev/msab358] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chromosomal fusions are hypothesized to facilitate adaptation to divergent environments, both by bringing together previously unlinked adaptive alleles and by creating regions of low recombination that facilitate the linkage of adaptive alleles; but, there is little empirical evidence to support this hypothesis. Here, we address this knowledge gap by studying threespine stickleback (Gasterosteus aculeatus), in which ancestral marine fish have repeatedly adapted to freshwater across the northern hemisphere. By comparing the threespine and ninespine stickleback (Pungitius pungitius) genomes to a de novo assembly of the fourspine stickleback (Apeltes quadracus) and an outgroup species, we find two chromosomal fusion events involving the same chromosomes have occurred independently in the threespine and ninespine stickleback lineages. On the fused chromosomes in threespine stickleback, we find an enrichment of quantitative trait loci underlying traits that contribute to marine versus freshwater adaptation. By comparing whole-genome sequences of freshwater and marine threespine stickleback populations, we also find an enrichment of regions under divergent selection on these two fused chromosomes. There is elevated genetic diversity within regions under selection in the freshwater population, consistent with a simulation study showing that gene flow can increase diversity in genomic regions associated with local adaptation and our demographic models showing gene flow between the marine and freshwater populations. Integrating our results with previous studies, we propose that these fusions created regions of low recombination that enabled the formation of adaptative clusters, thereby facilitating freshwater adaptation in the face of recurrent gene flow between marine and freshwater threespine sticklebacks.
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Affiliation(s)
- Zuyao Liu
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Marius Roesti
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - David Marques
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Department of Fish Ecology and Evolution, Centre for Ecology, Evolution, and Biogeochemistry, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, Switzerland.,Natural History Museum Basel, Basel, Switzerland
| | - Melanie Hiltbrunner
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Verena Saladin
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Catherine L Peichel
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
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12
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Herron SA, Rubin MJ, Albrecht MA, Long QG, Sandoval MC, Miller AJ. The role of genus and life span in predicting seed and vegetative trait variation and correlation in Lathyrus, Phaseolus, and Vicia. AMERICAN JOURNAL OF BOTANY 2021; 108:2388-2404. [PMID: 34634144 PMCID: PMC9306869 DOI: 10.1002/ajb2.1773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Annual and perennial life history transitions are abundant among angiosperms, and understanding the phenotypic variation underlying life span shifts is a key endeavor of plant evolutionary biology. Comparative analyses of trait variation and correlation networks among annual and perennial plants is increasingly important as new herbaceous perennial crops are being developed for edible seed. However, it remains unclear how seed to vegetative growth trait relationships correlate with life span. METHODS To assess the relative roles of genus and life span in predicting phenotypic variation and trait correlations, we measured seed size and shape, germination proportion, and early-life-stage plant height and leaf growth over 3 mo in 29 annual and perennial, herbaceous congeneric species from three legume genera (Lathyrus, Phaseolus, and Vicia). RESULTS Genus was the strongest predictor of seed size and shape variation, and life span consistently predicted plant height and leaf number at single time points. Correlation networks revealed that annual species had significant associations between seed traits and vegetative traits, whereas perennials had no significant seed-vegetative associations. Each genus also differed in the extent of integration between seed and vegetative traits, as well as within-vegetative-trait correlation patterns. CONCLUSIONS Genus and life span were important for predicting aspects of early-life-stage phenotypic variation and trait relationships. Differences in phenotypic correlation may indicate that selection on seed size traits will impact vegetative growth differently depending on life span, which has important implications for nascent perennial breeding programs.
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Affiliation(s)
- Sterling A. Herron
- Saint Louis University, Department of Biology3507 Laclede AvenueSt. LouisMissouri63103USA
| | - Matthew J. Rubin
- Donald Danforth Plant Science Center975 North Warson RoadSt. LouisMissouri63132USA
| | - Matthew A. Albrecht
- Missouri Botanical Garden, Center for Conservation and Sustainable Development4344 Shaw BoulevardSt. LouisMissouri63110USA
| | - Quinn G. Long
- Shaw Nature Reserve307 Pinetum Loop RoadGray SummitMissouri63039USA
| | - Marissa C. Sandoval
- University of California, Berkeley, Rausser College of Natural Resources319 Wellman Hall, BerkeleyCalifornia94704USA
| | - Allison J. Miller
- Saint Louis University, Department of Biology3507 Laclede AvenueSt. LouisMissouri63103USA
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13
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McCulloch GA, Guhlin J, Dutoit L, Harrop TWR, Dearden PK, Waters JM. Genomic signatures of parallel alpine adaptation in recently evolved flightless insects. Mol Ecol 2021; 30:6677-6686. [PMID: 34592029 DOI: 10.1111/mec.16204] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 09/16/2021] [Accepted: 09/27/2021] [Indexed: 12/01/2022]
Abstract
Natural selection along elevational gradients has potential to drive predictable adaptations across distinct lineages, but the extent of such repeated evolution remains poorly studied for many widespread alpine taxa. We present parallel genomic analyses of two recently evolved flightless alpine insect lineages to test for molecular signatures of repeated alpine adaptation. Specifically, we compare low-elevation vs. alpine stonefly ecotypes from parallel stream populations in which flightless upland ecotypes have been independently derived. We map 67,922 polymorphic genetic markers, generated across 176 Zelandoperla fenestrata specimens from two independent alpine stream populations in New Zealand's Rock and Pillar Range, to a newly developed plecopteran reference genome. Genome-wide scans revealed 31 regions with outlier single nucleotide polymorphisms (SNPs) differentiating lowland vs. alpine ecotypes in Lug Creek, and 37 regions with outliers differentiating ecotypes in Six Mile Creek. Of these regions, 13% (8/60) yielded outlier SNPs across both within-stream ecotype comparisons, implying comparable genomic shifts contribute to this repeated alpine adaptation. Candidate genes closely linked to repeated outlier regions include several with documented roles in insect wing-development (e.g., dishevelled), suggesting that they may contribute to repeated alpine wing reduction. Additional candidate genes have been shown to influence insect fecundity (e.g., ovo) and lifespan (e.g., Mrp4), implying that they might contribute to life history differentiation between upland and lowland ecotypes. Additional outlier genes have potential roles in the evolution of reproductive isolation among ecotypes (hedgehog and Desaturase 1). These results demonstrate how replicated outlier tests across independent lineages can potentially contribute to the discovery of genes underpinning repeated adaptation.
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Affiliation(s)
| | - Joseph Guhlin
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ludovic Dutoit
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Thomas W R Harrop
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Peter K Dearden
- Genomics Aotearoa and Department of Biochemistry, University of Otago, Dunedin, New Zealand
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14
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Vest K, Sobel JM. Variation in seasonal timing traits and life history along a latitudinal transect in Mimulus ringens. J Evol Biol 2021; 34:1803-1816. [PMID: 34582606 DOI: 10.1111/jeb.13941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
Seasonal timing traits are commonly under recurrent, spatially variable selection, and are therefore predicted to exhibit clinal variation. Temperate perennial plants often require vernalization to prompt growth and reproduction; however, little is known about whether vernalization requirements change across the range of a broadly distributed species. We performed a critical vernalization duration study in Mimulus ringens, coupled with population genomic analysis. Plants from eight populations spanning the latitudinal range were exposed to varying durations of 4°C vernalization between 0 and 56 days, and flowering response was assessed. RADSeq was also performed to generate 1179 polymorphic SNPs, which were used to examine population structure. We found unexpected life history variation, with some populations lacking vernalization requirement. Population genomic analyses show that these life history variants are highly divergent from perennials, potentially revealing a cryptic species. For perennial populations, minimum vernalization time was surprisingly consistent. However, once vernalized, northern populations flowered almost 3 weeks faster than southern. Furthermore, southern populations exhibited sensitivity to vernalization times beyond flowering competency, suggesting an ability to respond adaptively to different lengths of winter. Mimulus ringens, therefore, reveals evidence of clinal variation, and provides opportunities for future studies addressing mechanistic and ecological hypotheses both within and between incipient species.
