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Sabolić I, Mira Ó, Brandt DYC, Lisičić D, Stapley J, Novosolov M, Bakarić R, Cizelj I, Glogoški M, Hudina T, Taverne M, Allentoft ME, Nielsen R, Herrel A, Štambuk A. Plastic and genomic change of a newly established lizard population following a founder event. Mol Ecol 2024; 33:e17255. [PMID: 38133599 DOI: 10.1111/mec.17255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023]
Abstract
Understanding how phenotypic divergence arises among natural populations remains one of the major goals in evolutionary biology. As part of competitive exclusion experiment conducted in 1971, 10 individuals of Italian wall lizard (Podarcis siculus (Rafinesque-Schmaltz, 1810)) were transplanted from Pod Kopište Island to the nearby island of Pod Mrčaru (Adriatic Sea). Merely 35 years after the introduction, the newly established population on Pod Mrčaru Island had shifted their diet from predominantly insectivorous towards omnivorous and changed significantly in a range of morphological, behavioural, physiological and ecological characteristics. Here, we combine genomic and quantitative genetic approaches to determine the relative roles of genetic adaptation and phenotypic plasticity in driving this rapid phenotypic shift. Our results show genome-wide genetic differentiation between ancestral and transplanted population, with weak genetic erosion on Pod Mrčaru Island. Adaptive processes following the founder event are indicated by highly differentiated genomic loci associating with ecologically relevant phenotypic traits, and/or having a putatively adaptive role across multiple lizard populations. Diverged traits related to head size and shape or bite force showed moderate heritability in a crossing experiment, but between-population differences in these traits did not persist in a common garden environment. Our results confirm the existence of sufficient additive genetic variance for traits to evolve under selection while also demonstrating that phenotypic plasticity and/or genotype by environment interactions are the main drivers of population differentiation at this early evolutionary stage.
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Affiliation(s)
- Iva Sabolić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Óscar Mira
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Débora Y C Brandt
- Department of Integrative Biology, University of Berkeley, Berkeley, California, USA
| | - Duje Lisičić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Jessica Stapley
- Department of Environmental Sciences, ETH Zurich, Zurich, Switzerland
| | - Maria Novosolov
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Robert Bakarić
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Ivan Cizelj
- Zoological Garden of Zagreb, Zagreb, Croatia
| | - Marko Glogoški
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | | | - Maxime Taverne
- C.N.R.S/M.N.H.N., Département d'Ecologie et de Gestion de la Biodiversité, Paris, France
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Rasmus Nielsen
- Department of Integrative Biology, University of Berkeley, Berkeley, California, USA
| | - Anthony Herrel
- C.N.R.S/M.N.H.N., Département d'Ecologie et de Gestion de la Biodiversité, Paris, France
- Department of Biology, Evolutionary Morphology of Vertebrates, Ghent University, Ghent, Belgium
- Department of Biology, University of Antwerp, Wilrijk, Belgium
- Naturhistorisches Museum Bern, Bern, Switzerland
| | - Anamaria Štambuk
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
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Abstract
AbstractEvolutionary biologists have thought about the role of genetic variation during adaptation for a very long time-before we understood the organization of the genetic code, the provenance of genetic variation, and how such variation influenced the phenotypes on which natural selection acts. Half a century after the discovery of the structure of DNA and the unraveling of the genetic code, we have a rich understanding of these problems and the means to both delve deeper and widen our perspective across organisms and natural populations. The 2022 Vice Presidential Symposium of the American Society of Naturalists highlighted examples of recent insights into the role of genetic variation in adaptive processes, which are compiled in this special section. The work was conducted in different parts of the world, included theoretical and empirical studies with diverse organisms, and addressed distinct aspects of how genetic variation influences adaptation. In our introductory article to the special section, we discuss some important recent insights about the generation and maintenance of genetic variation, its impacts on phenotype and fitness, its fate in natural populations, and its role in driving adaptation. By placing the special section articles in the broader context of recent developments, we hope that this overview will also serve as a useful introduction to the field.
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Turba R, Richmond JQ, Fitz-Gibbon S, Morselli M, Fisher RN, Swift CC, Ruiz-Campos G, Backlin AR, Dellith C, Jacobs DK. Genetic structure and historic demography of endangered unarmoured threespine stickleback at southern latitudes signals a potential new management approach. Mol Ecol 2022; 31:6515-6530. [PMID: 36205603 PMCID: PMC10092051 DOI: 10.1111/mec.16722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/05/2022] [Accepted: 09/29/2022] [Indexed: 01/13/2023]
Abstract
Habitat loss, flood control infrastructure, and drought have left most of southern California and northern Baja California's native freshwater fish near extinction, including the endangered unarmoured threespine stickleback (Gasterosteus aculeatus williamsoni). This subspecies, an unusual morph lacking the typical lateral bony plates of the G. aculeatus complex, occurs at arid southern latitudes in the eastern Pacific Ocean and survives in only three inland locations. Managers have lacked molecular data to answer basic questions about the ancestry and genetic distinctiveness of unarmoured populations. These data could be used to prioritize conservation efforts. We sampled G. aculeatus from 36 localities and used microsatellites and whole genome data to place unarmoured populations within the broader evolutionary context of G. aculeatus across southern California/northern Baja California. We identified three genetic groups with none consisting solely of unarmoured populations. Unlike G. aculeatus at northern latitudes, where Pleistocene glaciation has produced similar historical demographic profiles across populations, we found markedly different demographics depending on sampling location, with inland unarmoured populations showing steeper population declines and lower heterozygosity compared to low armoured populations in coastal lagoons. One exception involved the only high elevation population in the region, where the demography and alleles of unarmoured fish were similar to low armoured populations near the coast, exposing one of several cases of artificial translocation. Our results suggest that the current "management-by-phenotype" approach, based on lateral plates, is incidentally protecting the most imperilled populations; however, redirecting efforts toward evolutionary units, regardless of phenotype, may more effectively preserve adaptive potential.
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Affiliation(s)
- Rachel Turba
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | | | - Sorel Fitz-Gibbon
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, USA
| | | | - Camm C Swift
- Emeritus, Section of Fishes, Natural History Museum of Los Angeles County, Los Angeles, California, USA
| | - Gorgonio Ruiz-Campos
- Ichthyological Collection, Facultad de Ciencias, Universidad Autónoma de Baja California, Ensenada, Baja California, Mexico
| | - Adam R Backlin
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station-Santa Ana Office, Santa Ana, California, USA
| | - Chris Dellith
- U.S. Fish and Wildlife Service, Ventura, California, USA
| | - David K Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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Yamamichi M. How does genetic architecture affect eco-evolutionary dynamics? A theoretical perspective. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200504. [PMID: 35634922 PMCID: PMC9149794 DOI: 10.1098/rstb.2020.0504] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies have revealed the importance of feedbacks between contemporary rapid evolution (i.e. evolution that occurs through changes in allele frequencies) and ecological dynamics. Despite its inherent interdisciplinary nature, however, studies on eco-evolutionary feedbacks have been mostly ecological and tended to focus on adaptation at the phenotypic level without considering the genetic architecture of evolutionary processes. In empirical studies, researchers have often compared ecological dynamics when the focal species under selection has a single genotype with dynamics when it has multiple genotypes. In theoretical studies, common approaches are models of quantitative traits where mean trait values change adaptively along the fitness gradient and Mendelian traits with two alleles at a single locus. On the other hand, it is well known that genetic architecture can affect short-term evolutionary dynamics in population genetics. Indeed, recent theoretical studies have demonstrated that genetic architecture (e.g. the number of loci, linkage disequilibrium and ploidy) matters in eco-evolutionary dynamics (e.g. evolutionary rescue where rapid evolution prevents extinction and population cycles driven by (co)evolution). I propose that theoretical approaches will promote the synthesis of functional genomics and eco-evolutionary dynamics through models that combine population genetics and ecology as well as nonlinear time-series analyses using emerging big data.
