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Chen H, Berg CS, Samuli M, Sotola VA, Sweigart AL, Yuan YW, Fishman L. The genetic architecture of floral trait divergence between hummingbird- and self-pollinated monkeyflower (Mimulus) species. THE NEW PHYTOLOGIST 2025; 245:2255-2267. [PMID: 39697054 DOI: 10.1111/nph.20348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 11/22/2024] [Indexed: 12/20/2024]
Abstract
Pollination syndromes are a key component of flowering plant diversification, prompting questions about the architecture of single traits and genetic coordination among traits. Here, we investigate the genetics of extreme floral divergence between naturally hybridizing monkeyflowers, Mimulus parishii (self-pollinated) and M. cardinalis (hummingbird-pollinated). We mapped quantitative trait loci (QTLs) for 18 pigment, pollinator reward/handling, and dimensional traits in parallel sets of F2 hybrids plus recombinant inbred lines and generated nearly isogenic lines (NILs) for two dimensional traits, pistil length and corolla size. Our multi-population approach revealed a highly polygenic basis (n = 190 QTLs total) for pollination syndrome divergence, capturing minor QTLs even for pigment traits with leading major loci. There was significant QTL overlap within pigment and dimensional categories. Nectar volume QTLs clustered with those for floral dimensions, suggesting a partially shared module. The NILs refined two pistil length QTLs, only one of which has tightly correlated effects on other dimensional traits. An overall polygenic architecture of floral divergence is partially coordinated by genetic modules formed by linkage (pigments) and likely pleiotropy (dimensions plus nectar). This work illuminates pollinator syndrome diversification in a model radiation and generates a robust framework for molecular and ecological genomics.
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Affiliation(s)
- Hongfei Chen
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06520, USA
| | - Colette S Berg
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Matthew Samuli
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - V Alex Sotola
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
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2
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Dopman EB, Shaw KL, Servedio MR, Butlin RK, Smadja CM. Coupling of Barriers to Gene Exchange: Causes and Consequences. Cold Spring Harb Perspect Biol 2024; 16:a041432. [PMID: 38191516 PMCID: PMC11293547 DOI: 10.1101/cshperspect.a041432] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Coupling has emerged as a concept to describe the transition from differentiated populations to newly evolved species through the strengthening of reproductive isolation. However, the term has been used in multiple ways, and relevant processes have sometimes not been clearly distinguished. Here, we synthesize existing uses of the concept of coupling and find three main perspectives: (1) coupling as the build-up of linkage disequilibrium among loci underlying barriers to gene exchange, (2) coupling as the build-up of genome-wide linkage disequilibrium, and (3) coupling as the process generating a coincidence of distinct barrier effects. We compare and contrast these views, show the diverse processes involved and the complexity of the relationships among recombination, linkage disequilibrium, and reproductive isolation, and, finally, we emphasize how each perspective can guide new directions in speciation research. Although the importance of coupling for evolutionary divergence and speciation is well established, many theoretical and empirical questions remain unanswered.
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Affiliation(s)
- Erik B Dopman
- Department of Biology, Tufts University, Medford, Massachusetts 02155, USA
| | - Kerry L Shaw
- Department of Neurobiology and Behavior, Cornell University, Ithaca, New York 14853, USA
| | - Maria R Servedio
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Roger K Butlin
- Ecology and Evolutionary Biology, School of Biosciences, The University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
- Department of Marine Sciences, University of Gothenburg, Gothenburg 40530, Sweden
| | - Carole M Smadja
- Institut des Sciences de l'Evolution de Montpellier ISEM, Universite de Montpellier, CNRS, IRD, Montpellier 34095, France
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3
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Merrill RM, Arenas-Castro H, Feller AF, Harenčár J, Rossi M, Streisfeld MA, Kay KM. Genetics and the Evolution of Prezygotic Isolation. Cold Spring Harb Perspect Biol 2024; 16:a041439. [PMID: 37848246 PMCID: PMC10835618 DOI: 10.1101/cshperspect.a041439] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
The significance of prezygotic isolation for speciation has been recognized at least since the Modern Synthesis. However, fundamental questions remain. For example, how are genetic associations between traits that contribute to prezygotic isolation maintained? What is the source of genetic variation underlying the evolution of these traits? And how do prezygotic barriers affect patterns of gene flow? We address these questions by reviewing genetic features shared across plants and animals that influence prezygotic isolation. Emerging technologies increasingly enable the identification and functional characterization of the genes involved, allowing us to test established theoretical expectations. Embedding these genes in their developmental context will allow further predictions about what constrains the evolution of prezygotic isolation. Ongoing improvements in statistical and computational tools will reveal how pre- and postzygotic isolation may differ in how they influence gene flow across the genome. Finally, we highlight opportunities for progress by combining theory with appropriate data.
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Affiliation(s)
- Richard M Merrill
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Henry Arenas-Castro
- School of Biological Sciences, University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Anna F Feller
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA
- Arnold Arboretum of Harvard University, Boston, Massachusetts 02131, USA
| | - Julia Harenčár
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
| | - Matteo Rossi
- Faculty of Biology, Division of Evolutionary Biology, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Matthew A Streisfeld
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403-5289, USA
| | - Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, California 95060, USA
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4
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Frachon L, Schiestl FP. Rapid genomic evolution in Brassica rapa with bumblebee selection in experimental evolution. BMC Ecol Evol 2024; 24:7. [PMID: 38195402 PMCID: PMC10775529 DOI: 10.1186/s12862-023-02194-y] [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: 10/04/2022] [Accepted: 12/20/2023] [Indexed: 01/11/2024] Open
Abstract
BACKGROUND Insect pollinators shape rapid phenotypic evolution of traits related to floral attractiveness and plant reproductive success. However, the underlying genomic changes remain largely unknown despite their importance in predicting adaptive responses to natural or to artificial selection. Based on a nine-generation experimental evolution study with fast cycling Brassica rapa plants adapting to bumblebees, we investigate the genomic evolution associated with the previously observed parallel phenotypic evolution. In this current evolve and resequencing (E&R) study, we conduct a genomic scan of the allele frequency changes along the genome in bumblebee-pollinated and hand-pollinated plants and perform a genomic principal component analysis (PCA). RESULTS We highlight rapid genomic evolution associated with the observed phenotypic evolution mediated by bumblebees. Controlling for genetic drift, we observe significant changes in allelic frequencies at multiple loci. However, this pattern differs according to the replicate of bumblebee-pollinated plants, suggesting putative non-parallel genomic evolution. Finally, our study underlines an increase in genomic variance implying the putative involvement of multiple loci in short-term pollinator adaptation. CONCLUSIONS Overall, our study enhances our understanding of the complex interactions between pollinator and plants, providing a stepping stone towards unravelling the genetic basis of plant genomic adaptation to biotic factors in the environment.
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Affiliation(s)
- Léa Frachon
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland.
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
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5
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Wessinger CA. How the switch to hummingbird pollination has greatly contributed to our understanding of evolutionary processes. THE NEW PHYTOLOGIST 2024; 241:59-64. [PMID: 37853523 PMCID: PMC10843001 DOI: 10.1111/nph.19335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 09/30/2023] [Indexed: 10/20/2023]
Abstract
The evolutionary switch to hummingbird pollination exemplifies complex adaptation, requiring evolutionary change in multiple component traits. Despite this complexity, diverse lineages have converged on hummingbird-adapted flowers on a relatively short evolutionary timescale. Here, I review how features of the genetic basis of adaptation contribute to this remarkable evolutionary lability. Large-effect substitutions, large mutational targets for adaptation, adaptive introgression, and concentrated architecture all contribute to the origin and maintenance of hummingbird-adapted flowers. The genetic features of adaptation are likely shaped by the ecological and geographic context of the switch to hummingbird pollination, with implications for future evolutionary trajectories.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
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Wessinger CA, Katzer AM, Hime PM, Rausher MD, Kelly JK, Hileman LC. A few essential genetic loci distinguish Penstemon species with flowers adapted to pollination by bees or hummingbirds. PLoS Biol 2023; 21:e3002294. [PMID: 37769035 PMCID: PMC10538765 DOI: 10.1371/journal.pbio.3002294] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 08/11/2023] [Indexed: 09/30/2023] Open
Abstract
In the formation of species, adaptation by natural selection generates distinct combinations of traits that function well together. The maintenance of adaptive trait combinations in the face of gene flow depends on the strength and nature of selection acting on the underlying genetic loci. Floral pollination syndromes exemplify the evolution of trait combinations adaptive for particular pollinators. The North American wildflower genus Penstemon displays remarkable floral syndrome convergence, with at least 20 separate lineages that have evolved from ancestral bee pollination syndrome (wide blue-purple flowers that present a landing platform for bees and small amounts of nectar) to hummingbird pollination syndrome (bright red narrowly tubular flowers offering copious nectar). Related taxa that differ in floral syndrome offer an attractive opportunity to examine the genomic basis of complex trait divergence. In this study, we characterized genomic divergence among 229 individuals from a Penstemon species complex that includes both bee and hummingbird floral syndromes. Field plants are easily classified into species based on phenotypic differences and hybrids displaying intermediate floral syndromes are rare. Despite unambiguous phenotypic differences, genome-wide differentiation between species is minimal. Hummingbird-adapted populations are more genetically similar to nearby bee-adapted populations than to geographically distant hummingbird-adapted populations, in terms of genome-wide dXY. However, a small number of genetic loci are strongly differentiated between species. These approximately 20 "species-diagnostic loci," which appear to have nearly fixed differences between pollination syndromes, are sprinkled throughout the genome in high recombination regions. Several map closely to previously established floral trait quantitative trait loci (QTLs). The striking difference between the diagnostic loci and the genome as whole suggests strong selection to maintain distinct combinations of traits, but with sufficient gene flow to homogenize the genomic background. A surprisingly small number of alleles confer phenotypic differences that form the basis of species identity in this species complex.
