151
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Brandvain Y, Wright SI. The Limits of Natural Selection in a Nonequilibrium World. Trends Genet 2016; 32:201-210. [PMID: 26874998 DOI: 10.1016/j.tig.2016.01.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/23/2015] [Accepted: 01/19/2016] [Indexed: 11/19/2022]
Abstract
Evolutionary theory predicts that factors such as a small population size or low recombination rate can limit the action of natural selection. The emerging field of comparative population genomics offers an opportunity to evaluate these hypotheses. However, classical theoretical predictions assume that populations are at demographic equilibrium. This assumption is likely to be violated in the very populations researchers use to evaluate selection's limits: populations that have experienced a recent shift in population size and/or effective recombination rates. Here we highlight theory and data analyses concerning limitations on the action of natural selection in nonequilibrial populations and argue that substantial care is needed to appropriately test whether species and populations show meaningful differences in selection efficacy. A move toward model-based inferences that explicitly incorporate nonequilibrium dynamics provides a promising approach to more accurately contrast selection efficacy across populations and interpret its significance.
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Affiliation(s)
- Yaniv Brandvain
- Department of Plant Biology, University of Minnesota, St Paul, MN 55108, USA
| | - Stephen I Wright
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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152
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Abstract
Many groups of closely related species have reticulate phylogenies. Recent genomic analyses are showing this in many insects and vertebrates, as well as in microbes and plants. In microbes, lateral gene transfer is the dominant process that spoils strictly tree-like phylogenies, but in multicellular eukaryotes hybridization and introgression among related species is probably more important. Because many species, including the ancestors of ancient major lineages, seem to evolve rapidly in adaptive radiations, some sexual compatibility may exist among them. Introgression and reticulation can thereby affect all parts of the tree of life, not just the recent species at the tips. Our understanding of adaptive evolution, speciation, phylogenetics, and comparative biology must adapt to these mostly recent findings. Introgression has important practical implications as well, not least for the management of genetically modified organisms in pest and disease control.
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Affiliation(s)
- James Mallet
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
- Department of Genetics, Evolution and EnvironmentUniversity College LondonLondonUK
| | - Nora Besansky
- Department of Biological Sciences and Eck Institute for Global HealthUniversity of Notre DameNotre DameINUSA
| | - Matthew W. Hahn
- Department of Biology and School of Informatics and ComputingIndiana UniversityBloomingtonINUSA
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153
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Davey JW, Chouteau M, Barker SL, Maroja L, Baxter SW, Simpson F, Merrill RM, Joron M, Mallet J, Dasmahapatra KK, Jiggins CD. Major Improvements to the Heliconius melpomene Genome Assembly Used to Confirm 10 Chromosome Fusion Events in 6 Million Years of Butterfly Evolution. G3 (BETHESDA, MD.) 2016; 6:695-708. [PMID: 26772750 PMCID: PMC4777131 DOI: 10.1534/g3.115.023655] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/06/2016] [Indexed: 12/30/2022]
Abstract
The Heliconius butterflies are a widely studied adaptive radiation of 46 species spread across Central and South America, several of which are known to hybridize in the wild. Here, we present a substantially improved assembly of the Heliconius melpomene genome, developed using novel methods that should be applicable to improving other genome assemblies produced using short read sequencing. First, we whole-genome-sequenced a pedigree to produce a linkage map incorporating 99% of the genome. Second, we incorporated haplotype scaffolds extensively to produce a more complete haploid version of the draft genome. Third, we incorporated ∼20x coverage of Pacific Biosciences sequencing, and scaffolded the haploid genome using an assembly of this long-read sequence. These improvements result in a genome of 795 scaffolds, 275 Mb in length, with an N50 length of 2.1 Mb, an N50 number of 34, and with 99% of the genome placed, and 84% anchored on chromosomes. We use the new genome assembly to confirm that the Heliconius genome underwent 10 chromosome fusions since the split with its sister genus Eueides, over a period of about 6 million yr.