This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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Attard CRM, Sandoval-Castillo J, Brauer CJ, Unmack PJ, Schmarr D, Bernatchez L, Beheregaray LB. Fish out of water: Genomic insights into persistence of rainbowfish populations in the desert. Evolution 2021; 76:171-183. [PMID: 34778944 DOI: 10.1111/evo.14399] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/22/2021] [Accepted: 10/31/2021] [Indexed: 11/26/2022]
Abstract
How populations of aquatic fauna persist in extreme desert environments is an enigma. Individuals often breed and disperse during favorable conditions. Theory predicts that adaptive capacity should be low in small populations, such as in desert fishes. We integrated satellite-derived surface water data and population genomic diversity from 20,294 single-nucleotide polymorphisms across 344 individuals to understand metapopulation persistence of the desert rainbowfish (Melanotaenia splendida tatei) in central Australia. Desert rainbowfish showed very small effective population sizes, especially at peripheral populations, and low connectivity between river catchments. Yet, there was no evidence of population-level inbreeding and a signal of possible adaptive divergence associated with aridity was detected. Candidate genes for local adaptation included functions related to environmental cues and stressful conditions. Eco-evolutionary modeling showed that positive selection in refugial subpopulations combined with connectivity during flood periods can enable retention of adaptive diversity. Our study suggests that adaptive variation can be maintained in small populations and integrate with neutral metapopulation processes to allow persistence in the desert.
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Affiliation(s)
- Catherine R M Attard
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Jonathan Sandoval-Castillo
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Chris J Brauer
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
| | - Peter J Unmack
- Centre for Applied Water Science, Institute for Applied Ecology, University of Canberra, Canberra, ACT, 2601, Australia
| | - David Schmarr
- Inland Waters and Catchment Ecology Program, SARDI Aquatic Sciences, Henley Beach, SA, 5022, Australia
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes, Université Laval Québec, Québec, QC, G1V 0A6, Canada
| | - Luciano B Beheregaray
- Molecular Ecology Laboratory, College of Science and Engineering, Flinders University, Adelaide, SA, 5001, Australia
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Cuenca‐Cambronero M, Pantel JH, Marshall H, Nguyen TTT, Tomero‐Sanz H, Orsini L. Evolutionary mechanisms underpinning fitness response to multiple stressors in Daphnia. Evol Appl 2021; 14:2457-2469. [PMID: 34745337 PMCID: PMC8549616 DOI: 10.1111/eva.13258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 05/13/2021] [Accepted: 05/19/2021] [Indexed: 11/28/2022] Open
Abstract
Multiple stressors linked to anthropogenic activities can influence how organisms adapt and evolve. So far, a consensus on how multiple stressors drive adaptive trajectories in natural populations has not been reached. Some meta-analysis reports show predominance of additive effects of stressors on ecological endpoints (e.g., fecundity, mortality), whereas others show synergistic effects more frequently. Moreover, it is unclear what mechanisms of adaptation underpin responses to complex environments. Here, we use populations of Daphnia magna resurrected from different times in the past to investigate mechanisms of adaptation to multiple stressors and to understand how historical exposure to environmental stress shapes adaptive responses of modern populations. Using common garden experiments on resurrected modern and historical populations, we investigate (1) whether exposure to one stress results in higher tolerance to a second stressor; (2) the mechanisms of adaptation underpinning long-term evolution to multistress (genetic evolution, plasticity, evolution of plasticity); and (3) the interaction effects of multiple stressors on fitness (synergism, antagonism, additivity). We measure the combined impact of different levels of resource availability (algae) and biocides on fitness-linked life-history traits and interpret these results in light of historical environmental exposures. We show that exposure to one stressor can alter tolerance to second stressors and that the interaction effect depends on the severity of either stressor. We also show that mechanisms of adaptation underpinning phenotypic evolution significantly differ in single-stress and multistress scenarios. These adaptive responses are driven largely by synergistic effects on fecundity and size at maturity, and additive effects on age at maturity. Exposure to multiple stressors shifts the trade-offs among fitness-linked life-history traits, with a stronger effect on Daphnia populations when low-resource availability and high biocide levels are experienced. Our study indicates that mitigation interventions based on single-stress analysis may not capture realistic threats.
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Affiliation(s)
- Maria Cuenca‐Cambronero
- Department of Fish Ecology and EvolutionEawagKastanienbaumSwitzerland
- Aquatic Ecology and EvolutionInstitute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
| | - Jelena H. Pantel
- Department of Computer Science, Mathematics, and Environmental ScienceThe American University of ParisParisFrance
| | - Hollie Marshall
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
- Institute of Evolutionary BiologyUniversity of EdinburghEdinburghUK
| | - Tien T. T. Nguyen
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
- Department of Animal and Plant SciencesUniversity of SheffieldSheffieldUK
| | - Henar Tomero‐Sanz
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
- Department of Molecular Cancer Pathology of IRYCISHospital Ramon y CajalMadridSpain
| | - Luisa Orsini
- Environmental Genomics Group, School of BiosciencesUniversity of BirminghamBirminghamUK
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7
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Wood ZT, Wiegardt AK, Barton KL, Clark JD, Homola JJ, Olsen BJ, King BL, Kovach AI, Kinnison MT. Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems. Evol Appl 2021; 14:2189-2205. [PMID: 34603492 PMCID: PMC8477602 DOI: 10.1111/eva.13264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/17/2023] Open
Abstract
Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.
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Affiliation(s)
- Zachary T. Wood
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| | - Andrew K. Wiegardt
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Kayla L. Barton
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Jonathan D. Clark
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Brian J. Olsen
- Maine Center for Genetics in the EnvironmentOronoMEUSA
- Department of Wildlife, Fisheries, and Conservation BiologyUniversity of MaineOronoMEUSA
| | - Benjamin L. King
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Michael T. Kinnison
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
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Meger J, Ulaszewski B, Burczyk J. Genomic signatures of natural selection at phenology-related genes in a widely distributed tree species Fagus sylvatica L. BMC Genomics 2021; 22:583. [PMID: 34332553 PMCID: PMC8325806 DOI: 10.1186/s12864-021-07907-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/20/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Diversity among phenology-related genes is predicted to be a contributing factor in local adaptations seen in widely distributed plant species that grow in climatically variable geographic areas, such as forest trees. European beech (Fagus sylvatica L.) is widespread, and is one of the most important broadleaved tree species in Europe; however, its potential for adaptation to climate change is a matter of uncertainty, and little is known about the molecular basis of climate change-relevant traits like bud burst. RESULTS We explored single nucleotide polymorphisms (SNP) at candidate genes related to bud burst in beech individuals sampled across 47 populations from Europe. SNP diversity was monitored for 380 candidate genes using a sequence capture approach, providing 2909 unlinked SNP loci. We used two complementary analytical methods to find loci significantly associated with geographic variables, climatic variables (expressed as principal components), or phenotypic variables (spring and autumn phenology, height, survival). Redundancy analysis (RDA) was used to detect candidate markers across two spatial scales (entire study area and within subregions). We revealed 201 candidate SNPs at the broadest scale, 53.2% of which were associated with phenotypic variables. Additive polygenic scores, which provide a measure of the cumulative signal across significant candidate SNPs, were correlated with a climate variable (first principal component, PC1) related to temperature and precipitation availability, and spring phenology. However, different genotype-environment associations were identified within Southeastern Europe as compared to the entire geographic range of European beech. CONCLUSIONS Environmental conditions play important roles as drivers of genetic diversity of phenology-related genes that could influence local adaptation in European beech. Selection in beech favors genotypes with earlier bud burst under warmer and wetter habitats within its range; however, selection pressures may differ across spatial scales.