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Affiliation(s)
- Kelly Vest
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, New York, USA
| | - James M Sobel
- Department of Biological Sciences, Binghamton University (SUNY), Binghamton, New York, USA
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15
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Wright SJ, Goad DM, Gross BL, Muñoz PR, Olsen KM. Genetic trade-offs underlie divergent life history strategies for local adaptation in white clover. Mol Ecol 2021; 31:3742-3760. [PMID: 34532899 DOI: 10.1111/mec.16180] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/25/2021] [Accepted: 09/02/2021] [Indexed: 01/26/2023]
Abstract
Local adaptation is common in plants, yet characterization of its underlying genetic basis is rare in herbaceous perennials. Moreover, while many plant species exhibit intraspecific chemical defence polymorphisms, their importance for local adaptation remains poorly understood. We examined the genetic architecture of local adaptation in a perennial, obligately-outcrossing herbaceous legume, white clover (Trifolium repens). This widespread species displays a well-studied chemical defence polymorphism for cyanogenesis (HCN release following tissue damage) and has evolved climate-associated cyanogenesis clines throughout its range. Two biparental F2 mapping populations, derived from three parents collected in environments spanning the U.S. latitudinal species range (Duluth, MN, St. Louis, MO and Gainesville, FL), were grown in triplicate for two years in reciprocal common garden experiments in the parental environments (6,012 total plants). Vegetative growth and reproductive fitness traits displayed trade-offs across reciprocal environments, indicating local adaptation. Genetic mapping of fitness traits revealed a genetic architecture characterized by allelic trade-offs between environments, with 100% and 80% of fitness QTL in the two mapping populations showing significant QTL×E interactions, consistent with antagonistic pleiotropy. Across the genome there were three hotspots of QTL colocalization. Unexpectedly, we found little evidence that the cyanogenesis polymorphism contributes to local adaptation. Instead, divergent life history strategies in reciprocal environments were major fitness determinants: selection favoured early investment in flowering at the cost of multiyear survival in the southernmost site versus delayed flowering and multiyear persistence in the northern environments. Our findings demonstrate that multilocus genetic trade-offs contribute to contrasting life history characteristics that allow for local adaptation in this outcrossing herbaceous perennial.
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Affiliation(s)
- Sara J Wright
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - David M Goad
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - Briana L Gross
- Biology Department, University of Minnesota-Duluth, Duluth, Minnesota, USA
| | - Patricio R Muñoz
- Horticultural Science Department, University of Florida, Gainesville, Florida, USA
| | - Kenneth M Olsen
- Department of Biology, Washington University, St. Louis, Missouri, USA
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16
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López-Goldar X, Agrawal AA. Ecological Interactions, Environmental Gradients, and Gene Flow in Local Adaptation. TRENDS IN PLANT SCIENCE 2021; 26:796-809. [PMID: 33865704 DOI: 10.1016/j.tplants.2021.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 06/12/2023]
Abstract
Despite long-standing interest in local adaptation of plants to their biotic and abiotic environment, existing theory, and many case studies, little work to date has addressed within-species evolution of concerted strategies and how these might contrast with patterns across species. Here we consider the interactions between pollinators, herbivores, and resource availability in shaping plant local adaptation, how these interactions impact plant phenotypes and gene flow, and the conditions where multiple traits align along major environmental gradients such as latitude and elevation. Continued work in emerging model systems will benefit from the melding of classic experimental approaches with novel population genetic analyses to reveal patterns and processes in plant local adaptation.
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Affiliation(s)
- Xosé López-Goldar
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA.
| | - Anurag A Agrawal
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
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17
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Nelson TC, Muir CD, Stathos AM, Vanderpool DD, Anderson K, Angert AL, Fishman L. Quantitative trait locus mapping reveals an independent genetic basis for joint divergence in leaf function, life-history, and floral traits between scarlet monkeyflower (Mimulus cardinalis) populations. AMERICAN JOURNAL OF BOTANY 2021; 108:844-856. [PMID: 34036561 DOI: 10.1002/ajb2.1660] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023]
Abstract
PREMISE Across taxa, vegetative and floral traits that vary along a fast-slow life-history axis are often correlated with leaf functional traits arrayed along the leaf economics spectrum, suggesting a constrained set of adaptive trait combinations. Such broad-scale convergence may arise from genetic constraints imposed by pleiotropy (or tight linkage) within species, or from natural selection alone. Understanding the genetic basis of trait syndromes and their components is key to distinguishing these alternatives and predicting evolution in novel environments. METHODS We used a line-cross approach and quantitative trait locus (QTL) mapping to characterize the genetic basis of twenty leaf functional/physiological, life history, and floral traits in hybrids between annualized and perennial populations of scarlet monkeyflower (Mimulus cardinalis). RESULTS We mapped both single and multi-trait QTLs for life history, leaf function and reproductive traits, but found no evidence of genetic co-ordination across categories. A major QTL for three leaf functional traits (thickness, photosynthetic rate, and stomatal resistance) suggests that a simple shift in leaf anatomy may be key to adaptation to seasonally dry habitats. CONCLUSIONS Our results suggest that the co-ordination of resource-acquisitive leaf physiological traits with a fast life-history and more selfing mating system results from environmental selection rather than functional or genetic constraint. Independent assortment of distinct trait modules, as well as a simple genetic basis to leaf physiological traits associated with drought escape, may facilitate adaptation to changing climates.
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Affiliation(s)
- Thomas C Nelson
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
| | - Christopher D Muir
- Departments of Botany and Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
- School of Life Sciences, University of Hawai'i, Honolulu, Hawai'i, 96822, USA
| | - Angela M Stathos
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
| | - Daniel D Vanderpool
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
| | - Kayli Anderson
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
| | - Amy L Angert
- Departments of Botany and Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana, 59812, USA
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18
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Coughlan JM, Brown MW, Willis JH. The genetic architecture and evolution of life-history divergence among perennials in the Mimulus guttatus species complex. Proc Biol Sci 2021; 288:20210077. [PMID: 33823671 PMCID: PMC8059554 DOI: 10.1098/rspb.2021.0077] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Ecological divergence is a fundamental source of phenotypic diversity between closely related species, yet the genetic architecture of most ecologically relevant traits is poorly understood. Differences in elevation can impose substantial divergent selection on both complex, correlated suites of traits (such as life-history), as well as novel adaptations. We use the Mimulus guttatus species complex to assess if the divergence in elevation is accompanied by trait divergence in a group of closely related perennials and determine the genetic architecture of this divergence. We find that divergence in elevation is associated with differences in life-history, as well as a unique trait, the production of rhizomes. The divergence between two perennials is largely explained by few mid-to-large effect quantitative trait loci (QTLs). However, the presence of QTLs with correlated, but opposing effects on multiple traits leads to some hybrids with transgressive trait combinations. Lastly, we find that the genetic architecture of the ability to produce rhizomes changes through development, wherein most hybrids produce rhizomes, but only later in development. Our results suggest that elevational differences may shape life-history divergence between perennials, but aspects of the genetic architecture of divergence may have implications for hybrid fitness in nature.