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Affiliation(s)
- John W Davey
- Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
| | - Mathieu Chouteau
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry, 34293 Montpellier 5, France
| | - Sarah L Barker
- Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
| | - Luana Maroja
- Department of Biology, Williams College, Williamstown, Massachusetts, 01267
| | - Simon W Baxter
- School of Biological Sciences, University of Adelaide, SA 5005 Australia
| | - Fraser Simpson
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom
| | | | - Mathieu Joron
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 CNRS - EPHE - Université de Montpellier - Université Paul Valéry, 34293 Montpellier 5, France
| | - James Mallet
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom
| | - Kanchon K Dasmahapatra
- Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, WC1E 6BT, United Kingdom
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
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154
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Shimizu KK, Tsuchimatsu T. Evolution of Selfing: Recurrent Patterns in Molecular Adaptation. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2015. [DOI: 10.1146/annurev-ecolsys-112414-054249] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Selfing has evolved in animals, fungi, and plants, and since Darwin's pioneering study, it is considered one of the most frequent evolutionary trends in flowering plants. Generally, the evolution of selfing is characterized by a loss of self-incompatibility, the selfing syndrome, and changes in genome-wide polymorphism patterns. Recent interdisciplinary studies involving molecular functional experiments, genome-wide data, experimental evolution, and evolutionary ecology using Arabidopsis thaliana, Caenorhabditis elegans, and other species show that the evolution of selfing is not merely a degradation of outcrossing traits but a model for studying the recurrent patterns underlying adaptive molecular evolution. For example, in wild Arabidopsis relatives, self-compatibility evolved from mutations in the male specificity gene, S-LOCUS CYSTEINE-RICH PROTEIN/S-LOCUS PROTEIN 11 (SCR/SP11), rather than the female specificity gene, S-LOCUS RECEPTOR KINASE (SRK), supporting the theoretical prediction of sexual asymmetry. Prevalence of dominant self-compatible mutations is consistent with Haldane's sieve, which acts against recessive adaptive mutations. Time estimates based on genome-wide polymorphisms and self-incompatibility genes generally support the recent origin of selfing.
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Affiliation(s)
- Kentaro K. Shimizu
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Takashi Tsuchimatsu
- Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Tokyo 153-8902, Japan
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155
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Martin CH, Cutler JS, Friel JP, Dening Touokong C, Coop G, Wainwright PC. Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation. Evolution 2015; 69:1406-1422. [PMID: 25929355 DOI: 10.1111/evo.12674] [Citation(s) in RCA: 106] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 04/20/2015] [Indexed: 12/19/2022]
Abstract
One of the most celebrated examples of sympatric speciation in nature are monophyletic radiations of cichlid fishes endemic to Cameroon crater lakes. However, phylogenetic inference of monophyly may not detect complex colonization histories involving some allopatric isolation, such as double invasions obscured by genome-wide gene flow. Population genomic approaches are better suited to test hypotheses of sympatric speciation in these cases. Here, we use comprehensive sampling from all four sympatric crater lake cichlid radiations in Cameroon and outgroups across Africa combined with next-generation sequencing to genotype tens of thousands of SNPs. We find considerable evidence of gene flow between all four radiations and neighboring riverine populations after initial colonization. In a few cases, some sympatric species are more closely related to outgroups than others, consistent with secondary gene flow facilitating their speciation. Our results do not rule out sympatric speciation in Cameroon cichlids, but rather reveal a complex history of speciation with gene flow, including allopatric and sympatric phases, resulting in both reproductively isolated species and incipient species complexes. The best remaining non-cichlid examples of sympatric speciation all involve assortative mating within microhabitats. We speculate that this feature may be necessary to complete the process of sympatric speciation in nature.
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Affiliation(s)
- Christopher H Martin
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina
| | - Joseph S Cutler
- Department of Conservation Biology, University of California, Santa Cruz, California
| | - John P Friel
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, Alabama
| | | | - Graham Coop
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
| | - Peter C Wainwright
- Center for Population Biology and Department of Evolution & Ecology, University of California, Davis, California
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156
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Twyford AD, Friedman J. Adaptive divergence in the monkey flower Mimulus guttatus is maintained by a chromosomal inversion. Evolution 2015; 69:1476-1486. [PMID: 25879251 PMCID: PMC5029580 DOI: 10.1111/evo.12663] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/01/2015] [Indexed: 12/15/2022]
Abstract
Organisms exhibit an incredible diversity of life history strategies as adaptive responses to environmental variation. The establishment of novel life history strategies involves multilocus polymorphisms, which will be challenging to establish in the face of gene flow and recombination. Theory predicts that adaptive allelic combinations may be maintained and spread if they occur in genomic regions of reduced recombination, such as chromosomal inversion polymorphisms, yet empirical support for this prediction is lacking. Here, we use genomic data to investigate the evolution of divergent adaptive ecotypes of the yellow monkey flower Mimulus guttatus. We show that a large chromosomal inversion polymorphism is the major region of divergence between geographically widespread annual and perennial ecotypes. In contrast, ∼40,000 single nucleotide polymorphisms in collinear regions of the genome show no signal of life history, revealing genomic patterns of diversity have been shaped by localized homogenizing gene flow and large-scale Pleistocene range expansion. Our results provide evidence for an inversion capturing and protecting loci involved in local adaptation, while also explaining how adaptive divergence can occur with gene flow.