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Affiliation(s)
- Joanna Meger
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Bartosz Ulaszewski
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland
| | - Jaroslaw Burczyk
- Department of Genetics, Faculty of Biological Sciences, Kazimierz Wielki University, Chodkiewicza 30, 85-064, Bydgoszcz, Poland.
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9
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Birkeland S, Gustafsson ALS, Brysting AK, Brochmann C, Nowak MD. Multiple Genetic Trajectories to Extreme Abiotic Stress Adaptation in Arctic Brassicaceae. Mol Biol Evol 2021; 37:2052-2068. [PMID: 32167553 PMCID: PMC7306683 DOI: 10.1093/molbev/msaa068] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/23/2020] [Accepted: 03/10/2020] [Indexed: 12/11/2022] Open
Abstract
Extreme environments offer powerful opportunities to study how different organisms have adapted to similar selection pressures at the molecular level. Arctic plants have adapted to some of the coldest and driest biomes on Earth and typically possess suites of similar morphological and physiological adaptations to extremes in light and temperature. Here, we compare patterns of molecular evolution in three Brassicaceae species that have independently colonized the Arctic and present some of the first genetic evidence for plant adaptations to the Arctic environment. By testing for positive selection and identifying convergent substitutions in orthologous gene alignments for a total of 15 Brassicaceae species, we find that positive selection has been acting on different genes, but similar functional pathways in the three Arctic lineages. The positively selected gene sets identified in the three Arctic species showed convergent functional profiles associated with extreme abiotic stress characteristic of the Arctic. However, there was little evidence for independently fixed mutations at the same sites and for positive selection acting on the same genes. The three species appear to have evolved similar suites of adaptations by modifying different components in similar stress response pathways, implying that there could be many genetic trajectories for adaptation to the Arctic environment. By identifying candidate genes and functional pathways potentially involved in Arctic adaptation, our results provide a framework for future studies aimed at testing for the existence of a functional syndrome of Arctic adaptation in the Brassicaceae and perhaps flowering plants in general.
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Affiliation(s)
- Siri Birkeland
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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Pespeni MH, Moczek AP. Signals of selection beyond bottlenecks between exotic populations of the bull-headed dung beetle, Onthophagus taurus. Evol Dev 2021; 23:86-99. [PMID: 33522675 DOI: 10.1111/ede.12367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 12/02/2020] [Accepted: 12/15/2020] [Indexed: 11/27/2022]
Abstract
Colonization of new environments can lead to population bottlenecks and rapid phenotypic evolution that could be due to neutral and selective processes. Exotic populations of the bull-headed dung beetle (Onthophagus taurus) have differentiated in opposite directions from native beetles in male horn-to-body size allometry and female fecundity. Here we test for genetic and transcriptional differences among two exotic and one native O. taurus populations after three generations in common garden conditions. We sequenced RNA from 24 individuals for each of the three populations including both sexes, and spanning four developmental stages for the two exotic, differentiated populations. Identifying 270,400 high-quality single nucleotide polymorphisms, we revealed a strong signal of genetic differentiation between the three populations, and evidence of recent bottlenecks within and an excess of outlier loci between exotic populations. Differences in gene expression between populations were greatest in prepupae and early adult life stages, stages during which differences in male horn development and female fecundity manifest. Finally, genes differentially expressed between exotic populations also had greater genetic differentiation and performed functions related to chitin biosynthesis and nutrient sensing, possibly underlying allometry and fecundity trait divergences. Our results suggest that beyond bottlenecks, recent introductions have led to genetic and transcriptional differences in genes correlated with observed phenotypic differences.
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Affiliation(s)
- Melissa H Pespeni
- Department of Biology, University of Vermont, Burlington, Vermont, USA.,Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Armin P Moczek
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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11
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Mendes PB, Faria LD. The eco-evolutionary dynamics of a predator-prey system across an r/K continuum. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Swift HF, Dawson MN. Demographic, Environmental, and Phenotypic Change but Genetic Consistency in the Jellyfish Mastigias papua. THE BIOLOGICAL BULLETIN 2020; 239:80-94. [PMID: 33151754 DOI: 10.1086/710663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
AbstractSpatiotemporal environmental change can produce phenotypic differences within and between populations. For scyphozoans, the effect of environmental variation on phenotype has been unclear because of multiple challenges, including difficulties delimiting populations. Marine lakes, bodies of seawater entirely surrounded by land, provide an opportunity to study discrete populations and capture responses to perturbations. We use this opportunity to compare Mastigias papua (Lesson, 1830) medusae before and after a demographic and environmental perturbation. We reconstructed mitochondrial DNA haplotype networks, measured morphological variation, and assessed swimming behavior of pre- and post-perturbation samples to evaluate two hypotheses about the source of variation: recolonization from an alternate location or endemic phenotypic variation. We found significant differences between samples in morphology (F > 9.5, P < 0.001) and in two of three behaviors (F > 8.45, P < 0.005) but no substantial genetic differentiation (ΦST = 0.03, P = 0.09). We reject the hypothesis of recolonization because pre- and post-perturbation lake medusae were genetically similar to each other and also significantly different from any potential source locations (ΦST > 0.48, P > 0.001). We could not distinguish the source of endemic variation; this will require genomic or experimental analyses. Increasing climatic variability emphasizes the need for understanding population-level responses to environmental change and how responses may be modified by sources of intraspecific variation.
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Kenthao A, Jearranaiprepame P. Ecomorphological diversification of some barbs and carps (Cyprininae, Cyprinidae) in the Lower Mekong Basin of Thailand. ZOOLOGY 2020; 143:125830. [PMID: 32916444 DOI: 10.1016/j.zool.2020.125830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 11/19/2022]
Abstract
Morphological variation is fundamentally related to various aspects of fish ecology, including foraging, locomotion, and habitat utilisation. Twenty-six species of closely related cyprinid fish (n = 502) were analysed for patterns of morphological variations by using geometric morphometric methods. Ecological data of feeding and habitat preferences were determined by the observations in fields and laboratory together with the gathering of bibliographic information. The findings of major variation displayed in all parts of the fish body and correlated with ecological parameters. Variations of head shape especially form and position of mouthpart involved with feeding behaviours, whereas the variations of body depth and length which affected swimming patterns reflected responsiveness of water currents and habitat uses. Adaptation of head shape and body elongation was remarkably related to the feeding regime, swimming manoeuvrability and habitat utilisation of the species. Some convergent variation was observed between the tribes Smiliogastrini and Poropuntiini. Therefore, we propose that the morphological diversity of cyprinine fish is mainly affected by ecological gradients, while phylogenetic effects on morphology are minor.