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Affiliation(s)
- Jenn M. Coughlan
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
- Biology Department, University of North Carolina, 250 Bell Tower Dr., Chapel Hill, NC 27599, USA
| | - Maya Wilson Brown
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI 48824, USA
| | - John H. Willis
- Biology Department, Duke University, 125 Science Dr., Durham, NC 27708, USA
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Population genomic and historical analysis suggests a global invasion by bridgehead processes in Mimulus guttatus. Commun Biol 2021; 4:327. [PMID: 33712659 PMCID: PMC7954805 DOI: 10.1038/s42003-021-01795-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/05/2021] [Indexed: 01/24/2023] Open
Abstract
Imperfect historical records and complex demographic histories present challenges for reconstructing the history of biological invasions. Here, we combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. By sampling 521 plants from 158 native and introduced populations genotyped at >44,000 loci, we determined that invasive M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range. We hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide. Our results emphasise the highly admixed nature of introduced M. guttatus and demonstrate the potential of introduced populations to serve as sources of secondary admixture, producing novel hybrids. Unravelling the history of biological invasions provides a starting point to understand how invasive populations adapt to novel environments. Vallejo-Marín et al. combine historical records, extensive worldwide and genome-wide sampling, and demographic analyses to investigate the global invasion of Mimulus guttatus from North America to Europe and the Southwest Pacific. They found that M. guttatus was first likely introduced to the British Isles from the Aleutian Islands (Alaska), followed by admixture from multiple parts of the native range, and hypothesise that populations in the British Isles then served as a bridgehead for vanguard invasions worldwide.
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20
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Kooyers NJ, Morioka KA, Colicchio JM, Clark KS, Donofrio A, Estill SK, Pascualy CR, Anderson IC, Hagler M, Cho C, Blackman BK. Population responses to a historic drought across the range of the common monkeyflower (Mimulus guttatus). AMERICAN JOURNAL OF BOTANY 2021; 108:284-296. [PMID: 33400274 DOI: 10.1002/ajb2.1589] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/26/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Due to climate change, more frequent and intense periodic droughts are predicted to increasingly pose major challenges to the persistence of plant populations. When a severe drought occurs over a broad geographical region, independent responses by individual populations provide replicated natural experiments for examining the evolution of drought resistance and the potential for evolutionary rescue. METHODS We used a resurrection approach to examine trait evolution in populations of the common monkeyflower, Mimulus guttatus, exposed to a record drought in California from 2011 to 2017. Specifically, we compared variation in traits related to drought escape and avoidance from seeds collected from 37 populations pre- and post-drought in a common garden. In a parallel experiment, we evaluated fitness in two populations, one which thrived and one which was nearly extirpated during the drought, under well-watered and dry-down conditions. RESULTS We observed substantial variation among populations in trait evolution. In the subset of populations where phenotypes changed significantly, divergence proceeded along trait correlations with some populations flowering rapidly with less vegetative tissue accumulation and others delaying flowering with greater vegetative tissue accumulation. The degree of trait evolution was only weakly correlated with drought intensity but strongly correlated with initial levels of standing variation. Fitness was higher in the post-drought than pre-drought accessions in both treatments for the thriving population, but lower in both treatments for the nearly extirpated population. CONCLUSIONS Together, our results indicate that evolutionary responses to drought are context dependent and reflect the standing genetic variation and genetic correlations present within populations.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA, 70503, USA
| | - Kelsie A Morioka
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jack M Colicchio
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Kaitlyn S Clark
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Abigail Donofrio
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Shayne K Estill
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Catalina R Pascualy
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ian C Anderson
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Megan Hagler
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Chloe Cho
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
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21
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Friedman J. The Evolution of Annual and Perennial Plant Life Histories: Ecological Correlates and Genetic Mechanisms. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-024638] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Flowering plants exhibit two principal life-history strategies: annuality (living and reproducing in one year) and perenniality (living more than one year). The advantages of either strategy depend on the relative benefits of immediate reproduction balanced against survivorship and future reproduction. This trade-off means that life-history strategies are associated with particular environments, with annuals being found more often in unpredictable habitats. Annuality and perenniality are the outcome of developmental genetic programs responding to their environment, with perennials being distinguished by their delayed competence to flower and reversion to growth after flowering. Evolutionary transitions between these strategies are frequent and have consequences for mating systems and genome evolution, with perennials being more likely to outcross with higher inbreeding depression and lower rates of molecular evolution. Integrating expectations from life-history theory with knowledge of the developmental genetics of flowering and seasonality is required to understand the mechanisms involved in the evolution of annual and perennial life histories.
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Affiliation(s)
- Jannice Friedman
- Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada
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22
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Lindberg CL, Hanslin HM, Schubert M, Marcussen T, Trevaskis B, Preston JC, Fjellheim S. Increased above-ground resource allocation is a likely precursor for independent evolutionary origins of annuality in the Pooideae grass subfamily. THE NEW PHYTOLOGIST 2020; 228:318-329. [PMID: 32421861 DOI: 10.1111/nph.16666] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/07/2020] [Indexed: 06/11/2023]
Abstract
Semelparous annual plants flower a single time during their 1-yr life cycle, investing much of their energy into rapid reproduction. By contrast, iteroparous perennial plants flower multiple times over several years, and partition their resources between reproduction and persistence. To which extent evolutionary transitions between life-cycle strategies are internally constrained at the developmental, genetic and phylogenetic level is unknown. Here we study the evolution of life-cycle strategies in the grass subfamily Pooideae and test if transitions between them are facilitated by evolutionary precursors. We integrate ecological, life-cycle strategy and growth data in a phylogenetic framework. We investigate if growth traits are candidates for a precursor. Species in certain Pooideae clades are predisposed to evolve annuality from perenniality, potentially due to the shared inheritance of specific evolutionary precursors. Seasonal dry climates, which have been linked to annuality, were only able to select for transitions to annuality when the precursor was present. Allocation of more resources to above-ground rather than below-ground growth is a candidate for the precursor. Our findings support the hypothesis that only certain lineages can respond quickly to changing external conditions by switching their life-cycle strategy, likely due to the presence of evolutionary precursors.
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Affiliation(s)
- Camilla Lorange Lindberg
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Hans Martin Hanslin
- Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, 1431, Norway
| | - Marian Schubert
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Thomas Marcussen
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1432, Norway
| | - Ben Trevaskis
- Commonwealth Scientific and Industrial Research Organization, Canberra, ACT, 2601, Australia
| | | | - Siri Fjellheim
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1432, Norway
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Archambeault SL, Bärtschi LR, Merminod AD, Peichel CL. Adaptation via pleiotropy and linkage: Association mapping reveals a complex genetic architecture within the stickleback Eda locus. Evol Lett 2020; 4:282-301. [PMID: 32774879 PMCID: PMC7403726 DOI: 10.1002/evl3.175] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 04/04/2020] [Accepted: 04/29/2020] [Indexed: 11/26/2022] Open
Abstract
Genomic mapping of the loci associated with phenotypic evolution has revealed genomic "hotspots," or regions of the genome that control multiple phenotypic traits. This clustering of loci has important implications for the speed and maintenance of adaptation and could be due to pleiotropic effects of a single mutation or tight genetic linkage of multiple causative mutations affecting different traits. The threespine stickleback (Gasterosteus aculeatus) is a powerful model for the study of adaptive evolution because the marine ecotype has repeatedly adapted to freshwater environments across the northern hemisphere in the last 12,000 years. Freshwater ecotypes have repeatedly fixed a 16 kilobase haplotype on chromosome IV that contains Ectodysplasin (Eda), a gene known to affect multiple traits, including defensive armor plates, lateral line sensory hair cells, and schooling behavior. Many additional traits have previously been mapped to a larger region of chromosome IV that encompasses the Eda freshwater haplotype. To identify which of these traits specifically map to this adaptive haplotype, we made crosses of rare marine fish heterozygous for the freshwater haplotype in an otherwise marine genetic background. Further, we performed fine-scale association mapping in a fully interbreeding, polymorphic population of freshwater stickleback to disentangle the effects of pleiotropy and linkage on the phenotypes affected by this haplotype. Although we find evidence that linked mutations have small effects on a few phenotypes, a small 1.4-kb region within the first intron of Eda has large effects on three phenotypic traits: lateral plate count, and both the number and patterning of the posterior lateral line neuromasts. Thus, the Eda haplotype is a hotspot of adaptation in stickleback due to both a small, pleiotropic region affecting multiple traits as well as multiple linked mutations affecting additional traits.