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Affiliation(s)
- Alex D Twyford
- Ashworth Laboratories, Institute of Evolutionary Biology, The University of Edinburgh, Charlotte Auerbach Road, Edinburgh, EH9 3FL, United Kingdom.,Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244
| | - Jannice Friedman
- Department of Biology, Syracuse University, 107 College Place, Syracuse, New York, 13244
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157
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Twyford AD, Streisfeld MA, Lowry DB, Friedman J. Genomic studies on the nature of species: adaptation and speciation inMimulus. Mol Ecol 2015; 24:2601-9. [DOI: 10.1111/mec.13190] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2015] [Revised: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/27/2022]
Affiliation(s)
- Alex D. Twyford
- Ashworth Laboratories; Institute of Evolutionary Biology; The University of Edinburgh; Charlotte Auerbach Road Edinburgh EH9 3FL UK
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
| | | | - David B. Lowry
- Plant Biology Laboratories; Department of Plant Biology; Michigan State University; 612 Wilson Road Room 166 East Lansing MI 48824 USA
| | - Jannice Friedman
- Department of Biology; Syracuse University; 107 College Place Syracuse NY 13244 USA
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158
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Thomas CG, Wang W, Jovelin R, Ghosh R, Lomasko T, Trinh Q, Kruglyak L, Stein LD, Cutter AD. Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis. Genome Res 2015; 25:667-78. [PMID: 25783854 PMCID: PMC4417115 DOI: 10.1101/gr.187237.114] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/12/2015] [Indexed: 12/19/2022]
Abstract
The nematode Caenorhabditis briggsae is a model for comparative developmental evolution with C. elegans. Worldwide collections of C. briggsae have implicated an intriguing history of divergence among genetic groups separated by latitude, or by restricted geography, that is being exploited to dissect the genetic basis to adaptive evolution and reproductive incompatibility; yet, the genomic scope and timing of population divergence is unclear. We performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae and applied a pairwise sequentially Markovian coalescent (PSMC) model to 703 combinations of genomic haplotypes to draw inferences about population history, the genomic scope of natural selection, and to compare with 40 wild isolates of C. elegans. We estimate that a diaspora of at least six distinct C. briggsae lineages separated from one another approximately 200,000 generations ago, including the “Temperate” and “Tropical” phylogeographic groups that dominate most samples worldwide. Moreover, an ancient population split in its history approximately 2 million generations ago, coupled with only rare gene flow among lineage groups, validates this system as a model for incipient speciation. Low versus high recombination regions of the genome give distinct signatures of population size change through time, indicative of widespread effects of selection on highly linked portions of the genome owing to extreme inbreeding by self-fertilization. Analysis of functional mutations indicates that genomic context, owing to selection that acts on long linkage blocks, is a more important driver of population variation than are the functional attributes of the individually encoded genes.
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Affiliation(s)
- Cristel G Thomas
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Wei Wang
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Richard Jovelin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Rajarshi Ghosh
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Tatiana Lomasko
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
| | - Quang Trinh
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3
| | - Leonid Kruglyak
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA; Departments of Human Genetics and Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, California 90095, USA; Howard Hughes Medical Institute, UCLA, Los Angeles, California 90095, USA
| | - Lincoln D Stein
- Informatics and Bio-Computing, Ontario Institute for Cancer Research, Toronto, Ontario, Canada, M5G 0A3; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Bioinformatics and Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Asher D Cutter
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2; Center for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
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159
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LaFountain AM, Frank HA, Yuan YW. Carotenoid composition of the flowers of Mimulus lewisii and related species: Implications regarding the prevalence and origin of two unique, allenic pigments. Arch Biochem Biophys 2015; 573:32-9. [PMID: 25778629 DOI: 10.1016/j.abb.2015.03.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/05/2015] [Accepted: 03/06/2015] [Indexed: 11/25/2022]
Abstract
The genus Mimulus has been used as a model system in a wide range of ecological and evolutionary studies and contains many species with carotenoid pigmented flowers. However, the detailed carotenoid composition of these flowers has never been reported. In this paper the floral carotenoid composition of 11 Mimulus species are characterized using high-performance liquid chromatography, mass spectrometry and chemical methods with a particular focus on the genetic model species, Mimulus lewisii. M. lewisii flowers have five major carotenoids: antheraxanthin, violaxanthin, neoxanthin, and the unique allenic carotenoids, deepoxyneoxanthin and mimulaxanthin. This carotenoid profile is consistent with the expression levels of putative carotenoid biosynthetic genes in the M. lewisii flower. The other 10 species possess the same five carotenoids or a subset of these. Comparison of the carotenoid profiles among species in a phylogenetic context provides new insights into the biosynthesis and evolution of deepoxyneoxanthin and mimulaxanthin. This work also lays the foundation for future studies regarding transcriptional control of the carotenoid biosynthesis pathway in Mimulus flowers.