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Affiliation(s)
- Anan Kenthao
- Department of Biology, Faculty of Science, Naresuan University, Mueang, Phitsanulok, 65000, Thailand.
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14
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The long-term restoration of ecosystem complexity. Nat Ecol Evol 2020; 4:676-685. [DOI: 10.1038/s41559-020-1154-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 02/19/2020] [Indexed: 12/25/2022]
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15
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Dissecting the Transcriptomic Basis of Phenotypic Evolution in an Aquatic Keystone Grazer. Mol Biol Evol 2019; 37:475-487. [DOI: 10.1093/molbev/msz234] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Knowledge of the molecular basis of phenotypic responses to environmental cues is key to understanding the process of adaptation. Insights to adaptation at an evolutionary time scale can be gained by observing organismal responses before and after a shift in environmental conditions, but such observations can rarely be made. Using the ecological and genomic model Daphnia, we linked transcriptomic responses and phosphorus (P)-related phenotypic traits under high and low P availability. We mapped weighted gene coexpression networks to traits previously assessed in resurrected ancient (600 years old) and modern Daphnia pulicaria from a lake with a historic shift in P-enrichment. Subsequently, we assessed evolutionary conservation or divergence in transcriptional networks of the same isolates. We discovered highly preserved gene networks shared between ancient genotypes and their modern descendants, but also detected clear evidence of transcriptional divergence between these evolutionarily separated genotypes. Our study highlights that phenotypic evolution is a result of molecular fine-tuning on different layers ranging from basic cellular responses to higher order phenotypes. In a broader context, these findings advance our understanding how populations are able to persist throughout major environmental shifts.
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16
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Mabin CJT, Johnson CR, Wright JT. Family-level variation in early life-cycle traits of kelp. JOURNAL OF PHYCOLOGY 2019; 55:380-392. [PMID: 30506918 DOI: 10.1111/jpy.12820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 11/16/2018] [Indexed: 06/09/2023]
Abstract
Temperate kelp forests (Laminarians) are threatened by temperature stress due to ocean warming and photoinhibition due to increased light associated with canopy loss. However, the potential for evolutionary adaptation in kelp to rapid climate change is not well known. This study examined family-level variation in physiological and photosynthetic traits in the early life-cycle stages of the ecologically important Australasian kelp Ecklonia radiata and the response of E. radiata families to different temperature and light environments using a family × environment design. There was strong family-level variation in traits relating to morphology (surface area measures, branch length, branch count) and photosynthetic performance (Fv /Fm ) in both haploid (gametophyte) and diploid (sporophyte) stages of the life-cycle. Additionally, the presence of family × environment interactions showed that offspring from different families respond differently to temperature and light in the branch length of male gametophytes and oogonia surface area of female gametophytes. Negative responses to high temperatures were stronger for females vs. males. Our findings suggest E. radiata may be able to respond adaptively to climate change but studies partitioning the narrow vs. broad sense components of heritable variation are needed to establish the evolutionary potential of E. radiata to adapt under climate change.
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Affiliation(s)
- Christopher J T Mabin
- Institute for Marine and Antarctic Studies, University of Tasmania, Launceston, Tasmania, 7250, Australia
| | - Craig R Johnson
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7001, Australia
| | - Jeffrey T Wright
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, 7001, Australia
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17
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Jones AG, Arnold SJ, Bürger R. The Effects of Epistasis and Pleiotropy on Genome-Wide Scans for Adaptive Outlier Loci. J Hered 2019; 110:494-513. [DOI: 10.1093/jhered/esz007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/31/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
With the advent of next-generation sequencing approaches, the search for individual loci underlying local adaptation has become a major enterprise in evolutionary biology. One promising method to identify such loci is to examine genome-wide patterns of differentiation, using an FST-outlier approach. The effects of pleiotropy and epistasis on this approach are not yet known. Here, we model 2 populations of a sexually reproducing, diploid organism with 2 quantitative traits, one of which is involved in local adaptation. We consider genetic architectures with and without pleiotropy and epistasis. We also model neutral marker loci on an explicit genetic map as the 2 populations diverge and apply FST outlier approaches to determine the extent to which quantitative trait loci (QTL) are detectable. Our results show, under a wide range of conditions, that only a small number of QTL are typically responsible for most of the trait divergence between populations, even when inheritance is highly polygenic. We find that the loci making the largest contributions to trait divergence tend to be detectable outliers. These loci also make the largest contributions to within-population genetic variance. The addition of pleiotropy reduces the extent to which quantitative traits can evolve independently but does not reduce the efficacy of outlier scans. The addition of epistasis, however, reduces the mean FST values for causative QTL, making these loci more difficult, but not impossible, to detect in outlier scans.
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Affiliation(s)
- Adam G Jones
- Department of Biological Sciences, University of Idaho, Moscow, ID
| | - Stevan J Arnold
- Department of Integrative Biology, Oregon State University, Corvallis, OR
| | - Reinhard Bürger
- Faculty of Mathematics, University of Vienna, Vienna, Austria
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18
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Affiliation(s)
- Andrew P. Hendry
- Redpath Museum and Department of BiologyMcGill University Montreal Quebec Canada
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19
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Burak MK, Monk JD, Schmitz OJ. Eco-Evolutionary Dynamics: The Predator-Prey Adaptive Play and the Ecological Theater. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2018; 91:481-489. [PMID: 30588213 PMCID: PMC6302632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The emerging field of eco-evolutionary dynamics has demonstrated that both ecological and evolutionary processes can occur contemporaneously. Ecological interactions, such as between predator and prey, are important focal areas where an eco-evolutionary perspective can advance understanding about phenotypically plastic and adaptive evolutionary responses. In predator-prey interactions, both species reciprocally respond and adapt to each other in order to simultaneously ensure resource consumption and predation avoidance. Here we sketch out a way to help unify experimental and analytical approaches to both eco-evolutionary dynamics and predator-prey interactions, with a specific focus on terrestrial systems. We discuss the need to view predator-prey eco-evolutionary dynamics as a perpetually adaptive interplay with constantly shifting pressures and feedbacks, rather than viewing it as driving a set evolutionary trajectory. We then outline our perspective on how to understand eco-evolutionary patterns in a predator-prey context. We propose initiating insight by distinguishing phenotypic plasticity against genetic change (i.e., "molecular reductionism") and further applying a landscape-scale perspective (i.e., "landscape holism"). We believe that studying predator-prey interactions under an eco-evolutionary lens can provide insights into how general and, consequently, predictable species' evolutionary responses are to their contemporary environments.