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Affiliation(s)
- Sophie L. Archambeault
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
- Graduate Program in Molecular and Cellular BiologyUniversity of WashingtonSeattleWashington98195
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWashington98109
| | - Luis R. Bärtschi
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
| | | | - Catherine L. Peichel
- Institute of Ecology and EvolutionUniversity of BernBern3012Switzerland
- Graduate Program in Molecular and Cellular BiologyUniversity of WashingtonSeattleWashington98195
- Divisions of Basic Sciences and Human BiologyFred Hutchinson Cancer Research CenterSeattleWashington98109
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24
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Multi-level patterns of genetic structure and isolation by distance in the widespread plant Mimulus guttatus. Heredity (Edinb) 2020; 125:227-239. [PMID: 32641721 DOI: 10.1038/s41437-020-0335-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 06/02/2020] [Accepted: 06/15/2020] [Indexed: 12/30/2022] Open
Abstract
An understanding of genetic structure is essential for answering many questions in population genetics. However, complex population dynamics and scale-dependent processes can make it difficult to detect if there are distinct genetic clusters present in natural populations. Inferring discrete population structure is particularly challenging in the presence of continuous genetic variation such as isolation by distance. Here, we use the plant species Mimulus guttatus as a case study for understanding genetic structure at three spatial scales. We use reduced-representation sequencing and marker-based genotyping to understand dispersal dynamics and to characterise genetic structure. Our results provide insight into the spatial scale of genetic structure in a widespread plant species, and demonstrate how dispersal affects spatial genetic variation at the local, regional, and range-wide scale. At a fine-spatial scale, we show dispersal is rampant with little evidence of spatial genetic structure within populations. At a regional-scale, we show continuous differentiation driven by isolation by distance over hundreds of kilometres, with broad geographic genetic clusters that span major barriers to dispersal. Across Western North America, we observe geographic genetic structure and the genetic signature of multiple postglacial recolonisation events, with historical gene flow linking isolated populations. Our genetic analyses show M. guttatus is highly dispersive and maintains large metapopulations with high intrapopulation variation. This high diversity and dispersal confounds the inference of genetic structure, with multi-level sampling and spatially-explicit analyses required to understand population history.
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25
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Kooyers NJ, Donofrio A, Blackman BK, Holeski LM. The Genetic Architecture of Plant Defense Trade-offs in a Common Monkeyflower. J Hered 2020; 111:333-345. [DOI: 10.1093/jhered/esaa015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Abstract
Determining how adaptive combinations of traits arose requires understanding the prevalence and scope of genetic constraints. Frequently observed phenotypic correlations between plant growth, defenses, and/or reproductive timing have led researchers to suggest that pleiotropy or strong genetic linkage between variants affecting independent traits is pervasive. Alternatively, these correlations could arise via independent mutations in different genes for each trait and extensive correlational selection. Here we evaluate these alternatives by conducting a quantitative trait loci (QTL) mapping experiment involving a cross between 2 populations of common monkeyflower (Mimulus guttatus) that differ in growth rate as well as total concentration and arsenal composition of plant defense compounds, phenylpropanoid glycosides (PPGs). We find no evidence that pleiotropy underlies correlations between defense and growth rate. However, there is a strong genetic correlation between levels of total PPGs and flowering time that is largely attributable to a single shared QTL. While this result suggests a role for pleiotropy/close linkage, several other QTLs also contribute to variation in total PPGs. Additionally, divergent PPG arsenals are influenced by a number of smaller-effect QTLs that each underlie variation in 1 or 2 PPGs. This result indicates that chemical defense arsenals can be finely adapted to biotic environments despite sharing a common biochemical precursor. Together, our results show correlations between defense and life-history traits are influenced by pleiotropy or genetic linkage, but genetic constraints may have limited impact on future evolutionary responses, as a substantial proportion of variation in each trait is controlled by independent loci.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Louisiana, Lafayette, LA
- Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Abigail Donofrio
- Department of Integrative Biology, University of South Florida, Tampa, FL
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA
| | - Liza M Holeski
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ
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26
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Brown MR, Frachon N, Wong ELY, Metherell C, Twyford AD. Life history evolution, species differences, and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia). AMERICAN JOURNAL OF BOTANY 2020; 107:456-465. [PMID: 32133624 DOI: 10.1002/ajb2.1445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 12/04/2019] [Indexed: 05/14/2023]
Abstract
PREMISE Species delimitation in parasitic organisms is challenging because traits used to identify species are often plastic and vary depending on the host. Here, we use species from a recent radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We tested whether Euphrasia species show reliable trait differences, investigated whether these differences correspond to life history trade-offs between growth and reproduction, and quantified plasticity in response to host species. METHODS Common garden experiments were used to evaluate trait differences between 11 Euphrasia taxa grown on a common host, document phenotypic plasticity when a single Euphrasia species is grown on eight different hosts, and relate observations to trait differences recorded in the wild. RESULTS Euphrasia exhibited variation in life history strategies; some individuals transitioned rapidly to flowering at the expense of early season growth, while others invested in vegetative growth and delayed flowering. Life history differences were present between some species, though many related taxa lacked clear trait differences. Species differences were further blurred by phenotypic plasticity-many traits were plastic and changed with host type or between environments. CONCLUSIONS Phenotypic plasticity in response to host and environment confounds species delimitation in Euphrasia. When grown in a common garden environment, some morphologically distinct taxa can be identified, though others represent morphologically similar shallow segregates. Trait differences present between some species and populations demonstrate the rapid evolution of distinct life history strategies in response to local ecological conditions.
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Affiliation(s)
- Max R Brown
- University of Edinburgh, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
| | - Natacha Frachon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Edgar L Y Wong
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, 4 High Firs Crescent, Harpenden, Hertfordshire, AL5 1NA, UK
| | - Alex D Twyford
- University of Edinburgh, Institute of Evolutionary Biology, Charlotte Auerbach Road, Edinburgh, EH9 3FL, UK
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
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27
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Popovic D, Lowry DB. Contrasting environmental factors drive local adaptation at opposite ends of an environmental gradient in the yellow monkeyflower (Mimulus guttatus). AMERICAN JOURNAL OF BOTANY 2020; 107:298-307. [PMID: 31989586 DOI: 10.1002/ajb2.1419] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/13/2019] [Indexed: 05/22/2023]
Abstract
PREMISE Identifying the environmental factors responsible for natural selection across different habitats is crucial for understanding the process of local adaptation in plants. Despite its importance, few studies have successfully isolated the environmental factors driving local adaptation in nature. In this study, we evaluated the agents of selection responsible for local adaptation of the monkeyflower Mimulus guttatus to California's coastal and inland habitats. METHODS We implemented a manipulative reciprocal transplant experiment at coastal and inland sites, where we excluded aboveground stressors in an effort to elucidate their role in the evolution of local adaptation. RESULTS Excluding aboveground stressors, most likely a combination of salt spray and herbivory, completely rescued inland annual plant fitness when transplanted to coastal habitat. The exclosures in inland habitat provided a benefit to the performance of coastal perennial plants. However, the exclosures are unlikely to provide much fitness benefit to the coastal plants at the inland site because of their general inability to flower in time to escape from the summer drought. CONCLUSIONS Our study demonstrates that a distinct set of selective agents (aboveground vs. belowground) are responsible for local adaptation at opposite ends of an environmental gradient.