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Affiliation(s)
- Carolyn A. Wessinger
- Department of Biological Sciences, University of South Carolina, Columbia, South Carolina, United States of America
| | - Amanda M. Katzer
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Paul M. Hime
- Biodiversity Institute and Natural History Museum, University of Kansas, Lawrence, Kansas, United States of America
| | - Mark D. Rausher
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - John K. Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Lena C. Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America
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7
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Binaghi M, Esfeld K, Mandel T, Freitas LB, Roesti M, Kuhlemeier C. Genetic architecture of a pollinator shift and its fate in secondary hybrid zones of two Petunia species. BMC Biol 2023; 21:58. [PMID: 36941631 PMCID: PMC10029178 DOI: 10.1186/s12915-023-01561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/10/2023] [Indexed: 03/23/2023] Open
Abstract
BACKGROUND Theory suggests that the genetic architecture of traits under divergent natural selection influences how easily reproductive barriers evolve and are maintained between species. Divergently selected traits with a simple genetic architecture (few loci with major phenotypic effects) should facilitate the establishment and maintenance of reproductive isolation between species that are still connected by some gene flow. While empirical support for this idea appears to be mixed, most studies test the influence of trait architectures on reproductive isolation only indirectly. Petunia plant species are, in part, reproductively isolated by their different pollinators. To investigate the genetic causes and consequences of this ecological isolation, we deciphered the genetic architecture of three floral pollination syndrome traits in naturally occurring hybrids between the widespread Petunia axillaris and the highly endemic and endangered P. exserta. RESULTS Using population genetics, Bayesian linear mixed modelling and genome-wide association studies, we found that the three pollination syndrome traits vary in genetic architecture. Few genome regions explain a majority of the variation in flavonol content (defining UV floral colour) and strongly predict the trait value in hybrids irrespective of interspecific admixture in the rest of their genomes. In contrast, variation in pistil exsertion and anthocyanin content (defining visible floral colour) is controlled by many genome-wide loci. Opposite to flavonol content, the genome-wide proportion of admixture between the two species predicts trait values in their hybrids. Finally, the genome regions strongly associated with the traits do not show extreme divergence between individuals representing the two species, suggesting that divergent selection on these genome regions is relatively weak within their contact zones. CONCLUSIONS Among the traits analysed, those with a more complex genetic architecture are best maintained in association with the species upon their secondary contact. We propose that this maintained genotype-phenotype association is a coincidental consequence of the complex genetic architectures of these traits: some of their many underlying small-effect loci are likely to be coincidentally linked with the actual barrier loci keeping these species partially isolated upon secondary contact. Hence, the genetic architecture of a trait seems to matter for the outcome of hybridization not only then when the trait itself is under selection.
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Affiliation(s)
- Marta Binaghi
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Marius Roesti
- Institute of Ecology and Evolution, University of Bern, 3012, Bern, Switzerland
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, 3013, Bern, Switzerland.
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8
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Li C, Binaghi M, Pichon V, Cannarozzi G, Brandão de Freitas L, Hanemian M, Kuhlemeier C. Tight genetic linkage of genes causing hybrid necrosis and pollinator isolation between young species. NATURE PLANTS 2023; 9:420-432. [PMID: 36805038 PMCID: PMC10027609 DOI: 10.1038/s41477-023-01354-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/19/2023] [Indexed: 05/18/2023]
Abstract
The mechanisms of reproductive isolation that cause phenotypic diversification and eventually speciation are a major topic of evolutionary research. Hybrid necrosis is a post-zygotic isolation mechanism in which cell death develops in the absence of pathogens. It is often due to the incompatibility between proteins from two parents. Here we describe a unique case of hybrid necrosis due to an incompatibility between loci on chromosomes 2 and 7 between two pollinator-isolated Petunia species. Typical immune responses as well as endoplasmic reticulum stress responses are induced in the necrotic line. The locus on chromosome 2 encodes ChiA1, a bifunctional GH18 chitinase/lysozyme. The enzymatic activity of ChiA1 is dispensable for the development of necrosis. We propose that the extremely high expression of ChiA1 involves a positive feedback loop between the loci on chromosomes 2 and 7. ChiA1 is tightly linked to major genes involved in the adaptation to different pollinators, a form of pre-zygotic isolation. This linkage of pre- and post-zygotic barriers strengthens reproductive isolation and probably contributes to rapid diversification and speciation.
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Affiliation(s)
- Chaobin Li
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Marta Binaghi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Vivien Pichon
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gina Cannarozzi
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
- Chemistry/Biology/Pharmacy Information Center, ETH Zürich, Zürich, Switzerland
| | - Loreta Brandão de Freitas
- Department of Genetics, Laboratory of Molecular Evolution, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Mathieu Hanemian
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
- Laboratoire des Interactions Plantes-Microbes-Environnement (LIPME), INRAE, CNRS, Université de Toulouse, Castanet-Tolosan, France.
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern, Switzerland.
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9
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Lüthi MN, Berardi AE, Mandel T, Freitas LB, Kuhlemeier C. Single gene mutation in a plant MYB transcription factor causes a major shift in pollinator preference. Curr Biol 2022; 32:5295-5308.e5. [PMID: 36473466 DOI: 10.1016/j.cub.2022.11.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/16/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
Understanding the molecular basis of reproductive isolation and speciation is a key goal of evolutionary genetics. In the South American genus Petunia, the R2R3-MYB transcription factor MYB-FL regulates the biosynthesis of UV-absorbing flavonol pigments, a major determinant of pollinator preference. MYB-FL is highly expressed in the hawkmoth-pollinated P. axillaris, but independent losses of its activity in sister taxa P. secreta and P. exserta led to UV-reflective flowers and associated pollinator shifts in each lineage (bees and hummingbirds, respectively). We created a myb-fl CRISPR mutant in P. axillaris and studied the effect of this single gene on innate pollinator preference. The mutation strongly reduced the expression of the two key flavonol-related biosynthetic genes but only affected the expression of few other genes. The mutant flowers were UV reflective as expected but additionally contained low levels of visible anthocyanin pigments. Hawkmoths strongly preferred the wild-type P. axillaris over the myb-fl mutant, whereas both social and solitary bee preference depended on the level of visible color of the mutants. MYB-FL, with its specific expression pattern, small number of target genes, and key position at the nexus of flavonol and anthocyanin biosynthetic pathways, provides a striking example of evolution by single mutations of large phenotypic effect.
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Affiliation(s)
- Martina N Lüthi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Andrea E Berardi
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Loreta B Freitas
- Department of Genetics, Universidade Federal do Rio Grande do Sul, POB 15053, Porto Alegre, 91501970 Rio Grande do Sul, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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10
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Berardi AE, Betancourt Morejón AC, Hopkins R. Convergence without divergence in North American red-flowering Silene. FRONTIERS IN PLANT SCIENCE 2022; 13:945806. [PMID: 36147235 PMCID: PMC9485837 DOI: 10.3389/fpls.2022.945806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/06/2022] [Indexed: 06/16/2023]
Abstract
Combinations of correlated floral traits have arisen repeatedly across angiosperms through convergent evolution in response to pollinator selection to optimize reproduction. While some plant groups exhibit very distinct combinations of traits adapted to specific pollinators (so-called pollination syndromes), others do not. Determining how floral traits diverge across clades and whether floral traits show predictable correlations in diverse groups of flowering plants is key to determining the extent to which pollinator-mediated selection drives diversification. The North American Silene section Physolychnis is an ideal group to investigate patterns of floral evolution because it is characterized by the evolution of novel red floral color, extensive floral morphological variation, polyploidy, and exposure to a novel group of pollinators (hummingbirds). We test for correlated patterns of trait evolution that would be consistent with convergent responses to selection in the key floral traits of color and morphology. We also consider both the role of phylogenic distance and geographic overlap in explaining patterns of floral trait variation. Inconsistent with phenotypically divergent pollination syndromes, we find very little clustering of North American Silene into distinct floral morphospace. We also find little evidence that phylogenetic history or geographic overlap explains patterns of floral diversity in this group. White- and pink-flowering species show extensive phenotypic diversity but are entirely overlapping in morphological variation. However, red-flowering species have much less phenotypic disparity and cluster tightly in floral morphospace. We find that red-flowering species have evolved floral traits that align with a traditional hummingbird syndrome, but that these trait values overlap with several white and pink species as well. Our findings support the hypothesis that convergent evolution does not always proceed through comparative phenotypic divergence, but possibly through sorting of standing ancestral variation.
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Affiliation(s)
- Andrea E. Berardi
- Harvard University Herbaria, Cambridge, MA, United States
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- The Arnold Arboretum, Boston, MA, United States
| | - Ana C. Betancourt Morejón
- Department of Biology, University of Puerto Rico - Rio Piedras Campus, San Juan, Puerto Rico
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, United States
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- The Arnold Arboretum, Boston, MA, United States
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11
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Abstract
The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.