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Affiliation(s)
- Mary K. Burak
- To whom all correspondence should be addressed: Mary Burak, 370 Prospect Street, New Haven, CT 06511; Tel: 203-436-5276,
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20
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Gaggiotti OE, Chao A, Peres‐Neto P, Chiu C, Edwards C, Fortin M, Jost L, Richards CM, Selkoe KA. Diversity from genes to ecosystems: A unifying framework to study variation across biological metrics and scales. Evol Appl 2018; 11:1176-1193. [PMID: 30026805 PMCID: PMC6050189 DOI: 10.1111/eva.12593] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 12/21/2017] [Indexed: 02/03/2023] Open
Abstract
Biological diversity is a key concept in the life sciences and plays a fundamental role in many ecological and evolutionary processes. Although biodiversity is inherently a hierarchical concept covering different levels of organization (genes, population, species, ecological communities and ecosystems), a diversity index that behaves consistently across these different levels has so far been lacking, hindering the development of truly integrative biodiversity studies. To fill this important knowledge gap, we present a unifying framework for the measurement of biodiversity across hierarchical levels of organization. Our weighted, information-based decomposition framework is based on a Hill number of order q = 1, which weights all elements in proportion to their frequency and leads to diversity measures based on Shannon's entropy. We investigated the numerical behaviour of our approach with simulations and showed that it can accurately describe complex spatial hierarchical structures. To demonstrate the intuitive and straightforward interpretation of our diversity measures in terms of effective number of components (alleles, species, etc.), we applied the framework to a real data set on coral reef biodiversity. We expect our framework will have multiple applications covering the fields of conservation biology, community genetics and eco-evolutionary dynamics.
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Affiliation(s)
- Oscar E. Gaggiotti
- School of BiologyScottish Oceans InstituteUniversity of St AndrewsSt AndrewsUK
| | - Anne Chao
- Institute of StatisticsNational Tsing Hua UniversityHsin‐ChuTaiwan
| | | | - Chun‐Huo Chiu
- Department of AgronomyNational Taiwan UniversityTaipeiTaiwan
| | - Christine Edwards
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSaint LouisMOUSA
| | - Marie‐Josée Fortin
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Lou Jost
- Ecominga FundationBanosTungurahuaEcuador
| | | | - Kimberly A. Selkoe
- National Center for Ecological Analysis and SynthesisUniversity of California Santa BarbaraSanta BarbaraCAUSA
- Hawai'i Institute of Marine BiologyUniversity of Hawai'i at MānoaKaneoheHIUSA
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21
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Morris MRJ, Bowles E, Allen BE, Jamniczky HA, Rogers SM. Contemporary ancestor? Adaptive divergence from standing genetic variation in Pacific marine threespine stickleback. BMC Evol Biol 2018; 18:113. [PMID: 30021523 PMCID: PMC6052716 DOI: 10.1186/s12862-018-1228-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 07/03/2018] [Indexed: 11/25/2022] Open
Abstract
Background Populations that have repeatedly colonized novel environments are useful for studying the role of ecology in adaptive divergence – particularly if some individuals persist in the ancestral habitat. Such “contemporary ancestors” can be used to demonstrate the effects of selection by comparing phenotypic and genetic divergence between the derived population and their extant ancestors. However, evolution and demography in these “contemporary ancestors” can complicate inferences about the source (standing genetic variation, de novo mutation) and pace of adaptive divergence. Marine threespine stickleback (Gasterosteus aculeatus) have colonized freshwater environments along the Pacific coast of North America, but have also persisted in the marine environment. To what extent are marine stickleback good proxies of the ancestral condition? Results We sequenced > 5800 variant loci in over 250 marine stickleback from eight locations extending from Alaska to California, and phenotyped them for platedness and body shape. Pairwise FST varied from 0.02 to 0.18. Stickleback were divided into five genetic clusters, with a single cluster comprising stickleback from Washington to Alaska. Plate number, Eda, body shape, and candidate loci showed evidence of being under selection in the marine environment. Comparisons to a freshwater population demonstrated that candidate loci for freshwater adaptation varied depending on the choice of marine populations. Conclusions Marine stickleback are structured into phenotypically and genetically distinct populations that have been evolving as freshwater stickleback evolved. This variation complicates their usefulness as proxies of the ancestors of freshwater populations. Lessons from stickleback may be applied to other “contemporary ancestor”-derived population studies. Electronic supplementary material The online version of this article (10.1186/s12862-018-1228-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew R J Morris
- Department of Biology, Ambrose University, 150 Ambrose Circle SW, Calgary, AB, T3H 0L5, Canada.
| | - Ella Bowles
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Brandon E Allen
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
| | - Heather A Jamniczky
- McCaig Institute for Bone and Joint Health, Department of Cell Biology & Anatomy, University of Calgary, 3330 Hospital Dr. NW, Calgary, AB, T2N 4Z6, Canada
| | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, AB, T2N 1N4, Canada
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22
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Morgan TJ, Herman MA, Johnson LC, Olson BJ, Ungerer MC. Ecological Genomics: genes in ecology and ecology in genes. Genome 2018; 61:v-vii. [DOI: 10.1139/gen-2018-0022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Theodore J. Morgan
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
| | - Michael A. Herman
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
| | - Loretta C. Johnson
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
| | - Bradley J.C.S. Olson
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
| | - Mark C. Ungerer
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
- Division of Biology and Ecological Genomics Institute, Kansas State University, Manhattan, KS 66506, USA
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23
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Okamoto KW, Amarasekare P. A framework for high‐throughput eco‐evolutionary simulations integrating multilocus forward‐time population genetics and community ecology. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Kenichi W. Okamoto
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
- Department of Entomology North Carolina State University Raleigh NC USA
- Department of Ecology and Evolutionary Biology Yale Institute for Biospheric Studies Yale University New Haven CT USA
| | - Priyanga Amarasekare
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
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24
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Patel S, Cortez MH, Schreiber SJ. Partitioning the Effects of Eco-Evolutionary Feedbacks on Community Stability. Am Nat 2018. [DOI: 10.1086/695834] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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25
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Rudman SM, Barbour MA, Csilléry K, Gienapp P, Guillaume F, Hairston Jr NG, Hendry AP, Lasky JR, Rafajlović M, Räsänen K, Schmidt PS, Seehausen O, Therkildsen NO, Turcotte MM, Levine JM. What genomic data can reveal about eco-evolutionary dynamics. Nat Ecol Evol 2017; 2:9-15. [DOI: 10.1038/s41559-017-0385-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 10/16/2017] [Indexed: 01/17/2023]
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26
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Ożgo M, Liew TS, Webster NB, Schilthuizen M. Inferring microevolution from museum collections and resampling: lessons learned from Cepaea. PeerJ 2017; 5:e3938. [PMID: 29093997 PMCID: PMC5661451 DOI: 10.7717/peerj.3938] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/26/2017] [Indexed: 01/08/2023] Open
Abstract
Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.