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Affiliation(s)
- Damian Popovic
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
- Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
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28
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Coughlan JM, Wilson Brown M, Willis JH. Patterns of Hybrid Seed Inviability in the Mimulus guttatus sp. Complex Reveal a Potential Role of Parental Conflict in Reproductive Isolation. Curr Biol 2020; 30:83-93.e5. [PMID: 31883810 PMCID: PMC7017923 DOI: 10.1016/j.cub.2019.11.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 11/06/2019] [Indexed: 11/19/2022]
Abstract
Genomic conflicts may play a central role in the evolution of reproductive barriers. Theory predicts that early-onset hybrid inviability may stem from conflict between parents for resource allocation to offspring. Here, we describe M. decorus: a group of cryptic species within the M. guttatus species complex that are largely reproductively isolated by hybrid seed inviability (HSI). HSI between M. guttatus and M. decorus is common and strong, but populations of M. decorus vary in the magnitude and directionality of HSI with M. guttatus. Patterns of HSI between M. guttatus and M. decorus, as well as within M. decorus, conform to the predictions of parental conflict: first, reciprocal F1s exhibit size differences and parent-of-origin-specific endosperm defects; second, the extent of asymmetry between reciprocal F1 seed size is correlated with asymmetry in HSI; and third, inferred differences in the extent of conflict predict the extent of HSI between populations. We also find that HSI is rapidly evolving, as populations that exhibit the most HSI are each others' closest relative. Lastly, although all populations appear largely outcrossing, we find that the differences in the inferred strength of conflict scale positively with π, suggesting that demographic or life history factors other than transitions to self-fertilization may influence the rate of parental-conflict-driven evolution. Overall, these patterns suggest the rapid evolution of parent-of-origin-specific resource allocation alleles coincident with HSI within and between M. guttatus and M. decorus. Parental conflict may therefore be an important evolutionary driver of reproductive isolation.
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Affiliation(s)
- Jenn M Coughlan
- Biological Sciences, Duke University, 25 Science Drive, Durham, NC 27708, USA; Biology Department, University of North Carolina, Chapel Hill, 120 South Road, Chapel Hill, NC 27599, USA.
| | - Maya Wilson Brown
- Biological Sciences, Duke University, 25 Science Drive, Durham, NC 27708, USA
| | - John H Willis
- Biological Sciences, Duke University, 25 Science Drive, Durham, NC 27708, USA
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29
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Peterson ML, Angert AL, Kay KM. Experimental migration upward in elevation is associated with strong selection on life history traits. Ecol Evol 2020; 10:612-625. [PMID: 32015830 PMCID: PMC6988539 DOI: 10.1002/ece3.5710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 08/10/2019] [Accepted: 09/05/2019] [Indexed: 12/26/2022] Open
Abstract
One of the strongest biological impacts of climate change has been the movement of species poleward and upward in elevation. Yet, what is not clear is the extent to which the spatial distribution of locally adapted lineages and ecologically important traits may also shift with continued climate change. Here, we take advantage of a transplant experiment mimicking up-slope seed dispersal for a suite of ecologically diverse populations of yellow monkeyflower (Mimulus guttatus sensu lato) into a high-elevation common garden during an extreme drought period in the Sierra Nevada mountains, California, USA. We use a demographic approach to quantify fitness and test for selection on life history traits in local versus lower-elevation populations and in normal versus drought years to test the potential for up-slope migration and phenotypic selection to alter the distribution of key life history traits in montane environments. We find that lower-elevation populations tend to outperform local populations, confirming the potential for up-slope migration. Although selection generally favored some local montane traits, including larger flowers and larger stem size at flowering, drought conditions tended to select for earlier flowering typical of lower-elevation genotypes. Taken together, this suggests that monkeyflower lineages moving upward in elevation could experience selection for novel trait combinations, particularly under warmer and drier conditions that are predicted to occur with continued climate change.
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Affiliation(s)
- Megan L. Peterson
- Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
| | - Amy L. Angert
- Department of Botany and ZoologyUniversity of British ColumbiaVancouverBCCanada
| | - Kathleen M. Kay
- Ecology and Evolutionary BiologyUniversity of California Santa CruzSanta CruzCalifornia
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30
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Kooyers NJ, Colicchio JM, Greenlee AB, Patterson E, Handloser NT, Blackman BK. Lagging Adaptation to Climate Supersedes Local Adaptation to Herbivory in an Annual Monkeyflower. Am Nat 2019; 194:541-557. [DOI: 10.1086/702312] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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31
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Mantel SJ, Sweigart AL. Divergence in drought-response traits between sympatric species of Mimulus. Ecol Evol 2019; 9:10291-10304. [PMID: 31632643 PMCID: PMC6787937 DOI: 10.1002/ece3.5549] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 07/19/2019] [Accepted: 07/24/2019] [Indexed: 12/26/2022] Open
Abstract
Differential adaptation to local environmental conditions is thought to be an important driver of speciation. Plants, whose sedentary lifestyle necessitates fine-tuned adaptation to edaphic conditions such as water availability, are often distributed based on these conditions. Populations occupying water-limited habitats may employ a variety of strategies, involving numerous phenotypes, to prevent and withstand desiccation. In sympatry, two closely related Mimulus species-M. guttatus and M. nasutus-occupy distinct microhabitats that differ in seasonal water availability. In a common garden experiment, we characterized natural variation within and between sympatric M. guttatus and M. nasutus in the ability to successfully set seed under well-watered and drought conditions. We also measured key phenotypes for drought adaptation, including developmental timing, plant size, flower size, and stomatal density. Consistent with their microhabitat associations in nature, M. nasutus set seed much more successfully than M. guttatus under water-limited conditions. This divergence in reproductive output under drought was due to differences in mortality after the onset of flowering, with M. nasutus surviving at a much higher rate than M. guttatus. Higher seed set in M. nasutus was mediated, at least in part, by a plastic increase in the rate of late-stage development (i.e., fruit maturation), consistent with the ability of this species to inhabit more ephemeral habitats in the field. Our results suggest adaptation to water availability may be an important factor in species maintenance of these Mimulus taxa in sympatry.
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32
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Lowry DB, Popovic D, Brennan DJ, Holeski LM. Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in
Mimulus guttatus
*. Evolution 2019; 73:1168-1181. [DOI: 10.1111/evo.13699] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/21/2019] [Accepted: 01/31/2019] [Indexed: 12/24/2022]
Affiliation(s)
- David B. Lowry
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
- Plant Resilience Institute,Michigan State University East Lansing Michigan 48824
| | - Damian Popovic
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
- Program in Ecology, Evolutionary Biology, and BehaviorMichigan State University East Lansing Michigan 48824
| | - Darlene J. Brennan
- Department of Plant BiologyMichigan State University East Lansing Michigan 48824
| | - Liza M. Holeski
- Department of Biological SciencesNorthern Arizona University Flagstaff Arizona 86011
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33
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Rubin MJ, Schmid KM, Friedman J. Assortative mating by flowering time and its effect on correlated traits in variable environments. Ecol Evol 2019; 9:471-481. [PMID: 30680129 PMCID: PMC6342113 DOI: 10.1002/ece3.4765] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 11/13/2018] [Accepted: 11/13/2018] [Indexed: 11/10/2022] Open
Abstract
Reproductive timing is a key life-history trait that impacts the pool of available mates, the environment experienced during flowering, and the expression of other traits through genetic covariation. Selection on phenology, and its consequences on other life-history traits, has considerable implications in the context of ongoing climate change and shifting growing seasons. To test this, we grew field-collected seed from the wildflower Mimulus guttatus in a greenhouse to assess the standing genetic variation for flowering time and covariation with other traits. We then created full-sib families through phenological assortative mating and grew offspring in three photoperiod treatments representing seasonal variation in daylength. We find substantial quantitative genetic variation for the onset of flowering time, which covaried with vegetative traits. The assortatively-mated offspring varied in their critical photoperiod by over two hours, so that families differed in their probability of flowering across treatments Allocation to flowering and vegetative growth changed across the daylength treatments, with consistent direction and magnitude of covariation among flowering time and other traits. Our results suggest that future studies of flowering time evolution should consider the joint evolution of correlated traits and shifting seasonal selection to understand how environmental variation influences life histories.