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12
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Smit SJ, Lichman BR. Plant biosynthetic gene clusters in the context of metabolic evolution. Nat Prod Rep 2022; 39:1465-1482. [PMID: 35441651 PMCID: PMC9298681 DOI: 10.1039/d2np00005a] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 12/17/2022]
Abstract
Covering: up to 2022Plants produce a wide range of structurally and biosynthetically diverse natural products to interact with their environment. These specialised metabolites typically evolve in limited taxonomic groups presumably in response to specific selective pressures. With the increasing availability of sequencing data, it has become apparent that in many cases the genes encoding biosynthetic enzymes for specialised metabolic pathways are not randomly distributed on the genome. Instead they are physically linked in structures such as arrays, pairs and clusters. The exact function of these clusters is debated. In this review we take a broad view of gene arrangement in plant specialised metabolism, examining types of structures and variation. We discuss the evolution of biosynthetic gene clusters in the wider context of metabolism, populations and epigenetics. Finally, we synthesise our observations to propose a new hypothesis for biosynthetic gene cluster formation in plants.
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Affiliation(s)
- Samuel J Smit
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
| | - Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, YO10 5DD, UK.
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13
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Poulin V, Amesefe D, Gonzalez E, Alexandre H, Joly S. Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae). PLoS One 2022; 17:e0267540. [PMID: 35853078 PMCID: PMC9295946 DOI: 10.1371/journal.pone.0267540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.
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Affiliation(s)
- Valérie Poulin
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Delase Amesefe
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G), McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Hermine Alexandre
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Simon Joly
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Montreal Botanical Garden, Montréal, Canada
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14
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Li Q, Lindtke D, Rodríguez-Ramírez C, Kakioka R, Takahashi H, Toyoda A, Kitano J, Ehrlich RL, Chang Mell J, Yeaman S. Local Adaptation and the Evolution of Genome Architecture in Threespine Stickleback. Genome Biol Evol 2022; 14:6589818. [PMID: 35594844 PMCID: PMC9178229 DOI: 10.1093/gbe/evac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 12/11/2022] Open
Abstract
Theory predicts that local adaptation should favor the evolution of a concentrated genetic architecture, where the alleles driving adaptive divergence are tightly clustered on chromosomes. Adaptation to marine versus freshwater environments in threespine stickleback has resulted in an architecture that seems consistent with this prediction: divergence among populations is mainly driven by a few genomic regions harboring multiple quantitative trait loci for environmentally adapted traits, as well as candidate genes with well-established phenotypic effects. One theory for the evolution of these "genomic islands" is that rearrangements remodel the genome to bring causal loci into tight proximity, but this has not been studied explicitly. We tested this theory using synteny analysis to identify micro- and macro-rearrangements in the stickleback genome and assess their potential involvement in the evolution of genomic islands. To identify rearrangements, we conducted a de novo assembly of the closely related tubesnout (Aulorhyncus flavidus) genome and compared this to the genomes of threespine stickleback and two other closely related species. We found that small rearrangements, within-chromosome duplications, and lineage-specific genes (LSGs) were enriched around genomic islands, and that all three chromosomes harboring large genomic islands have experienced macro-rearrangements. We also found that duplicates and micro-rearrangements are 9.9× and 2.9× more likely to involve genes differentially expressed between marine and freshwater genotypes. While not conclusive, these results are consistent with the explanation that strong divergent selection on candidate genes drove the recruitment of rearrangements to yield clusters of locally adaptive loci.
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Affiliation(s)
- Qiushi Li
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Dorothea Lindtke
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
| | - Carlos Rodríguez-Ramírez
- Division of Evolutionary Ecology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Ryo Kakioka
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Nakagami-gun, Okinawa 903-0213, Japan
| | - Hiroshi Takahashi
- National Fisheries University, 2-7-1 Nagata-honmachi, Shimonoseki, Yamaguchi 759-6595, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Jun Kitano
- Ecological Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Rachel L Ehrlich
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Joshua Chang Mell
- Department of Microbiology & Immunology, Drexel University College of Medicine, Philadelphia 19102, PA, USA
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Canada T2N 1N4
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15
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Yeaman S. Evolution of polygenic traits under global vs local adaptation. Genetics 2022; 220:iyab134. [PMID: 35134196 PMCID: PMC8733419 DOI: 10.1093/genetics/iyab134] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/05/2021] [Indexed: 12/14/2022] Open
Abstract
Observations about the number, frequency, effect size, and genomic distribution of alleles associated with complex traits must be interpreted in light of evolutionary process. These characteristics, which constitute a trait's genetic architecture, can dramatically affect evolutionary outcomes in applications from agriculture to medicine, and can provide a window into how evolution works. Here, I review theoretical predictions about the evolution of genetic architecture under spatially homogeneous, global adaptation as compared with spatially heterogeneous, local adaptation. Due to the tension between divergent selection and migration, local adaptation can favor "concentrated" genetic architectures that are enriched for alleles of larger effect, clustered in a smaller number of genomic regions, relative to expectations under global adaptation. However, the evolution of such architectures may be limited by many factors, including the genotypic redundancy of the trait, mutation rate, and temporal variability of environment. I review the circumstances in which predictions differ for global vs local adaptation and discuss where progress can be made in testing hypotheses using data from natural populations and lab experiments. As the field of comparative population genomics expands in scope, differences in architecture among traits and species will provide insights into how evolution works, and such differences must be interpreted in light of which kind of selection has been operating.
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Affiliation(s)
- Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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16
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Kay KM, Surget-Groba Y. The genetic basis of floral mechanical isolation between two hummingbird-pollinated Neotropical understorey herbs. Mol Ecol 2021; 31:4351-4363. [PMID: 34487383 DOI: 10.1111/mec.16165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/29/2021] [Accepted: 08/31/2021] [Indexed: 12/29/2022]
Abstract
Floral divergence can contribute to reproductive isolation among plant lineages, and thus provides an opportunity to study the genetics of speciation, including the number, effect size, mode of action and interactions of quantitative trait loci (QTL). Moreover, flowers represent suites of functionally interrelated traits, but it is unclear to what extent the phenotypic integration of the flower is underlain by a shared genetic architecture, which could facilitate or constrain correlated evolution of floral traits. Here, we examine the genetic architecture of floral morphological traits involved in an evolutionary switch from bill to forehead pollen placement between two species of hummingbird-pollinated Neotropical understorey herbs that are reproductively isolated by these floral differences. For the majority of traits, we find multiple QTL of relatively small effect spread throughout the genome. We also find substantial colocalization and alignment of effects of QTL underlying different floral traits that function together to promote outcrossing and reduce heterospecific pollen transfer. Our results are consistent with adaptive pleiotropy or linkage of many co-adapted genes, either of which could have facilitated a response to correlated selection and helped to stabilize divergent phenotypes in the face of low levels of hybridization. Moreover, our results indicate that floral mechanical isolation can be consistent with an infinitesimal model of adaptation.
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Affiliation(s)
- Kathleen M Kay
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Yann Surget-Groba
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, USA.,Département de Biologie, Université du Québec en Outaouais, Ripon, QC, Canada
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17
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Berardi AE, Esfeld K, Jäggi L, Mandel T, Cannarozzi GM, Kuhlemeier C. Complex evolution of novel red floral color in Petunia. THE PLANT CELL 2021; 33:2273-2295. [PMID: 33871652 PMCID: PMC8364234 DOI: 10.1093/plcell/koab114] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/12/2021] [Indexed: 05/20/2023]
Abstract
Red flower color has arisen multiple times and is generally associated with hummingbird pollination. The majority of evolutionary transitions to red color proceeded from purple lineages and tend to be genetically simple, almost always involving a few loss-of-function mutations of major phenotypic effect. Here we report on the complex evolution of a novel red floral color in the hummingbird-pollinated Petunia exserta (Solanaceae) from a colorless ancestor. The presence of a red color is remarkable because the genus cannot synthesize red anthocyanins and P. exserta retains a nonfunctional copy of the key MYB transcription factor AN2. We show that moderate upregulation and a shift in tissue specificity of an AN2 paralog, DEEP PURPLE, restores anthocyanin biosynthesis in P. exserta. An essential shift in anthocyanin hydroxylation occurred through rebalancing the expression of three hydroxylating genes. Furthermore, the downregulation of an acyltransferase promotes reddish hues in typically purple pigments by preventing acyl group decoration of anthocyanins. This study presents a rare case of a genetically complex evolutionary transition toward the gain of a novel red color.