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Affiliation(s)
- Małgorzata Ożgo
- Department of Evolutionary Biology, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Thor-Seng Liew
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia.,Institute Biology Leiden, Leiden University, Leiden, The Netherlands.,Endless Forms Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Nicole B Webster
- Institute Biology Leiden, Leiden University, Leiden, The Netherlands.,Endless Forms Group, Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Menno Schilthuizen
- Institute for Tropical Biology and Conservation, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia.,Institute Biology Leiden, Leiden University, Leiden, The Netherlands.,Endless Forms Group, Naturalis Biodiversity Center, Leiden, The Netherlands
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27
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Saastamoinen M, Bocedi G, Cote J, Legrand D, Guillaume F, Wheat CW, Fronhofer EA, Garcia C, Henry R, Husby A, Baguette M, Bonte D, Coulon A, Kokko H, Matthysen E, Niitepõld K, Nonaka E, Stevens VM, Travis JMJ, Donohue K, Bullock JM, Del Mar Delgado M. Genetics of dispersal. Biol Rev Camb Philos Soc 2017; 93:574-599. [PMID: 28776950 PMCID: PMC5811798 DOI: 10.1111/brv.12356] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/12/2022]
Abstract
Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal‐related phenotypes or evidence for the micro‐evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment‐dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non‐additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non‐equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context‐dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.
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Affiliation(s)
- Marjo Saastamoinen
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | - Julien Cote
- Laboratoire Évolution & Diversité Biologique UMR5174, CNRS, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Delphine Legrand
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Christopher W Wheat
- Population Genetics, Department of Zoology, Stockholm University, S-10691 Stockholm, Sweden
| | - Emanuel A Fronhofer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland
| | - Cristina Garcia
- CIBIO-InBIO, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Roslyn Henry
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K.,School of GeoSciences, University of Edinburgh, Edinburgh EH89XP, U.K
| | - Arild Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Michel Baguette
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France.,Museum National d'Histoire Naturelle, Institut Systématique, Evolution, Biodiversité, UMR 7205, F-75005 Paris, France
| | - Dries Bonte
- Department of Biology, Ghent University, B-9000 Ghent, Belgium
| | - Aurélie Coulon
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Biogéographie et Ecologie des Vertébrés, 34293 Montpellier, France.,CESCO UMR 7204, Bases écologiques de la conservation, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Kristjan Niitepõld
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Etsuko Nonaka
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Justin M J Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | | | - James M Bullock
- NERC Centre for Ecology & Hydrology, Wallingford OX10 8BB, U.K
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28
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Lindberg CD, Jayasundara N, Kozal JS, Leuthner TC, Di Giulio RT. Resistance to polycyclic aromatic hydrocarbon toxicity and associated bioenergetic consequences in a population of Fundulus heteroclitus. ECOTOXICOLOGY (LONDON, ENGLAND) 2017; 26:435-448. [PMID: 28213827 PMCID: PMC5398948 DOI: 10.1007/s10646-017-1775-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/02/2017] [Indexed: 05/20/2023]
Abstract
Several locations in the Elizabeth River, VA, USA are highly contaminated with polycyclic aromatic hydrocarbons (PAHs) due to the release of creosote mixtures from wood treatment facilities. Interestingly, some populations of Atlantic killifish (Fundulus heteroclitus) inhabiting the Elizabeth River (ER) are resistant to PAH-induced teratogenesis. However, evolutionary resistance to PAHs due to chronic PAH exposure is associated with reduced fitness and increased susceptibility to other environmental stressors in at least one PAH-resistant ER killifish population. More specifically, wild-caught and first generation PAH-resistant juvenile killifish have altered metabolic demands when compared to non-resistant fish. Herein, we investigated this association further by examining a previously under-studied population captured from the creosote-contaminated site Republic Creosoting (Rep). We assessed PAH toxicity and effects on energy metabolism in Rep killifish in comparison with killifish from the reference site Kings Creek (KC). Following exposures to simple and complex PAH mixtures, Rep killifish exhibited several phenotypes associated with PAH resistance including decreased incidences of developmental cardiovascular deformities and recalcitrant cytochrome P450 1A (CYP1A) activity. We evaluated bioenergetics in killifish embryos throughout development and found elevated basal oxygen consumption rates in Rep embryos relative to KC embryos. Furthermore, juvenile F1 Rep fish had significantly lower maximal metabolic rates and aerobic scopes than KC juveniles. These results suggest that populations of killifish that have adapted or evolved to withstand the toxicity associated with PAHs consequently have altered energetic metabolism or demands. Such consequences could result in an enhanced vulnerability to other environmental and anthropogenic stressors in PAH-resistant killifish.
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Affiliation(s)
- C D Lindberg
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA.
- Integrated Toxicology and Environmental Health Program, Duke University, Durham, NC, 27708, USA.
| | - N Jayasundara
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
| | - J S Kozal
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
- Integrated Toxicology and Environmental Health Program, Duke University, Durham, NC, 27708, USA
| | - T C Leuthner
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
- Integrated Toxicology and Environmental Health Program, Duke University, Durham, NC, 27708, USA
| | - R T Di Giulio
- Nicholas School of the Environment, Duke University, Durham, NC, 27708, USA
- Integrated Toxicology and Environmental Health Program, Duke University, Durham, NC, 27708, USA
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29
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Henning F, Machado-Schiaffino G, Baumgarten L, Meyer A. Genetic dissection of adaptive form and function in rapidly speciating cichlid fishes. Evolution 2017; 71:1297-1312. [PMID: 28211577 DOI: 10.1111/evo.13206] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 02/04/2017] [Indexed: 12/14/2022]
Abstract
Genes of major phenotypic effects and strong genetic correlations can facilitate adaptation, direct selective responses, and potentially lead to phenotypic convergence. However, the preponderance of this type of genetic architecture in repeatedly evolved adaptations remains unknown. Using hybrids between Haplochromis chilotes (thick-lipped) and Pundamilia nyererei (thin-lipped) we investigated the genetics underlying hypertrophied lips and elongated heads, traits that evolved repeatedly in cichlids. At least 25 loci of small-to-moderate and mainly additive effects were detected. Phenotypic variation in lip and head morphology was largely independent. Although several QTL overlapped for lip and head morphology traits, they were often of opposite effects. The distribution of effect signs suggests strong selection on lips. The fitness implications of several detected loci were demonstrated using a laboratory assay testing for the association between genotype and variation in foraging performance. The persistence of low fitness alleles in head morphology appears to be maintained through antagonistic pleiotropy/close linkage with positive-effect lip morphology alleles. Rather than being based on few major loci with strong positive genetic correlations, our results indicate that the evolution of the Lake Victoria thick-lipped ecomorph is the result of selection on numerous loci distributed throughout the genome.
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Affiliation(s)
- Frederico Henning
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany.,Department of Genetics, CCS, Federal University of Rio de Janeiro, Ilha do Fundão, 21941-599, Rio de Janeiro, Brazil
| | | | - Lukas Baumgarten
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, 78464, Konstanz, Germany
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Rodríguez-Verdugo A, Buckley J, Stapley J. The genomic basis of eco-evolutionary dynamics. Mol Ecol 2017; 26:1456-1464. [PMID: 28160333 DOI: 10.1111/mec.14045] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/22/2017] [Accepted: 01/25/2017] [Indexed: 12/30/2022]
Abstract
Recent recognition that ecological and evolutionary processes can operate on similar timescales has led to a rapid increase in theoretical and empirical studies on eco-evolutionary dynamics. Progress in the fields of evolutionary biology, genomics and ecology is greatly enhancing our understanding of rapid adaptive processes, the predictability of adaptation and the genetics of ecologically important traits. However, progress in these fields has proceeded largely independently of one another. In an attempt to better integrate these fields, the centre for 'Adaptation to a Changing Environment' organized a conference entitled 'The genomic basis of eco-evolutionary change' and brought together experts in ecological genomics and eco-evolutionary dynamics. In this review, we use the work of the invited speakers to summarize eco-evolutionary dynamics and discuss how they are relevant for understanding and predicting responses to contemporary environmental change. Then, we show how recent advances in genomics are contributing to our understanding of eco-evolutionary dynamics. Finally, we highlight the gaps in our understanding of eco-evolutionary dynamics and recommend future avenues of research in eco-evolutionary dynamics.