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34
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Tang W, Huang L, Bu S, Zhang X, Wu W. Estimation of QTL heritability based on pooled sequencing data. Bioinformatics 2019; 34:978-984. [PMID: 29106443 DOI: 10.1093/bioinformatics/btx703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022] Open
Abstract
Motivation Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem. Results In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation. Availability and implementation The R scripts of our method are open source under GPLv3 license at http://genetics.fafu.edu.cn/PQHE or https://github.com/biotangweiqi/PQHE. The R scripts require the R package rootSolve. Contact wuwr@fafu.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Weiqi Tang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Likun Huang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Suhong Bu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xuzhang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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35
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Gould BA, Chen Y, Lowry DB. Gene regulatory divergence between locally adapted ecotypes in their native habitats. Mol Ecol 2018; 27:4174-4188. [PMID: 30168223 DOI: 10.1111/mec.14852] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 08/15/2018] [Accepted: 08/19/2018] [Indexed: 01/04/2023]
Abstract
Local adaptation is a key driver of ecological specialization and the formation of new species. Despite its importance, the evolution of gene regulatory divergence among locally adapted populations is poorly understood, especially how that divergence manifests in nature. Here, we evaluate gene expression divergence and allele-specific gene expression responses for locally adapted coastal perennial and inland annual accessions of the yellow monkeyflower, Mimulus guttatus, in a field reciprocal transplant experiment. Overall, 6765 (73%) of surveyed genes were differentially expressed between coastal and inland habitats, while 7213 (77%) were differentially expressed between the coastal perennial and inland annual accessions. Cis-regulatory variation was pervasive, affecting 79% (5532) of differentially expressed genes. We detected trans effects for 52% (3611) of differentially expressed genes. Expression plasticity of alleles across habitats (G × E interactions) appears to be relatively common (affecting 18% of transcripts) and could minimize fitness trade-offs at loci that contribute to local adaptation. We also found evidence that at least one chromosomal inversion may act as supergene by holding together haplotypes of differentially expressed genes, but this pattern depends on habitat context. Our results highlight multiple key patterns regarding the relationship between gene expression and the evolution of locally adapted populations.
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Affiliation(s)
- Billie A Gould
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Myriad Women's Health, South San Francisco, California
| | - Yani Chen
- Department of Plant Biology, Michigan State University, East Lansing, Michigan
| | - David B Lowry
- Department of Plant Biology, Michigan State University, East Lansing, Michigan.,Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, Michigan.,Plant Resilience Institute, Michigan State University, East Lansing, Michigan
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36
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Coughlan JM, Willis JH. Dissecting the role of a large chromosomal inversion in life history divergence throughout the Mimulus guttatus species complex. Mol Ecol 2018; 28:1343-1357. [PMID: 30028906 DOI: 10.1111/mec.14804] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
Chromosomal inversions can play an important role in adaptation, but the mechanism of their action in many natural populations remains unclear. An inversion could suppress recombination between locally beneficial alleles, thereby preventing maladaptive reshuffling with less-fit, migrant alleles. The recombination suppression hypothesis has gained much theoretical support but empirical tests are lacking. Here, we evaluated the evolutionary history and phenotypic effects of a chromosomal inversion which differentiates annual and perennial forms of Mimulus guttatus. We found that perennials likely possess the derived orientation of the inversion. In addition, this perennial orientation occurs in a second perennial species, M. decorus, where it is strongly associated with life history differences between co-occurring M. decorus and annual M. guttatus. One prediction of the recombination suppression hypothesis is that loci contributing to local adaptation will predate the inversion. To test whether the loci influencing perenniality pre-date this inversion, we mapped QTLs for life history traits that differ between annual M. guttatus and a more distantly related, collinear perennial species, M. tilingii. Consistent with the recombination suppression hypothesis, we found that this region is associated with life history in the absence of the inversion, and this association can be broken into at least two QTLs. However, the absolute phenotypic effect of the LG8 inversion region on life history is weaker in M. tilingii than in perennials which possess the inversion. Thus, while we find support for the recombination suppression hypothesis, the contribution of this inversion to life history divergence in this group is likely complex.
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Affiliation(s)
| | - John H Willis
- Biology Department, Duke University, Durham, North Carolina
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37
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Rubin MJ, Brock MT, Baker RL, Wilcox S, Anderson K, Davis SJ, Weinig C. Circadian rhythms are associated with shoot architecture in natural settings. THE NEW PHYTOLOGIST 2018; 219:246-258. [PMID: 29672861 DOI: 10.1111/nph.15162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/11/2018] [Indexed: 06/08/2023]
Abstract
Circadian rhythms are key regulators of diverse biological processes under controlled settings. Yet, the phenotypic and fitness consequences of quantitative variation in circadian rhythms remain largely unexplored in the field. As with other pathways, phenotypic characterization of circadian outputs in the field may reveal novel clock functions. Across consecutive growing seasons, we test for associations between clock variation and flowering phenology, plant size, shoot architecture, and fruit set in clock mutants and segregating progenies of Arabidopsis thaliana expressing quantitative variation in circadian rhythms. Using structural equation modeling, we find that genotypic variation in circadian rhythms within a growing season is associated directly with branching, which in turn affects fruit production. Consistent with direct associations between the clock and branching in segregating progenies, cauline branch number is lower and rosette branch number higher in a short-period mutant relative to wild-type and long-period genotypes, independent of flowering time. Differences in branching arise from variation in meristem fate as well as leaf production rate before flowering and attendant increases in meristem number. Our results suggest that clock variation directly affects shoot architecture in the field, suggesting a novel clock function and means by which the clock affects performance.
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Affiliation(s)
- Matthew J Rubin
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
| | - Marcus T Brock
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Robert L Baker
- Biology Department, Miami University, Oxford, OH, 45056, USA
| | - Stephanie Wilcox
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Kyle Anderson
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
| | - Seth J Davis
- Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, WY, 82071, USA
- Program in Ecology, University of Wyoming, Laramie, WY, 82071, USA
- Department of Molecular Biology, University of Wyoming, Laramie, WY, 82071, USA
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38
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Twyford AD, Caola AM, Choudhary P, Raina R, Friedman J. Loss of Color Pigmentation Is Maintained at High Frequency in a Monkey Flower Population. Am Nat 2018; 191:135-145. [DOI: 10.1086/694853] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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39
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Muir CD, Angert AL. Grow with the flow: a latitudinal cline in physiology is associated with more variable precipitation in Erythranthe cardinalis. J Evol Biol 2017; 30:2189-2203. [PMID: 28977720 DOI: 10.1111/jeb.13184] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/24/2017] [Accepted: 09/28/2017] [Indexed: 01/19/2023]
Abstract
Local adaptation is commonly observed in nature: organisms perform well in their natal environment, but poorly outside it. Correlations between traits and latitude, or latitudinal clines, are among the most common pieces of evidence for local adaptation, but identifying the traits under selection and the selective agents is challenging. Here, we investigated a latitudinal cline in growth and photosynthesis across 16 populations of the perennial herb Erythranthe cardinalis (Phrymaceae). Using machine learning methods, we identify interannual variation in precipitation as a likely selective agent: southern populations from more variable environments had higher photosynthetic rates and grew faster. We hypothesize that selection may favour a more annualized life history - grow now rather than save for next year - in environments where severe droughts occur more often. Thus, our study provides insight into how species may adapt if Mediterranean climates become more variable due to climate change.