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Affiliation(s)
- Andrea E. Berardi
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Korinna Esfeld
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Lea Jäggi
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
| | | | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Bern 3013, Switzerland
- Author for correspondence:
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18
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Cozzolino S, Scopece G, Lussu M, Cortis P, Schiestl FP. Do floral and ecogeographic isolation allow the co-occurrence of two ecotypes of Anacamptis papilionacea (Orchidaceae)? Ecol Evol 2021; 11:9917-9931. [PMID: 34367549 PMCID: PMC8328454 DOI: 10.1002/ece3.7432] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 11/08/2022] Open
Abstract
Ecotypes are relatively frequent in flowering plants and considered central in ecological speciation as local adaptation can promote the insurgence of reproductive isolation. Without geographic isolation, gene flow usually homogenizes the allopatrically generated phenotypic and ecological divergences, unless other forms of reproductive isolation keep them separated. Here, we investigated two orchid ecotypes with marked phenotypic floral divergence that coexist in contact zones. We found that the two ecotypes show different ecological habitat preferences with one being more climatically restricted than the other. The ecotypes remain clearly morphologically differentiated both in allopatry and in sympatry and differed in diverse floral traits. Despite only slightly different flowering times, the two ecotypes achieved floral isolation thanks to different pollination strategies. We found that both ecotypes attract a wide range of insects, but the ratio of male/female attracted by the two ecotypes was significantly different, with one ecotype mainly attracts male pollinators, while the other mainly attracts female pollinators. As a potential consequence, the two ecotypes show different pollen transfer efficiency. Experimental plots with pollen staining showed a higher proportion of intra- than interecotype movements confirming floral isolation between ecotypes in sympatry while crossing experiments excluded evident postmating barriers. Even if not completely halting the interecotypes pollen flow in sympatry, such incipient switch in pollination strategy between ecotypes may represent a first step on the path toward evolution of sexual mimicry in Orchidinae.
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Affiliation(s)
| | - Giovanni Scopece
- Department of BiologyUniversity Federico II of NaplesNapoliItaly
| | - Michele Lussu
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
- Istituto Regionale per la Floricoltura (IRF)SanremoItaly
| | - Pierluigi Cortis
- Department of Life and Environmental SciencesUniversity of CagliariCagliariItaly
| | - Florian P. Schiestl
- Department of Systematic and Evolutionary Botany and Botanical GardensUniversity of ZurichZurichSwitzerland
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19
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Frachon L, Stirling SA, Schiestl FP, Dudareva N. Combining biotechnology and evolution for understanding the mechanisms of pollinator attraction. Curr Opin Biotechnol 2021; 70:213-219. [PMID: 34217123 DOI: 10.1016/j.copbio.2021.06.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 11/15/2022]
Abstract
Many flowering plants rely on pollinators for their reproductive success. Plant-pollinator interactions usually depend on a complex combination of traits based on a fine-tuned biosynthetic machinery, with many structural and regulatory genes involved. Yet, the physiological mechanisms in plants are the product of evolutionary processes. While evolution has been modifying flowers through millions of years, it is also a rapid process that can change plant traits within few generations. Here we discuss both mechanistic and evolutionary aspects of pollinator attraction. We also propose how latest advances in biotechnology and evolutionary studies, and their combination, will improve the elucidation of molecular mechanisms and evolutionary dynamics of pollinator attraction in changing environments.
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Affiliation(s)
- Léa Frachon
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - Shannon A Stirling
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN 47907-2063, USA
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland.
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, 175 South University St., West Lafayette, IN 47907-2063, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
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20
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Leidinger L, Vedder D, Cabral JS. Temporal environmental variation may impose differential selection on both genomic and ecological traits. OIKOS 2021. [DOI: 10.1111/oik.08172] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ludwig Leidinger
- Center for Computational and Theoretical Biology, Faculty of Biology, Univ. of Würzburg Würzburg Germany
| | - Daniel Vedder
- Center for Computational and Theoretical Biology, Faculty of Biology, Univ. of Würzburg Würzburg Germany
| | - Juliano Sarmento Cabral
- Center for Computational and Theoretical Biology, Faculty of Biology, Univ. of Würzburg Würzburg Germany
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21
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Byers KJRP, Bradshaw HD. Rational Design of a Novel Hawkmoth Pollinator Interaction in Mimulus Section Erythranthe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.658710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Diversification of theca. 275,000 extant flowering plant species has been driven in large part by coevolution with animal pollinators. A recurring pattern of pollinator shifts from hummingbird to hawkmoth pollination has characterized plant speciation in many western North American plant taxa, but in the genusMimulus(monkeyflowers) sectionErythranthethe evolution of hawkmoth pollination from hummingbird-pollinated ancestors has not occurred. We manipulated two flower color loci and tested the attractiveness of the resulting four color phenotypes (red, yellow, pink, and white) to naïve hawkmoths (Manduca sexta). Hawkmoths strongly prefer derived colors (yellow, pink, white) over the ancestral red when choosing an initial flower to visit, and generally preferred derived colors when total visits and total visit time were considered, with no hawkmoth preferring ancestral red over derived colors. The simple flower color genetics underlying this innate pollinator preference suggests a potential path for speciation into an unfilled hawkmoth-pollinated niche inMimulussectionErythranthe, and the deliberate design of a hawkmoth-pollinated flower demonstrates a new, predictive method for studying pollination syndrome evolution.
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22
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Dellinger AS. Pollination syndromes in the 21 st century: where do we stand and where may we go? THE NEW PHYTOLOGIST 2020; 228:1193-1213. [PMID: 33460152 DOI: 10.1111/nph.16793] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/31/2020] [Indexed: 06/12/2023]
Abstract
Pollination syndromes, recurring suites of floral traits appearing in connection with specific functional pollinator groups, have served for decades to organise floral diversity under a functional-ecological perspective. Some potential caveats, such as over-simplification of complex plant-animal interactions or lack of empirical observations, have been identified and discussed in recent years. Which of these caveats do indeed cause problems, which have been solved and where do future possibilities lie? I address these questions in a review of the pollination-syndrome literature of 2010 to 2019. I show that the majority of studies was based on detailed empirical pollinator observations and could reliably predict pollinators based on a few floral traits such as colour, shape or reward. Some traits (i.e. colour) were less reliable in predicting pollinators than others (i.e. reward, corolla width), however. I stress that future studies should consider floral traits beyond those traditionally recorded to expand our understanding of mechanisms of floral evolution. I discuss statistical methods suitable for objectively analysing the interplay of system-specific evolutionary constraints, pollinator-mediated selection and adaptive trade-offs at microecological and macroecological scales. I exemplify my arguments on an empirical dataset of floral traits of a neotropical plant radiation in the family Melastomataceae.
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23
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Guo Y, Warner RM. Dissecting genetic diversity and genomic background of Petunia cultivars with contrasting growth habits. HORTICULTURE RESEARCH 2020; 7:155. [PMID: 33082962 PMCID: PMC7528118 DOI: 10.1038/s41438-020-00373-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 05/15/2023]
Abstract
The cultivated petunia (Petunia ×hybrida) is derived from the progenitor species P. axillaris and P. integrifolia. The hybridization dates back only to the 1830s, though intensive breeding efforts have yielded cultivars exhibiting incredible diversity for many traits, including growth habit, flower color, and flower size. Until now, little is known about the genetic diversity and genomic background of modern cultivars. Here we selected a panel of 13 cultivars with contrasting growth habits and three wild species (the progenitors and P. exserta) to estimate the genomic contribution from the ancestral species and to study whether the variation of the genetic origin could be associated with different breeding programs or morphological variability. Transcriptome sequencing identified 1,164,566 SNPs representing 98.4% (32,451) of the transcripts that cover 99.2% (of 52,697,361 bp) of the P. axillaris transcriptome. Cultivars with an upright growth habit had more homozygous alleles and more P. axillaris-derived alleles than trailing cultivars, while mounded cultivars had intermediate heterozygosity. Unlike previous studies, we found the proportions of alleles derived from each progenitor species varied across cultivars but overall were not biased toward one progenitor species, suggesting diverse selection during cultivar development. For trailing cultivars, alleles potentially introgressed from other wild species ("out" alleles) were enriched. The "out" alleles were clustered in particular regions of chromosomes, suggesting that these regions may be hotspots of introgression. Transcripts in these regions were enriched with gene ontology terms associated with growth habit. This study provides novel insight into the contributions of progenitor species to the genomic background of modern petunia cultivars and identifies genome regions that may harbor genes conferring the trailing growth habit for further exploration.
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Affiliation(s)
- Yufang Guo
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Ryan M. Warner
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
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24
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Yarahmadov T, Robinson S, Hanemian M, Pulver V, Kuhlemeier C. Identification of transcription factors controlling floral morphology in wild Petunia species with contrasting pollination syndromes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:289-301. [PMID: 32780443 PMCID: PMC7693086 DOI: 10.1111/tpj.14962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 07/15/2020] [Indexed: 05/29/2023]
Abstract
Adaptation to different pollinators is an important driver of speciation in the angiosperms. Genetic approaches such as QTL mapping have been successfully used to identify the underlying speciation genes. However, these methods are often limited by widespread suppression of recombination due to divergence between species. While the mutations that caused the interspecific differences in floral color and scent have been elucidated in a variety of plant genera, the genes that are responsible for morphological differences remain mostly unknown. Differences in floral organ length determine the pollination efficiency of hawkmoths and hummingbirds, and therefore the genes that control these differences are potential speciation genes. Identifying such genes is challenging, especially in non-model species and when studying complex traits for which little prior genetic and biochemical knowledge is available. Here we combine transcriptomics with detailed growth analysis to identify candidate transcription factors underlying interspecific variation in the styles of Petunia flowers. Starting from a set of 2284 genes, stepwise filtering for expression in styles, differential expression between species, correlation with growth-related traits, allele-specific expression in interspecific hybrids, and/or high-impact polymorphisms resulted in a set of 43 candidate speciation genes. Validation by virus-induced gene silencing identified two MYB transcription factors, EOBI and EOBII, that were previously shown to regulate floral scent emission, a trait associated with pollination by hawkmoths.