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Affiliation(s)
- Alejandra Rodríguez-Verdugo
- Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland.,Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland
| | - James Buckley
- Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
| | - Jessica Stapley
- Adaptation to a Changing Environment, ETH Zürich, 8092, Zürich, Switzerland
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Chirgwin E, Marshall DJ, Sgrò CM, Monro K. The other 96%: Can neglected sources of fitness variation offer new insights into adaptation to global change? Evol Appl 2017; 10:267-275. [PMID: 28250811 PMCID: PMC5322406 DOI: 10.1111/eva.12447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/31/2016] [Indexed: 01/07/2023] Open
Abstract
Mounting research considers whether populations may adapt to global change based on additive genetic variance in fitness. Yet selection acts on phenotypes, not additive genetic variance alone, meaning that persistence and evolutionary potential in the near term, at least, may be influenced by other sources of fitness variation, including nonadditive genetic and maternal environmental effects. The fitness consequences of these effects, and their environmental sensitivity, are largely unknown. Here, applying a quantitative genetic breeding design to an ecologically important marine tubeworm, we examined nonadditive genetic and maternal environmental effects on fitness (larval survival) across three thermal environments. We found that these effects are nontrivial and environment dependent, explaining at least 44% of all parentally derived effects on survival at any temperature and 96% of parental effects at the most stressful temperature. Unlike maternal environmental effects, which manifested at the latter temperature only, nonadditive genetic effects were consistently significant and covaried positively across temperatures (i.e., parental combinations that enhanced survival at one temperature also enhanced survival at elevated temperatures). Thus, while nonadditive genetic and maternal environmental effects have long been neglected because their evolutionary consequences are complex, unpredictable, or seen as transient, we argue that they warrant further attention in a rapidly warming world.
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Affiliation(s)
- Evatt Chirgwin
- Centre for Geometric BiologyMonash UniversityMelbourneVICAustralia
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
| | - Dustin J. Marshall
- Centre for Geometric BiologyMonash UniversityMelbourneVICAustralia
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
| | - Carla M. Sgrò
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
| | - Keyne Monro
- Centre for Geometric BiologyMonash UniversityMelbourneVICAustralia
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
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Vertacnik KL, Linnen CR. Evolutionary genetics of host shifts in herbivorous insects: insights from the age of genomics. Ann N Y Acad Sci 2017; 1389:186-212. [DOI: 10.1111/nyas.13311] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/16/2016] [Accepted: 12/22/2016] [Indexed: 12/25/2022]
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Betini GS, McAdam AG, Griswold CK, Norris DR. A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size. eLife 2017; 6:e18770. [PMID: 28164780 PMCID: PMC5340529 DOI: 10.7554/elife.18770] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 02/06/2017] [Indexed: 11/17/2022] Open
Abstract
Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles.
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Affiliation(s)
- Gustavo S Betini
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | - Andrew G McAdam
- Department of Integrative Biology, University of Guelph, Guelph, Canada
| | | | - D Ryan Norris
- Department of Integrative Biology, University of Guelph, Guelph, Canada
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Population Genetics and Demography Unite Ecology and Evolution. Trends Ecol Evol 2017; 32:141-152. [DOI: 10.1016/j.tree.2016.12.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 12/08/2016] [Accepted: 12/10/2016] [Indexed: 12/31/2022]
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Species-rich networks and eco-evolutionary synthesis at the metacommunity level. Nat Ecol Evol 2017; 1:24. [DOI: 10.1038/s41559-016-0024] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/25/2016] [Indexed: 12/21/2022]
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Pearse DE. Saving the spandrels? Adaptive genomic variation in conservation and fisheries management. JOURNAL OF FISH BIOLOGY 2016; 89:2697-2716. [PMID: 27723095 DOI: 10.1111/jfb.13168] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 09/06/2016] [Indexed: 06/06/2023]
Abstract
As highlighted by many of the papers in this issue, research on the genomic basis of adaptive phenotypic variation in natural populations has made spectacular progress in the past few years, largely due to the advances in sequencing technology and analysis. Without question, the resulting genomic data will improve the understanding of regions of the genome under selection and extend knowledge of the genetic basis of adaptive evolution. What is far less clear, but has been the focus of active discussion, is how such information can or should transfer into conservation practice to complement more typical conservation applications of genetic data. Before such applications can be realized, the evolutionary importance of specific targets of selection relative to the genome-wide diversity of the species as a whole must be evaluated. The key issues for the incorporation of adaptive genomic variation in conservation and management are discussed here, using published examples of adaptive genomic variation associated with specific phenotypes in salmonids and other taxa to highlight practical considerations for incorporating such information into conservation programmes. Scenarios are described in which adaptive genomic data could be used in conservation or restoration, constraints on its utility and the importance of validating inferences drawn from new genomic data before applying them in conservation practice. Finally, it is argued that an excessive focus on preserving the adaptive variation that can be measured, while ignoring the vast unknown majority that cannot, is a modern twist on the adaptationist programme that Gould and Lewontin critiqued almost 40 years ago.
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Affiliation(s)
- D E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, 110 Shaffer Road, Santa Cruz, CA, 95060, U.S.A
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37
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Nacci D, Proestou D, Champlin D, Martinson J, Waits ER. Genetic basis for rapidly evolved tolerance in the wild: adaptation to toxic pollutants by an estuarine fish species. Mol Ecol 2016; 25:5467-5482. [DOI: 10.1111/mec.13848] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 08/22/2016] [Accepted: 08/30/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Diane Nacci
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Dina Proestou
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - Denise Champlin
- U.S. Environmental Protection Agency Office of Research and Development National Health and Environmental Effects Research Laboratory Atlantic Ecology Division 27 Tarzwell Dr. Narragansett RI 02882 USA
| | - John Martinson
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
| | - Eric R. Waits
- U.S. Environmental Protection Agency Office of Research and Development National Exposure Research Laboratory Ecological Exposure Research Division 26 W. Martin Luther King Dr. Cincinnati OH 45268 USA
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Bybee S, Córdoba-Aguilar A, Duryea MC, Futahashi R, Hansson B, Lorenzo-Carballa MO, Schilder R, Stoks R, Suvorov A, Svensson EI, Swaegers J, Takahashi Y, Watts PC, Wellenreuther M. Odonata (dragonflies and damselflies) as a bridge between ecology and evolutionary genomics. Front Zool 2016; 13:46. [PMID: 27766110 PMCID: PMC5057408 DOI: 10.1186/s12983-016-0176-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 09/16/2016] [Indexed: 12/21/2022] Open
Abstract
Odonata (dragonflies and damselflies) present an unparalleled insect model to integrate evolutionary genomics with ecology for the study of insect evolution. Key features of Odonata include their ancient phylogenetic position, extensive phenotypic and ecological diversity, several unique evolutionary innovations, ease of study in the wild and usefulness as bioindicators for freshwater ecosystems worldwide. In this review, we synthesize studies on the evolution, ecology and physiology of odonates, highlighting those areas where the integration of ecology with genomics would yield significant insights into the evolutionary processes that would not be gained easily by working on other animal groups. We argue that the unique features of this group combined with their complex life cycle, flight behaviour, diversity in ecological niches and their sensitivity to anthropogenic change make odonates a promising and fruitful taxon for genomics focused research. Future areas of research that deserve increased attention are also briefly outlined.