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Affiliation(s)
- C D Muir
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - A L Angert
- Biodiversity Research Centre and Department of Botany, University of British Columbia, Vancouver, BC, Canada.,Department of Zoology, University of British Columbia, Vancouver, BC, Canada
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40
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Roda F, Walter GM, Nipper R, Ortiz‐Barrientos D. Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. Mol Ecol 2017; 26:3687-3699. [DOI: 10.1111/mec.14150] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/07/2017] [Accepted: 04/03/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Federico Roda
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
- Harvard University Boston MA USA
| | - Greg M. Walter
- School of Biological Sciences The University of Queensland St. Lucia QLD Australia
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41
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Kooyers NJ, James B, Blackman BK. Competition drives trait evolution and character displacement between Mimulus species along an environmental gradient. Evolution 2017; 71:1205-1221. [PMID: 28186619 DOI: 10.1111/evo.13200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 01/24/2017] [Accepted: 01/27/2017] [Indexed: 01/31/2023]
Abstract
Closely related species may evolve to coexist stably in sympatry through niche differentiation driven by in situ competition, a process termed character displacement. Alternatively, past evolution in allopatry may have already sufficiently reduced niche overlap to permit establishment in sympatry, a process called ecological sorting. The relative importance of each process to niche differentiation is contentious even though they are not mutually exclusive and are both mediated via multivariate trait evolution. We explore how competition has impacted niche differentiation in two monkeyflowers, Mimulus alsinoides and M. guttatus, which often co-occur. Through field observations, common gardens, and competition experiments, we demonstrate that M. alsinoides is restricted to marginal habitats in sympatry and that the impacts of character displacement on niche differentiation are complex. Competition with M. guttatus alters selection gradients and has favored taller M. alsinoides with earlier seasonal flowering at low elevation and floral shape divergence at high elevation. However, no trait exhibits the pattern typically associated with character displacement, higher divergence between species in sympatry than allopatry. Thus, although character displacement was unlikely the process driving initial divergence along niche axes necessary for coexistence, we conclude that competition in sympatry has likely driven trait evolution along additional niche axes.
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Affiliation(s)
- Nicholas J Kooyers
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904.,Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720.,Department of Integrative Biology, University of South Florida, Tampa, Florida, 33620
| | - Brooke James
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, Charlottesville, Virginia, 22904.,Department of Plant and Microbial Biology, University of California, Berkeley, California, 94720
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42
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Hughes KA, Leips J. Pleiotropy, constraint, and modularity in the evolution of life histories: insights from genomic analyses. Ann N Y Acad Sci 2017; 1389:76-91. [PMID: 27936291 PMCID: PMC5318229 DOI: 10.1111/nyas.13256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 08/10/2016] [Accepted: 08/22/2016] [Indexed: 12/20/2022]
Abstract
Multicellular organisms display an enormous range of life history (LH) strategies and present an evolutionary conundrum; despite strong natural selection, LH traits are characterized by high levels of genetic variation. To understand the evolution of life histories and maintenance of this variation, the specific phenotypic effects of segregating alleles and the genetic networks in which they act need to be elucidated. In particular, the extent to which LH evolution is constrained by the pleiotropy of alleles contributing to LH variation is generally unknown. Here, we review recent empirical results that shed light on this question, with an emphasis on studies employing genomic analyses. While genome-scale analyses are increasingly practical and affordable, they face limitations of genetic resolution and statistical power. We describe new research approaches that we believe can produce new insights and evaluate their promise and applicability to different kinds of organisms. Two approaches seem particularly promising: experiments that manipulate selection in multiple dimensions and measure phenotypic and genomic response and analytical approaches that take into account genome-wide associations between markers and phenotypes, rather than applying a traditional marker-by-marker approach.
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Affiliation(s)
- Kimberly A. Hughes
- Department of Biological Science, Florida State University, Tallahassee, Florida
| | - Jeff Leips
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland
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43
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Puzey JR, Willis JH, Kelly JK. Population structure and local selection yield high genomic variation in Mimulus guttatus. Mol Ecol 2017; 26:519-535. [PMID: 27859786 PMCID: PMC5274581 DOI: 10.1111/mec.13922] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 09/30/2016] [Accepted: 11/07/2016] [Indexed: 12/30/2022]
Abstract
Across western North America, Mimulus guttatus exists as many local populations adapted to site-specific environmental challenges. Gene flow between locally adapted populations will affect genetic diversity both within demes and across the larger metapopulation. Here, we analyse 34 whole-genome sequences from the intensively studied Iron Mountain population (IM) in conjunction with sequences from 22 Mimulus individuals sampled from across western North America. Three striking features of these data address hypotheses about migration and selection in a locally adapted population. First, we find very high levels of intrapopulation polymorphism (synonymous π = 0.033). Variation outside of genes is likely even higher but difficult to estimate because excessive divergence reduces the efficiency of read mapping. Second, IM exhibits a significantly positive genomewide average for Tajima's D. This indicates allele frequencies are typically more intermediate than expected from neutrality, opposite the pattern observed in many other species. Third, IM exhibits a distinctive haplotype structure with a genomewide excess of positive associations between rarer alleles at linked loci. This suggests an important effect of gene flow from other Mimulus populations, although a residual effect of population founding might also contribute. The combination of multiple analyses, including a novel tree-based analytic method, illustrates how the balance of local selection, limited dispersal and metapopulation dynamics manifests across the genome. The overall genomic pattern of sequence diversity suggests successful gene flow of divergent immigrant genotypes into IM. However, many loci show patterns indicative of local adaptation, particularly at SNPs associated with chromosomal inversions.
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Affiliation(s)
- Joshua R. Puzey
- Department of Biology, College of William and Mary, Williamsburg, Virginia, 23187
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - John H. Willis
- Department of Biology, Duke University, Durham, North Carolina, 27708
| | - John K. Kelly
- Department of Ecology and Evolution, University of Kansas, Lawrence, Kansas, 27708
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Gould BA, Chen Y, Lowry DB. Pooled ecotype sequencing reveals candidate genetic mechanisms for adaptive differentiation and reproductive isolation. Mol Ecol 2016; 26:163-177. [DOI: 10.1111/mec.13881] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 08/22/2016] [Accepted: 08/29/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Billie A. Gould
- Department of Plant Biology; Michigan State University; Plant Biology Laboratories; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Yani Chen
- Department of Plant Biology; Michigan State University; Plant Biology Laboratories; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - David B. Lowry
- Department of Plant Biology; Michigan State University; Plant Biology Laboratories; 612 Wilson Road Room 166 East Lansing MI 48824 USA
- Program in Ecology, Evolutionary Biology and Behavior; Michigan State University; Giltner Hall 293 Farm Ln Rm 103 East Lansing MI 48824 USA
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45
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Ivey CT, Dudley LS, Hove AA, Emms SK, Mazer SJ. Outcrossing and photosynthetic rates vary independently within two Clarkia species: implications for the joint evolution of drought escape physiology and mating system. ANNALS OF BOTANY 2016; 118:897-905. [PMID: 27443300 PMCID: PMC5055815 DOI: 10.1093/aob/mcw134] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 05/19/2016] [Indexed: 05/11/2023]
Abstract
Background and Aims Mating systems of plants are diverse and evolutionarily labile. Abiotic environmental factors, such as seasonal drought, may impose selection on physiological traits that could lead to transitions in mating system if physiological traits are genetically correlated with traits that influence mating system. Within Clarkia, self-fertilizing taxa have higher photosynthetic rates, earlier flowering phenology, faster individual floral development and more compressed flowering periods than their outcrossing sister taxa, potentially reducing the selfing taxa's exposure to drought. In theory, this contrast in trait combinations between sister taxa could have arisen via correlated evolution due to pleiotropy or genetic linkage. Alternatively, each trait may evolve independently as part of a life history that is adaptive in seasonally dry environments. Methods To evaluate these hypotheses, we examined relationships between photosynthetic rates (adjusted for plant height and leaf node position) and outcrossing rates (estimated by allozyme variation in progeny arrays) during two consecutive years in multiple wild populations of two mixed-mating Clarkia taxa, each of which is sister to a derived selfing taxon. If the negative association between photosynthetic rate and outcrossing previously observed between sister taxa reflects correlated evolution due to a strong negative genetic correlation between these traits, then a similarly negative relationship would be observed within populations of each taxon. By contrast, if the combination of elevated photosynthetic rates and reduced outcrossing evolved independently within taxa, we predicted no consistent relationship between photosynthetic rate and outcrossing rate. Key Results We found no significant difference in outcrossing rates within populations between groups of plants with high versus low photosynthetic rates. Conclusions Overall, these results provide support for the hypothesis that the joint divergence in photosynthetic rate and mating system observed between Clarkia sister taxa is the result of independent evolutionary transitions.