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Affiliation(s)
- Tural Yarahmadov
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
- Department of BioMedical ResearchUniversity of BernBernCH‐3008Switzerland
| | - Sarah Robinson
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
- Sainsbury LaboratoryUniversity of CambridgeCambridgeCB2 1LRUK
| | - Mathieu Hanemian
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
- LIPMUniversité de ToulouseINRAECNRSCastanet‐TolosanFrance
| | - Valentin Pulver
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
| | - Cris Kuhlemeier
- Institute of Plant SciencesUniversity of BernAltenbergrain 21BernCH‐3013Switzerland
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25
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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: 5.4] [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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26
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Schnitzler CK, Turchetto C, Teixeira MC, Freitas LB. What could be the fate of secondary contact zones between closely related plant species? Genet Mol Biol 2020; 43:e20190271. [PMID: 32556035 PMCID: PMC7299303 DOI: 10.1590/1678-4685-gmb-2019-0271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 03/24/2020] [Indexed: 11/26/2022] Open
Abstract
Interspecific hybridization has been fundamental in plant evolution.
Nevertheless, the fate of hybrid zones throughout the generations remains poorly
addressed. We analyzed a pair of recently diverged, interfertile, and sympatric
Petunia species to ask what fate the interspecific hybrid
population has met over time. We analyzed the genetic diversity in two
generations from two contact sites and evaluated the effect of introgression. To
do this, we collected all adult plants from the contact zones, including
canonicals and intermediary colored individuals, and compared them with purebred
representatives of both species based on seven highly informative microsatellite
loci. We compared the genetic diversity observed in the contact zones with what
is seen in isolated populations of each species, considering two generations of
these annual species. Our results have confirmed the genetic differentiation
between the species and the hybrid origin of the majority of the intermediary
colored individuals. We also observed a differentiation related to genetic
variability and inbreeding levels among the populations. Over time, there were
no significant differences per site related to genetic diversity or phenotype
composition. We found two stable populations kept by high inbreeding and
backcross rates that influence the genetic diversity of their parental species
through introgression.
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Affiliation(s)
- Carolina K Schnitzler
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Caroline Turchetto
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Marcelo C Teixeira
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Evolução Molecular, Porto Alegre, RS, Brazil
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27
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Hämälä T, Gorton AJ, Moeller DA, Tiffin P. Pleiotropy facilitates local adaptation to distant optima in common ragweed (Ambrosia artemisiifolia). PLoS Genet 2020; 16:e1008707. [PMID: 32210431 PMCID: PMC7135370 DOI: 10.1371/journal.pgen.1008707] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/06/2020] [Accepted: 03/05/2020] [Indexed: 12/23/2022] Open
Abstract
Pleiotropy, the control of multiple phenotypes by a single locus, is expected to slow the rate of adaptation by increasing the chance that beneficial alleles also have deleterious effects. However, a prediction arising from classical theory of quantitative trait evolution states that pleiotropic alleles may have a selective advantage when phenotypes are distant from their selective optima. We examine the role of pleiotropy in regulating adaptive differentiation among populations of common ragweed (Ambrosia artemisiifolia); a species that has recently expanded its North American range due to human-mediated habitat change. We employ a phenotype-free approach by using connectivity in gene networks as a proxy for pleiotropy. First, we identify loci bearing footprints of local adaptation, and then use genotype-expression mapping and co-expression networks to infer the connectivity of the genes. Our results indicate that the putatively adaptive loci are highly pleiotropic, as they are more likely than expected to affect the expression of other genes, and they reside in central positions within the gene networks. We propose that the conditionally advantageous alleles at these loci avoid the cost of pleiotropy by having large phenotypic effects that are beneficial when populations are far from their selective optima. We further use evolutionary simulations to show that these patterns are in agreement with a model where populations face novel selective pressures, as expected during a range expansion. Overall, our results suggest that highly connected genes may be targets of positive selection during environmental change, even though they likely experience strong purifying selection in stable selective environments.
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Affiliation(s)
- Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Amanda J. Gorton
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, Minnesota, United States of America
| | - David A. Moeller
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America
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Babiychuk E, Teixeira JG, Tyski L, Guimaraes JTF, Romeiro LA, da Silva EF, Dos Santos JF, Vasconcelos S, da Silva DF, Castilho A, Siqueira JO, Fonseca VLI, Kushnir S. Geography is essential for reproductive isolation between florally diversified morning glory species from Amazon canga savannahs. Sci Rep 2019; 9:18052. [PMID: 31792228 PMCID: PMC6889514 DOI: 10.1038/s41598-019-53853-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 11/06/2019] [Indexed: 11/29/2022] Open
Abstract
The variety, relative importance and eco-evolutionary stability of reproductive barriers are critical to understanding the processes of speciation and species persistence. Here we evaluated the strength of the biotic prezygotic and postzygotic isolation barriers between closely related morning glory species from Amazon canga savannahs. The flower geometry and flower visitor assemblage analyses supported pollination by the bees in lavender-flowered Ipomoea marabaensis and recruitment of hummingbirds as pollinators in red-flowered Ipomoea cavalcantei. Nevertheless, native bee species and alien honeybees foraged on flowers of both species. Real-time interspecific hybridization underscored functionality of the overlap in flower visitor assemblages, questioning the strength of prezygotic isolation underpinned by diversification in flower colour and geometry. Interspecific hybrids were fertile and produced offspring in nature. No significant asymmetry in interspecific hybridization and hybrid incompatibilities among offspring were found, indicating weak postmating and postzygotic isolation. The results suggested that despite floral diversification, the insular-type geographic isolation remains a major barrier to gene flow. Findings set a framework for the future analysis of contemporary evolution of plant-pollinator networks at the population, community, and ecosystem levels in tropical ecosystems that are known to be distinct from the more familiar temperate climate models.
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Affiliation(s)
- Elena Babiychuk
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil.
| | | | - Lourival Tyski
- Parque Zoobotânico Vale, VALE S.A., Rod. Raimundo Mascarenhas, Km 26, S/N., Núcleo Urbano de Carajás, CEP 68516-000, Parauapebas, Pará, Brazil
| | | | - Luiza Araújo Romeiro
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil
| | | | | | - Santelmo Vasconcelos
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil
| | - Delmo Fonseca da Silva
- Parque Zoobotânico Vale, VALE S.A., Rod. Raimundo Mascarenhas, Km 26, S/N., Núcleo Urbano de Carajás, CEP 68516-000, Parauapebas, Pará, Brazil
| | - Alexandre Castilho
- Gerência de Meio Ambiente, Departamento de Ferrosos Corredor Norte, Vale S.A., Rua Guamá n 60, Núcleo Urbano, CEP 68516-000, Parauapebas, Pará, Brazil
| | - José Oswaldo Siqueira
- Instituto Tecnológico Vale, Rua Boaventura da Silva 955, CEP 66055-090, Belém, Pará, Brazil
| | | | - Sergei Kushnir
- Unaffiliated, Belém, Pará, Brazil.,Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12, Ireland
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Saenko SV, Chouteau M, Piron-Prunier F, Blugeon C, Joron M, Llaurens V. Unravelling the genes forming the wing pattern supergene in the polymorphic butterfly Heliconius numata. EvoDevo 2019; 10:16. [PMID: 31406559 PMCID: PMC6686539 DOI: 10.1186/s13227-019-0129-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/12/2019] [Indexed: 11/25/2022] Open
Abstract
Background Unravelling the genetic basis of polymorphic characters is central to our understanding of the origins and diversification of living organisms. Recently, supergenes have been implicated in a wide range of complex polymorphisms, from adaptive colouration in butterflies and fish to reproductive strategies in birds and plants. The concept of a supergene is now a hot topic in biology, and identification of its functional elements is needed to shed light on the evolution of highly divergent adaptive traits. Here, we apply different gene expression analyses to study the supergene P that controls polymorphism of mimetic wing colour patterns in the neotropical butterfly Heliconius numata. Results We performed de novo transcriptome assembly and differential expression analyses using high-throughput Illumina RNA sequencing on developing wing discs of different H. numata morphs. Within the P interval, 30 and 17 of the 191 transcripts were expressed differentially in prepupae and day-1 pupae, respectively. Among these is the gene cortex, known to play a role in wing pattern formation in Heliconius and other Lepidoptera. Our in situ hybridization experiments confirmed the relationship between cortex expression and adult wing patterns. Conclusions This study found the majority of genes in the P interval to be expressed in the developing wing discs during the critical stages of colour pattern formation, and detect drastic changes in expression patterns in multiple genes associated with structural variants. The patterns of expression of cortex only partially recapitulate the variation in adult phenotype, suggesting that the remaining phenotypic variation could be controlled by other genes within the P interval. Although functional studies on cortex are now needed to determine its exact developmental role, our results are in accordance with the classical supergene hypothesis, whereby several genes inherited together due to tight linkage control a major developmental switch. Electronic supplementary material The online version of this article (10.1186/s13227-019-0129-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Suzanne V Saenko
- 1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France
| | - Mathieu Chouteau
- 2Laboratoire Ecologie, Evolution, Interactions Des Systèmes Amazoniens (LEEISA), USR 3456, CNRS Guyane, Université De Guyane, 275 route de Montabo, 97334 Cayenne, French Guiana
| | - Florence Piron-Prunier
- 1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France
| | - Corinne Blugeon
- Genomic Facility, Institut de Biologie de l'Ecole normale superieure (IBENS), École normale supérieure, CNRS, INSERM, PSL Université Paris, 75005 Paris, France
| | - Mathieu Joron
- 4Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS-Université de Montpellier, École Pratique des Hautes Études, Université Paul Valéry, 34293 Montpellier 5, France
| | - Violaine Llaurens
- 1Institut de Systématique, Evolution et Biodiversité, UMR 7205 (CNRS, MNHN, Sorbonne Université, EPHE), Muséum National d'Histoire Naturelle CP50, 57 rue Cuvier, 75005 Paris, France
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Kostyun JL, Gibson MJS, King CM, Moyle LC. A simple genetic architecture and low constraint allow rapid floral evolution in a diverse and recently radiating plant genus. THE NEW PHYTOLOGIST 2019; 223:1009-1022. [PMID: 30972773 DOI: 10.1111/nph.15844] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Genetic correlations among different components of phenotypes, especially those resulting from pleiotropy, can constrain or facilitate trait evolution. These factors could especially influence the evolution of traits that are functionally integrated, such as those comprising the flower. Indeed, pleiotropy is proposed as a main driver of repeated convergent trait transitions, including the evolution of phenotypically similar pollinator syndromes. We assessed the role of pleiotropy in the differentiation of floral and other reproductive traits between two species - Jaltomata sinuosa and J. umbellata (Solanaceae) - that have divergent suites of floral traits consistent with bee and hummingbird pollination, respectively. To do so, we generated a hybrid population and examined the genetic architecture (trait segregation and quantitative trait locus (QTL) distribution) underlying 25 floral and fertility traits. We found that most floral traits had a relatively simple genetic basis (few, predominantly additive, QTLs of moderate to large effect), as well as little evidence of antagonistic pleiotropy (few trait correlations and QTL colocalization, particularly between traits of different classes). However, we did detect a potential case of adaptive pleiotropy among floral size and nectar traits. These mechanisms may have facilitated the rapid floral trait evolution observed within Jaltomata, and may be a common component of rapid phenotypic change more broadly.