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Affiliation(s)
- Amy M LaFountain
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269-3060, USA.
| | - Harry A Frank
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269-3060, USA
| | - Yao-Wu Yuan
- Department of Ecology and Evolutionary Biology and the Institute for Systems Genomics, University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3043, USA
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160
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Peterson ML, Miller TJ, Kay KM. An ultraviolet floral polymorphism associated with life history drives pollinator discrimination in Mimulus guttatus. AMERICAN JOURNAL OF BOTANY 2015; 102:396-406. [PMID: 25784473 DOI: 10.3732/ajb.1400415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
UNLABELLED • PREMISE OF THE STUDY Ultraviolet (UV) floral patterns are common in angiosperms and mediate pollinator attraction, efficiency, and constancy. UV patterns may vary within species, yet are cryptic to human observers. Thus, few studies have explicitly described the distribution or ecological significance of intraspecific variation in UV floral patterning. Here, we describe the geographic distribution and pattern of inheritance of a UV polymorphism in the model plant species Mimulus guttatus (Phrymaceae). We then test whether naturally occurring UV phenotypes influence pollinator interactions within M. guttatus.• METHODS We document UV patterns in 18 annual and 19 perennial populations and test whether UV pattern is associated with life history. To examine the pattern of inheritance, we conducted crosses within and between UV phenotypes. Finally, we tested whether bee pollinators discriminate among naturally occurring UV phenotypes in two settings: wild bee communities and captive Bombus impatiens.• KEY RESULTS Within M. guttatus, perennial populations exhibit a small bulls-eye pattern, whereas a bilaterally symmetric runway pattern occurs mainly in annual populations. Inheritance of UV patterning is consistent with a single-locus Mendelian model in which the runway phenotype is dominant. Bee pollinators discriminate against unfamiliar UV patterns in both natural and controlled settings.• CONCLUSIONS We describe a widespread UV polymorphism associated with life history divergence within Mimulus guttatus. UV pattern influences pollinator visitation and should be considered when estimating reproductive barriers between life history ecotypes. This work develops a new system to investigate the ecology and evolution of UV floral patterning in a species with extensive genomic resources.
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Affiliation(s)
- Megan L Peterson
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064 USA
| | - Timothy J Miller
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064 USA
| | - Kathleen M Kay
- Ecology and Evolutionary Biology, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064 USA
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161
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Sweigart AL, Flagel LE. Evidence of natural selection acting on a polymorphic hybrid incompatibility locus in Mimulus. Genetics 2015; 199:543-54. [PMID: 25428983 PMCID: PMC4317661 DOI: 10.1534/genetics.114.171819] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 11/18/2014] [Indexed: 12/30/2022] Open
Abstract
As a common cause of reproductive isolation in diverse taxa, hybrid incompatibilities are fundamentally important to speciation. A key question is which evolutionary forces drive the initial substitutions within species that lead to hybrid dysfunction. Previously, we discovered a simple genetic incompatibility that causes nearly complete male sterility and partial female sterility in hybrids between the two closely related yellow monkeyflower species Mimulus guttatus and M. nasutus. In this report, we fine map the two major incompatibility loci-hybrid male sterility 1 (hms1) and hybrid male sterility 2 (hms2)-to small nuclear genomic regions (each <70 kb) that include strong candidate genes. With this improved genetic resolution, we also investigate the evolutionary dynamics of hms1 in a natural population of M. guttatus known to be polymorphic at this locus. Using classical genetic crosses and population genomics, we show that a 320-kb region containing the hms1 incompatibility allele has risen to intermediate frequency in this population by strong natural selection. This finding provides direct evidence that natural selection within plant species can lead to hybrid dysfunction between species.
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Affiliation(s)
- Andrea L Sweigart
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Lex E Flagel
- Department of Biology, Duke University, Durham, North Carolina 27708 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
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162
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Puzey J, Vallejo-Marín M. Genomics of invasion: diversity and selection in introduced populations of monkeyflowers (Mimulus guttatus). Mol Ecol 2014; 23:4472-85. [DOI: 10.1111/mec.12875] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/02/2014] [Accepted: 07/22/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Joshua Puzey
- Department of Biology; Duke University; Durham NC 27705 USA
- Department of Biology; College of William and Mary; Williamsburg VA 23185 USA
| | - Mario Vallejo-Marín
- Biological and Environmental Sciences; University of Stirling; Stirling FK9 4LA UK
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163
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Oneal E, Lowry DB, Wright KM, Zhu Z, Willis JH. Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex. Mol Ecol 2014; 23:2844-60. [PMID: 24796267 DOI: 10.1111/mec.12778] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/14/2014] [Accepted: 04/26/2014] [Indexed: 12/12/2022]
Abstract
Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favourable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M. guttatus species complex. We tested whether annual and perennial M. guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M. guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M. guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M. guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex.
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Affiliation(s)
- Elen Oneal
- Department of Biology, Duke University, PO Box 90338, Durham, NC 27708, USA
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