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Affiliation(s)
- Christopher T. Ivey
- California State University, Chico, CA 95929-0515, USA
- *For correspondence. E-mail
| | - Leah S. Dudley
- University of Wisconsin, Stout, Menomonie, WI 54751, USA
| | - Alisa A. Hove
- Warren Wilson College, Asheville, NC 28815-6217, USA
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Yuan W, Flowers JM, Sahraie DJ, Ehrenreich IM, Purugganan MD. Extreme QTL mapping of germination speed in Arabidopsis thaliana. Mol Ecol 2016; 25:4177-96. [DOI: 10.1111/mec.13768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2015] [Revised: 07/01/2016] [Accepted: 07/06/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Wei Yuan
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - Jonathan M. Flowers
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
- Center for Genomics and Systems Biology; NYU Abu Dhabi Research Institute; New York University Abu Dhabi; Saadiyat Island Abu Dhabi United Arab Emirates
| | - Dustin J. Sahraie
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
| | - Ian M. Ehrenreich
- Molecular and Computational Biology Section; University of Southern California; Ray R. Irani Hall 201 Los Angeles CA 90089-2910 USA
| | - Michael D. Purugganan
- Department of Biology; Center for Genomics and Systems Biology; New York University; 12 Waverly Place New York NY 10003 USA
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Ferris KG, Barnett LL, Blackman BK, Willis JH. The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex. Mol Ecol 2016; 26:208-224. [PMID: 27439150 DOI: 10.1111/mec.13763] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 06/30/2016] [Accepted: 07/05/2016] [Indexed: 01/05/2023]
Abstract
The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters of smaller effect loci. In this study, we investigate the genetic architecture of divergence in flowering time, mating system-related traits, and leaf shape between Mimulus laciniatus and a sympatric population of its close relative M. guttatus. These three traits are probably involved in M. laciniatus' adaptation to a dry, exposed granite outcrop environment. Flowering time and mating system differences are also reproductive isolating barriers making them 'magic traits'. Phenotypic hybrids in this population provide evidence of recent gene flow. Using next-generation sequencing, we generate dense SNP markers across the genome and map quantitative trait loci (QTLs) involved in flowering time, flower size and leaf shape. We find that interspecific divergence in all three traits is due to few QTL of large effect including a highly pleiotropic QTL on chromosome 8. This QTL region contains the pleiotropic candidate gene TCP4 and is involved in ecologically important phenotypes in other Mimulus species. Our results are consistent with theory, indicating that local adaptation and reproductive isolation with gene flow should be due to few loci with large and pleiotropic effects.
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Affiliation(s)
- Kathleen G Ferris
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
| | - Laryssa L Barnett
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, 485 McCormick Road, Charlottesville, VA, 22904, USA
| | - John H Willis
- Department of Biology, Duke University, 125 Science Drive, Durham, NC, 27705, USA
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48
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DeMarche ML, Kay KM, Angert AL. The scale of local adaptation in Mimulus guttatus: comparing life history races, ecotypes, and populations. THE NEW PHYTOLOGIST 2016; 211:345-356. [PMID: 27102088 DOI: 10.1111/nph.13971] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/16/2016] [Indexed: 06/05/2023]
Abstract
Fitness trade-offs between environments are central to the evolution of biodiversity. Although transplant studies often document fitness trade-offs consistent with local adaptation (LA), many have also found an advantage of foreign genotypes (foreign advantage (FA)). Understanding the mechanisms driving the magnitude and distribution of fitness variation requires comparative approaches that test the ecological scales at which these different patterns emerge. We used a common garden transplant experiment to compare the relative fitnesses of native vs foreign genotypes at three nested ecological scales within Mimulus guttatus: annual vs perennial life history races, perennial ecotypes across an elevational range, and populations within perennial elevational ecotypes. We integrated fitness across the life-cycle and decomposed LA vs FA into contributions from different fitness components. We found LA, measured as home-site advantage, between annual and perennial races and a trend towards LA among populations within montane habitats. Conversely, we found strong FA of low-elevation perennials in a montane environment. LA between life history races reflects the fitness advantages of adult survival and vegetative growth in a mesic environment. Within the perennial race, recent climate conditions or nonselective processes, such as dispersal limitation or mutational load, could explain FA of low-elevation perennials in a montane environment.
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Affiliation(s)
- Megan L DeMarche
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Kathleen M Kay
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Amy L Angert
- Departments of Botany and Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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49
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Ferris KG, Rushton T, Greenlee AB, Toll K, Blackman BK, Willis JH. Leaf shape evolution has a similar genetic architecture in three edaphic specialists within the Mimulus guttatus species complex. ANNALS OF BOTANY 2015; 116:213-23. [PMID: 26070644 PMCID: PMC4512191 DOI: 10.1093/aob/mcv080] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/06/2015] [Accepted: 04/24/2015] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS The genetic basis of leaf shape has long interested botanists because leaf shape varies extensively across the plant kingdom and this variation is probably adaptive. However, knowledge of the genetic architecture of leaf shape variation in natural populations remains limited. This study examined the genetic architecture of leaf shape diversification among three edaphic specialists in the Mimulus guttatus species complex. Lobed and narrow leaves have evolved from the entire, round leaves of M. guttatus in M. laciniatus, M. nudatus and a polymorphic serpentine M. guttatus population (M2L). METHODS Bulk segregant analysis and next-generation sequencing were used to map quantitative trait loci (QTLs) that underlie leaf shape in an M. laciniatus × M. guttatus F2 population. To determine whether the same QTLs contribute to leaf shape variation in M. nudatus and M2L, F2s from M. guttatus × M. nudatus and lobed M2L × unlobed M. guttatus crosses were genotyped at QTLs from the bulk segregant analysis. KEY RESULTS Narrow and lobed leaf shapes in M. laciniatus, M. nudatus and M. guttatus are controlled by overlapping genetic regions. Several promising leaf shape candidate genes were found under each QTL. CONCLUSIONS The evolution of divergent leaf shape has taken place multiple times in the M. guttatus species complex and is associated with the occupation of dry, rocky environments. The genetic architecture of elongated and lobed leaves is similar across three species in this group. This may indicate that parallel genetic evolution from standing variation or new mutations is responsible for the putatively adaptive leaf shape variation in Mimulus.
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Affiliation(s)
- Kathleen G Ferris
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
| | - Tullia Rushton
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
| | - Anna B Greenlee
- Department of Biology, University of Virginia, 485 McCormick Road Charlottesville, VA 22904, USA
| | - Katherine Toll
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
| | - Benjamin K Blackman
- Department of Biology, University of Virginia, 485 McCormick Road Charlottesville, VA 22904, USA
| | - John H Willis
- Department of Biology, Duke University, 125 Science Drive, Durham, NC 27705, USA and
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50
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Twyford AD, Friedman J. Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion. Evolution 2015; 69:1476-1486. [PMID: 25879251 PMCID: PMC5029580 DOI: 10.1111/evo.12663] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/01/2015] [Indexed: 12/15/2022]
Abstract
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.
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Affiliation(s)
- Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom.,Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244
| | - Jannice Friedman
- Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244
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