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Affiliation(s)
- Jamie L Kostyun
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Plant Biology, The University of Vermont, Burlington, VT, 05405, USA
| | | | - Christian M King
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA
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Trevoy SAL, Janes JK, Muirhead K, Sperling FAH. Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle ( Dendroctonus ponderosae). Ecol Evol 2019; 9:1147-1159. [PMID: 30805148 PMCID: PMC6374669 DOI: 10.1002/ece3.4803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 11/20/2018] [Accepted: 11/21/2018] [Indexed: 12/11/2022] Open
Abstract
Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome-wide single-nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted resampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principal components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex-linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research.
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Affiliation(s)
| | - Jasmine K. Janes
- School of Environmental & Rural SciencesUniversity of New EnglandArmidaleNew South WalesAustralia
- Biology DepartmentVancouver Island UniversityNanaimoBritish ColumbiaCanada
| | - Kevin Muirhead
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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Plus ça change, plus c'est la même chose: The developmental evolution of flowers. Curr Top Dev Biol 2019; 131:211-238. [DOI: 10.1016/bs.ctdb.2018.11.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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The Genetics of a Behavioral Speciation Phenotype in an Island System. Genes (Basel) 2018; 9:genes9070346. [PMID: 29996514 PMCID: PMC6070818 DOI: 10.3390/genes9070346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/30/2022] Open
Abstract
Mating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variations in the crickets Laupala eukolea and Laupala cerasina, which occur on different islands (Maui and Hawaii). We then compare these results with a similar study of an independently evolving species pair that diverged within the same island. Finally, we annotate the L. cerasina transcriptome and test whether the QTL fall in functionally enriched genomic regions. We document a polygenic architecture behind the song rhythm divergence in the inter-island species pair that is remarkably similar to that previously found for an intra-island species pair in the same genus. Importantly, the QTL regions were significantly enriched for potential homologs of the genes involved in pathways that may be modulating the cricket song rhythm. These clusters of loci could constrain the spatial genomic distribution of the genetic variation underlying the cricket song variation and harbor several candidate genes that merit further study.
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Roesti M. Varied Genomic Responses to Maladaptive Gene Flow and Their Evidence. Genes (Basel) 2018; 9:E298. [PMID: 29899287 PMCID: PMC6027369 DOI: 10.3390/genes9060298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/17/2018] [Accepted: 05/30/2018] [Indexed: 12/02/2022] Open
Abstract
Adaptation to a local environment often occurs in the face of maladaptive gene flow. In this perspective, I discuss several ideas on how a genome may respond to maladaptive gene flow during adaptation. On the one hand, selection can build clusters of locally adaptive alleles at fortuitously co-localized loci within a genome, thereby facilitating local adaptation with gene flow ('allele-only clustering'). On the other hand, the selective pressure to link adaptive alleles may drive co-localization of the actual loci relevant for local adaptation within a genome through structural genome changes or an evolving intra-genomic crossover rate ('locus clustering'). While the expected outcome is, in both cases, a higher frequency of locally adaptive alleles in some genome regions than others, the molecular units evolving in response to gene flow differ (i.e., alleles versus loci). I argue that, although making this distinction is important, we commonly lack the critical empirical evidence to do so. This is mainly because many current approaches are biased towards detecting local adaptation in genome regions with low crossover rates. The importance of low-crossover genome regions for adaptation with gene flow, such as in co-localizing relevant loci within a genome, thus remains unclear. Future empirical investigations should address these questions by making use of comparative genomics, where multiple de novo genome assemblies from species evolved under different degrees of genetic exchange are compared. This research promises to advance our understanding of how a genome adapts to maladaptive gene flow, thereby promoting adaptive divergence and reproductive isolation.
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Affiliation(s)
- Marius Roesti
- Biodiversity Research Centre and Zoology Department, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Genetic Dissection of a Supergene Implicates Tfap2a in Craniofacial Evolution of Threespine Sticklebacks. Genetics 2018; 209:591-605. [PMID: 29593029 DOI: 10.1534/genetics.118.300760] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 03/26/2018] [Indexed: 02/07/2023] Open
Abstract
In nature, multiple adaptive phenotypes often coevolve and can be controlled by tightly linked genetic loci known as supergenes. Dissecting the genetic basis of these linked phenotypes is a major challenge in evolutionary genetics. Multiple freshwater populations of threespine stickleback fish (Gasterosteus aculeatus) have convergently evolved two constructive craniofacial traits, longer branchial bones and increased pharyngeal tooth number, likely as adaptations to dietary differences between marine and freshwater environments. Prior QTL mapping showed that both traits are partially controlled by overlapping genomic regions on chromosome 21 and that a regulatory change in Bmp6 likely underlies the tooth number QTL. Here, we mapped the branchial bone length QTL to a 155 kb, eight-gene interval tightly linked to, but excluding the coding regions of Bmp6 and containing the candidate gene Tfap2a Further recombinant mapping revealed this bone length QTL is separable into at least two loci. During embryonic and larval development, Tfap2a was expressed in the branchial bone primordia, where allele specific expression assays revealed the freshwater allele of Tfap2a was expressed at lower levels relative to the marine allele in hybrid fish. Induced loss-of-function mutations in Tfap2a revealed an essential role in stickleback craniofacial development and show that bone length is sensitive to Tfap2a dosage in heterozygotes. Combined, these results suggest that closely linked but genetically separable changes in Bmp6 and Tfap2a contribute to a supergene underlying evolved skeletal gain in multiple freshwater stickleback populations.
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Abstract
Pollinator-mediated selection on plants can favor transitions to a new pollinator depending on the relative abundances and efficiencies of pollinators present in the community. A frequently observed example is the transition from bee pollination to hummingbird pollination. We present a population genetic model that examines whether the ability to inbreed can influence evolutionary change in traits that underlie pollinator attraction. We find that a transition to a more efficient but less abundant pollinator is favored under a broadened set of ecological conditions if plants are capable of delayed selfing rather than obligately outcrossing. Delayed selfing allows plants carrying an allele that attracts the novel pollinator to reproduce even when this pollinator is rare, providing reproductive assurance. In addition, delayed selfing weakens the effects of Haldane's sieve by increasing the fixation probability for recessive alleles that confer adaptation to the new pollinator. Our model provides novel insight into the paradoxical abundance of recessive mutations in adaptation to hummingbird attraction. It further predicts that transitions to efficient but less abundant pollinators (such as hummingbirds in certain communities) should disproportionately occur in self-compatible lineages. Currently available mating system data sets are consistent with this prediction, and we suggest future areas of research that will enable a rigorous test of this theory.
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Reimegård J, Kundu S, Pendle A, Irish VF, Shaw P, Nakayama N, Sundström JF, Emanuelsson O. Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana. Nucleic Acids Res 2017; 45:3253-3265. [PMID: 28175342 PMCID: PMC5389543 DOI: 10.1093/nar/gkx087] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 01/31/2017] [Indexed: 12/02/2022] Open
Abstract
Co-expression of physically linked genes occurs surprisingly frequently in eukaryotes. Such chromosomal clustering may confer a selective advantage as it enables coordinated gene regulation at the chromatin level. We studied the chromosomal organization of genes involved in male reproductive development in Arabidopsis thaliana. We developed an in-silico tool to identify physical clusters of co-regulated genes from gene expression data. We identified 17 clusters (96 genes) involved in stamen development and acting downstream of the transcriptional activator MS1 (MALE STERILITY 1), which contains a PHD domain associated with chromatin re-organization. The clusters exhibited little gene homology or promoter element similarity, and largely overlapped with reported repressive histone marks. Experiments on a subset of the clusters suggested a link between expression activation and chromatin conformation: qRT-PCR and mRNA in situ hybridization showed that the clustered genes were up-regulated within 48 h after MS1 induction; out of 14 chromatin-remodeling mutants studied, expression of clustered genes was consistently down-regulated only in hta9/hta11, previously associated with metabolic cluster activation; DNA fluorescence in situ hybridization confirmed that transcriptional activation of the clustered genes was correlated with open chromatin conformation. Stamen development thus appears to involve transcriptional activation of physically clustered genes through chromatin de-condensation.
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Affiliation(s)
- Johan Reimegård
- Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Solna SE-171 65, Sweden
| | - Snehangshu Kundu
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Ali Pendle
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Vivian F Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Peter Shaw
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Naomi Nakayama
- Institute of Molecular Plant Science, SynthSys Centre for Synthetic and Systems Biology, and Centre for Science at Extreme Conditions, University of Edinburgh, King's Buildings, Edinburgh, UK
| | - Jens F Sundström
- Department of Plant Biology, Uppsala BioCenter, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Uppsala SE-750 07, Sweden
| | - Olof Emanuelsson
- Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, KTH Royal Institute of Technology, Solna SE-171 65, Sweden
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Fernández-Mazuecos M, Glover BJ. The evo-devo of plant speciation. Nat Ecol Evol 2017; 1:110. [DOI: 10.1038/s41559-017-0110] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/07/2017] [Indexed: 11/09/2022]
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40
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Llaurens V, Whibley A, Joron M. Genetic architecture and balancing selection: the life and death of differentiated variants. Mol Ecol 2017; 26:2430-2448. [PMID: 28173627 DOI: 10.1111/mec.14051] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023]
Abstract
Balancing selection describes any form of natural selection, which results in the persistence of multiple variants of a trait at intermediate frequencies within populations. By offering up a snapshot of multiple co-occurring functional variants and their interactions, systems under balancing selection can reveal the evolutionary mechanisms favouring the emergence and persistence of adaptive variation in natural populations. We here focus on the mechanisms by which several functional variants for a given trait can arise, a process typically requiring multiple epistatic mutations. We highlight how balancing selection can favour specific features in the genetic architecture and review the evolutionary and molecular mechanisms shaping this architecture. First, balancing selection affects the number of loci underlying differentiated traits and their respective effects. Control by one or few loci favours the persistence of differentiated functional variants by limiting intergenic recombination, or its impact, and may sometimes lead to the evolution of supergenes. Chromosomal rearrangements, particularly inversions, preventing adaptive combinations from being dissociated are increasingly being noted as features of such systems. Similarly, due to the frequency of heterozygotes maintained by balancing selection, dominance may be a key property of adaptive variants. High heterozygosity and limited recombination also influence associated genetic load, as linked recessive deleterious mutations may be sheltered. The capture of deleterious elements in a locus under balancing selection may reinforce polymorphism by further promoting heterozygotes. Finally, according to recent genomewide scans, balanced polymorphism might be more pervasive than generally thought. We stress the need for both functional and ecological studies to characterize the evolutionary mechanisms operating in these systems.
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Affiliation(s)
- Violaine Llaurens
- Institut de Systématique Evolution et Biodiversité (UMR 7205 CNRS, MNHN, UPMC, EPHE), Muséum National d'Histoire Naturelle - CP50, 45 rue Buffon, 75005, Paris, France
| | - Annabel Whibley
- Cell and Developmental Biology, John Innes Centre, Norwich, Norfolk, NR4 7UH, UK
| | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive (UMR 5175 CNRS, Université de Montpellier, Université Paul Valéry Montpellier, EPHE), 1919 route de Mende, 34293, Montpellier, France
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Saltz JB, Hessel FC, Kelly MW. Trait Correlations in the Genomics Era. Trends Ecol Evol 2017; 32:279-290. [PMID: 28139251 DOI: 10.1016/j.tree.2016.12.008] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 01/30/2023]
Abstract
Thinking about the evolutionary causes and consequences of trait correlations has been dominated by quantitative genetics theory that is focused on hypothetical loci. Since this theory was initially developed, technology has enabled the identification of specific genetic variants that contribute to trait correlations. Here, we review studies of the genetic basis of trait correlations to ask: What has this new information taught us? We find that causal variants can be pleiotropic and/or linked in different ways, indicating that pleiotropy and linkage are not alternative genetic mechanisms. Further, many trait correlations have a polygenic basis, suggesting that both pleiotropy and linkage likely contribute. We discuss implications of these findings for the evolutionary causes and consequences of trait correlations.
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Affiliation(s)
- Julia B Saltz
- Rice University,6100 Main Street, Houston, TX 77005, USA.
| | - Frances C Hessel
- Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Morgan W Kelly
- Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
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Ruiz-Hernández V, Hermans B, Weiss J, Egea-Cortines M. Genetic Analysis of Natural Variation in Antirrhinum Scent Profiles Identifies BENZOIC ACID CARBOXYMETHYL TRANSFERASE As the Major Locus Controlling Methyl Benzoate Synthesis. FRONTIERS IN PLANT SCIENCE 2017; 8:27. [PMID: 28154577 PMCID: PMC5244254 DOI: 10.3389/fpls.2017.00027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 01/05/2017] [Indexed: 05/31/2023]
Abstract
The Antirrhinum genus has a considerable complexity in the scent profiles produced by different species. We have analyzed the genetic differences between A. majus and A. linkianum, two species divergent in the emission of methyl benzoate, methyl cinnamate, acetophenone, and ocimene. The genetic analysis showed that all compounds segregated in a Mendelian fashion attributable to one or two loci with simple or epistatic interactions. Several lines lacked methyl benzoate, a major Volatile Organic Compound emitted by A. majus but missing in A. linkianum. Using a candidate gene approach, we found that the BENZOIC ACID CARBOXYMETHYL TRANSFERASE from A. linkianum appeared to be a null allele as we could not detect mRNA expression. The coding region did not show significant differences that could explain the loss of expression. The intron-exon boundaries was also conserved indicating that there is no alternative splicing in A. linkianum as compared to A. majus. However, it showed multiple polymorphisms in the 5' promoter region including two insertions, one harboring an IDLE MITE transposon with additional sequences with high homology to the PLENA locus and a second one with somewhat lower homology to the regulatory region of the VENOSA locus. It also had a 778 bp deletion as compared to the A. majus BAMT promoter region. Our results show that the differences in scent emission between A. majus and A. linkianum may be traced back to single genes involved in discrete biosynthetic reactions such as benzoic acid methylation. Thus, natural variation of this complex trait maybe the result of combinations of wild type, and loss of function alleles in different genes involved in discrete VOCs biosynthesis. Furthermore, the presence of active transposable elements in the genus may account for rapid evolution and instability, raising the possibility of adaptation to local pollinators.
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Amrad A, Moser M, Mandel T, de Vries M, Schuurink RC, Freitas L, Kuhlemeier C. Gain and Loss of Floral Scent Production through Changes in Structural Genes during Pollinator-Mediated Speciation. Curr Biol 2016; 26:3303-3312. [PMID: 27916524 DOI: 10.1016/j.cub.2016.10.023] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
Abstract
The interactions of plants with their pollinators are thought to be a driving force in the evolution of angiosperms. Adaptation to a new pollinator involves coordinated changes in multiple floral traits controlled by multiple genes. Surprisingly, such complex genetic shifts have happened numerous times during evolution. Here we report on the genetic basis of the changes in one such trait, floral scent emission, in the genus Petunia (Solanaceae). The increase in the quantity and complexity of the volatiles during the shift from bee to hawkmoth pollination was due to de novo expression of the genes encoding benzoic acid/salicylic acid carboxyl methyltransferase (BSMT) and benzoyl-CoA:benzylalcohol/2-phenylethanol benzoyltransferase (BPBT) together with moderately increased transcript levels for most enzymes of the phenylpropanoid/benzenoid pathway. Loss of cinnamate-CoA ligase (CNL) function as well as a reduction in the expression of the MYB transcription factor ODO1 explain the loss of scent during the transition from moth to hummingbird pollination. The CNL gene in the hummingbird-adapted species is inactive due to a stop codon, but also appears to have undergone further degradation over time. Therefore, we propose that loss of scent happened relatively early in the transition toward hummingbird pollination, and probably preceded the loss of UV-absorbing flavonols. The discovery that CNL is also involved in the loss of scent during the transition from outcrossing to selfing in Capsella (Brassicaceae) (see the accompanying paper) raises interesting questions about the possible causes of deep evolutionary conservation of the targets of evolutionary change.
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Affiliation(s)
- Avichai Amrad
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Michel Moser
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Therese Mandel
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Michel de Vries
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Robert C Schuurink
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Loreta Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, P.O. Box 15053, Avenida Bento Goncalves, 9500 Porto Alegre, Brazil
| | - Cris Kuhlemeier
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland.
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44
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Cai J, Zu P, Schiestl FP. The molecular bases of floral scent evolution under artificial selection: insights from a transcriptome analysis in Brassica rapa. Sci Rep 2016; 6:36966. [PMID: 27841366 PMCID: PMC5107913 DOI: 10.1038/srep36966] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 10/13/2016] [Indexed: 12/24/2022] Open
Abstract
In an artificial selection experiment using fast-cycling Brassica rapa plants it was recently shown that floral VOCs respond rapidly to selection for increased amounts. Here we carried out transcriptome analysis in these plants to explore the molecular bases of the augmentation in the artificially selected scent compound, phenylacetaldehyde (PAA), as well as other compounds that increased through pleiotropy. In the transcriptome data, we found up-regulation of genes likely underlying PAA synthesis, but also several genes of the shikimate pathway and the related phenylalanine metabolism. As phenylalanine is the precursor of many aromatic volatiles that showed increased emission, this result could explain some of the pleiotropic evolutionary responses. In addition, we found that ribosomal protein genes were up-regulated in “high” (high PAA amount) selection line plants, a mechanism that might further augment the effect of elevated gene expression at the proteomic level. Our study shows that selection on an individual trait can impose changes in the expression of several different genes, which could explain pleiotropic responses in the biosynthetic network of floral volatiles.
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Affiliation(s)
- Jing Cai
- Department of Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Pengjuan Zu
- Department of Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
| | - Florian P Schiestl
- Department of Systematic and Evolutionary Botany, University of Zürich, Zollikerstrasse 107, CH-8008 Zürich, Switzerland
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45
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Gates DJ, Strickler SR, Mueller LA, Olson BJSC, Smith SD. Diversification of R2R3-MYB Transcription Factors in the Tomato Family Solanaceae. J Mol Evol 2016; 83:26-37. [PMID: 27364496 DOI: 10.1007/s00239-016-9750-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 06/15/2016] [Indexed: 11/26/2022]
Abstract
MYB transcription factors play an important role in regulating key plant developmental processes involving defense, cell shape, pigmentation, and root formation. Within this gene family, sequences containing an R2R3 MYB domain are the most abundant type and exhibit a wide diversity of functions. In this study, we identify 559 R2R3 MYB genes using whole genome data from four species of Solanaceae and reconstruct their evolutionary relationships. We compare the Solanaceae R2R3 MYBs to the well-characterized Arabidopsis thaliana sequences to estimate functional diversity and to identify gains and losses of MYB clades in the Solanaceae. We identify numerous R2R3 MYBs that do not appear closely related to Arabidopsis MYBs, and thus may represent clades of genes that have been lost along the Arabidopsis lineage or gained after the divergence of Rosid and Asterid lineages. Despite differences in the distribution of R2R3 MYBs across functional subgroups and species, the overall size of the R2R3 subfamily has changed relatively little over the roughly 50 million-year history of Solanaceae. We added our information regarding R2R3 MYBs in Solanaceae to other data and performed a meta-analysis to trace the evolution of subfamily size across land plants. The results reveal many shifts in the number of R2R3 genes, including a 54 % increase along the angiosperm stem lineage. The variation in R2R3 subfamily size across land plants is weakly positively correlated with genome size and strongly positively correlated with total number of genes. The retention of such a large number of R2R3 copies over long evolutionary time periods suggests that they have acquired new functions and been maintained by selection. Discovering the nature of this functional diversity will require integrating forward and reverse genetic approaches on an -omics scale.
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Affiliation(s)
- Daniel J Gates
- School of Biological Sciences, University of Nebraska, Lincoln, 68588, USA.
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, USA.
| | | | - Lukas A Mueller
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Bradley J S C Olson
- Division of Molecular, Cellular and Developmental Biology, Kansas State University, Manhattan,, KS, 66506, USA
| | - Stacey D Smith
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, 80309, USA
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46
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Byers KJRP, Xu S, Schlüter PM. Molecular mechanisms of adaptation and speciation: why do we need an integrative approach? Mol Ecol 2016; 26:277-290. [DOI: 10.1111/mec.13678] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 04/18/2016] [Accepted: 04/21/2016] [Indexed: 01/06/2023]
Affiliation(s)
- Kelsey J. R. P. Byers
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
| | - Shuqing Xu
- Max Planck Institute for Chemical Ecology; Hans-Knöll-Straße 8 D-07745 Jena Germany
| | - Philipp M. Schlüter
- Department of Systematic and Evolutionary Botany; University of Zurich; Zollikerstrasse 107 CH-8008 Zurich Switzerland
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47
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Wessinger CA, Hileman LC. Accessibility, constraint, and repetition in adaptive floral evolution. Dev Biol 2016; 419:175-183. [PMID: 27153988 DOI: 10.1016/j.ydbio.2016.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
Adaptive phenotypic evolution is shaped by natural selection on multiple organismal traits as well as by genetic correlations among traits. Genetic correlations can arise through pleiotropy and can bias the production of phenotypic variation to certain combinations of traits. This phenomenon is referred to as developmental bias or constraint. Developmental bias may accelerate or constrain phenotypic evolution, depending on whether selection acts parallel or in opposition to genetic correlations among traits. We discuss examples from floral evolution where genetic correlations among floral traits contribute to rapid, coordinated evolution in multiple floral organ phenotypes and suggest future research directions that will explore the relationship between the genetic basis of adaptation and the pre-existing structure of genetic correlations. On the other hand, natural selection may act perpendicular to a strong genetic correlation, for example when two traits are encoded by a subset of the same genes and natural selection favors change in one trait and stability in the second trait. In such cases, adaptation is constrained by the availability of genetic variation that can influence the focal trait with minimal pleiotropic effects. Examples from plant diversification suggest that the origin of certain adaptations depends on the prior evolution of a gene copy with reduced pleiotropic effects, generated through the process of gene duplication followed by subfunctionalization or neofunctionalization. A history of gene duplication in some developmental pathways appears to have allowed particular flowering plant linages to have repeatedly evolved adaptations that might otherwise have been developmentally constrained.
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Affiliation(s)
- Carolyn A Wessinger
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66044, United States.
| | - Lena C Hileman
- Department of Ecology and Evolutionary Biology, University of Kansas, 1200 Sunnyside Avenue, Lawrence, KS 66044, United States.
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48
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Lee YW, Fishman L, Kelly JK, Willis JH. A Segregating Inversion Generates Fitness Variation in Yellow Monkeyflower (Mimulus guttatus). Genetics 2016; 202:1473-84. [PMID: 26868767 PMCID: PMC4905537 DOI: 10.1534/genetics.115.183566] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/01/2016] [Indexed: 11/18/2022] Open
Abstract
Polymorphic chromosomal rearrangements can bind hundreds of genes into single genetic loci with diverse effects. Rearrangements are often associated with local adaptation and speciation and may also be an important component of genetic variation within populations. We genetically and phenotypically characterize a segregating inversion (inv6) in the Iron Mountain (IM) population of Mimulus guttatus (yellow monkeyflower). We initially mapped inv6 as a region of recombination suppression in three F2 populations resulting from crosses among IM plants. In each case, the F1 parent was heterozygous for a derived haplotype, homogenous across markers spanning over 5 Mb of chromsome 6. In the three F2 populations, inv6 reduced male and female fitness components. In addition,i nv6 carriers suffered an ∼30% loss of pollen viability in the field. Despite these costs, inv6 exists at moderate frequency (∼8%) in the natural population, suggesting counterbalancing fitness benefits that maintain the polymorphism. Across 4 years of monitoring in the field, inv6 had an overall significant positive effect on seed production (lifetime female fitness) of carriers. This benefit was particularly strong in harsh years and may be mediated (in part) by strong positive effects on flower production. These data suggest that opposing fitness effects maintain an intermediate frequency, and as a consequence, inv6 generates inbreeding depression and high genetic variance. We discuss these findings in relation to the theory of inbreeding depression and the maintenance of fitness variation.
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Affiliation(s)
- Young Wha Lee
- Biology Department, Duke University, Durham, North Carolina 27708
| | - Lila Fishman
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas 66045
| | - John H Willis
- Biology Department, Duke University, Durham, North Carolina 27708
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49
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Lafon-Placette C, Vallejo-Marín M, Parisod C, Abbott RJ, Köhler C. Current plant speciation research: unravelling the processes and mechanisms behind the evolution of reproductive isolation barriers. THE NEW PHYTOLOGIST 2016; 209:29-33. [PMID: 26625345 DOI: 10.1111/nph.13756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- Clément Lafon-Placette
- Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala BioCenter, Uppsala, SE-75007, Sweden
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, UK
| | - Christian Parisod
- Laboratory of Evolutionary Botany, Institute of Biology, University of Neuchâtel, Neuchâtel, CH-2000, Switzerland
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Claudia Köhler
- Swedish University of Agricultural Sciences and Linnean Center of Plant Biology, Uppsala BioCenter, Uppsala, SE-75007, Sweden
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50
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Prinsi B, Negri AS, Quattrocchio FM, Koes RE, Espen L. Proteomics of red and white corolla limbs in petunia reveals a novel function of the anthocyanin regulator ANTHOCYANIN1 in determining flower longevity. J Proteomics 2016; 131:38-47. [DOI: 10.1016/j.jprot.2015.10.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 09/23/2015] [Accepted: 10/08/2015] [Indexed: 01/11/2023]
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