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Affiliation(s)
- Seth Bybee
- Brigham Young University, Provo, UT 84606 USA
| | - Alex Córdoba-Aguilar
- Departmento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Apdo, Postal 70-275, Ciudad Universitaria, 04510 Mexico City, Mexico
| | - M. Catherine Duryea
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Ryo Futahashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Central 6, Tsukuba, Ibaraki 305-8566 Japan
| | - Bengt Hansson
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - M. Olalla Lorenzo-Carballa
- Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool, L69 7ZB UK
| | - Ruud Schilder
- Departments of Entomology and Biology, Pennsylvania State University, University Park, PA 16802 USA
| | - Robby Stoks
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, University of Leuven, 3000 Leuven, Belgium
| | - Anton Suvorov
- Department of Biology, Brigham Young University, LSB 4102, Provo, UT 84602 USA
| | - Erik I. Svensson
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
| | - Janne Swaegers
- Laboratory of Aquatic Ecology, Evolution and Conservation, Department of Biology, University of Leuven, 3000 Leuven, Belgium
| | - Yuma Takahashi
- Division of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba, Sendai, Miyagi 980-8578 Japan
| | | | - Maren Wellenreuther
- Evolutionary Ecology Unit, Department of Biology, Lund University, 223 62 Lund, Sweden
- Plant and Food Research Limited, Nelson, 7010 New Zealand
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Govaert L, Pantel JH, De Meester L. Eco-evolutionary partitioning metrics: assessing the importance of ecological and evolutionary contributions to population and community change. Ecol Lett 2016; 19:839-53. [DOI: 10.1111/ele.12632] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 04/28/2016] [Accepted: 05/15/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven, Ch. Deberiotstraat 32 B-3000 Leuven Belgium
| | - Jelena H. Pantel
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven, Ch. Deberiotstraat 32 B-3000 Leuven Belgium
- Centre d'Ecologie fonctionelle et Evolutive; UMR 5175 CNRS Université de Montpellier EPHE; Campus CNRS; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution and Conservation; KU Leuven, Ch. Deberiotstraat 32 B-3000 Leuven Belgium
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40
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Roux F, Bergelson J. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology. Curr Top Dev Biol 2016; 119:111-56. [PMID: 27282025 DOI: 10.1016/bs.ctdb.2016.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity.
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Affiliation(s)
- F Roux
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.
| | - J Bergelson
- University of Chicago, Chicago, IL, United States
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41
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Kinnison MT, Hairston NG, Hendry AP. Cryptic eco-evolutionary dynamics. Ann N Y Acad Sci 2016; 1360:120-44. [PMID: 26619300 DOI: 10.1111/nyas.12974] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 12/17/2022]
Abstract
Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them.
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Affiliation(s)
| | - Nelson G Hairston
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York
| | - Andrew P Hendry
- Redpath Museum and Department of Biology, McGill University, Montreal, Quebec, Canada
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42
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Thomas GE, Geetha KA, Augustine L, Mamiyil S, Thomas G. Analyses between Reproductive Behavior, Genetic Diversity and Pythium Responsiveness in Zingiber spp. Reveal an Adaptive Significance for Hemiclonality. FRONTIERS IN PLANT SCIENCE 2016; 7:1913. [PMID: 28066470 PMCID: PMC5167741 DOI: 10.3389/fpls.2016.01913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 12/02/2016] [Indexed: 05/09/2023]
Abstract
Mode of reproduction is generally considered to have long-range evolutionary implications on population survival. Because sexual reproduction produces genetically diverse genotypes, this mode of reproduction is predicted to positively influence the success potential of offspring in evolutionary arms race with parasites (Red queen) whereas, without segregation and recombination, the obligate asexual multiplication may push a species into extinction due to the steady accumulation of deleterious mutations (Muller's ratchet). However, the extent of linearity between reproductive strategies, genetic diversity and population fitness, and the contributions of different breeding strategies to population fitness are yet to be understood clearly. Genus Zingiber belonging to the pan-tropic family Zingiberaceae represents a good system to study contributions of different breeding behavior on genetic diversity and population fitness, as this genus comprises species with contrasting breeding systems. In this study, we analyzed breeding behavior, amplified fragment length polymorphism diversity and response to the soft-rot pathogen Pythium aphanidermatum in 18 natural populations of three wild Zingiber spp.: Z. neesanum, Z. nimmonii, and Z. zerumbet, together with the obligately asexual cultivated congener, ginger (Z. officinale). Ginger showed an exceptionally narrow genetic base, and adding to this, all the tested cultivars were uniformly susceptible to soft-rot. Concordant with the postulates of Muller's ratchet, the background selection may be continuously pushing ginger into the ancestral state, rendering it inefficient in host-pathogen coevolution. Z. neesanum and Z. nimmonii populations were sexual and genetically diverse; however, contrary to Red Queen expectations, the populations were highly susceptible to soft-rot. Z. zerumbet showed a hemiclonal breeding behavior. The populations inhabiting forest understory were large and continuous, sexual and genetically diverse, but were susceptible, whereas populations inhabiting the revenue land were fragmented and monoclonal, but were resistant. It may be possible that, when genetic recombination becomes at a premium due to the genetic constraints imparted by habitat fragmentation or pathogen pressure, Z. zerumbet.
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Affiliation(s)
| | - Kiran A. Geetha
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram, India
| | - Lesly Augustine
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram, India
| | - Sabu Mamiyil
- Department of Botany, University of CalicutMalappuram, India
| | - George Thomas
- Plant Disease Biology and Biotechnology, Rajiv Gandhi Centre for BiotechnologyThiruvananthapuram, India
- *Correspondence: George Thomas,
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Hornoy B, Pavy N, Gérardi S, Beaulieu J, Bousquet J. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes. Genome Biol Evol 2015; 7:3269-85. [PMID: 26560341 PMCID: PMC4700950 DOI: 10.1093/gbe/evv218] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources.
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Affiliation(s)
- Benjamin Hornoy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Sébastien Gérardi
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
| | - Jean Beaulieu
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada Natural Resources Canada, Canadian Wood Fibre Centre, Québec City, QC, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest and Environmental Genomics, Centre for Forest Research and Institute for Systems and Integrative Biology, Université Laval, Québec City, QC, Canada
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Hendry AP. Key Questions on the Role of Phenotypic Plasticity in Eco-Evolutionary Dynamics. J Hered 2015; 107:25-41. [PMID: 26297912 DOI: 10.1093/jhered/esv060] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 07/16/2015] [Indexed: 11/13/2022] Open
Abstract
Ecology and evolution have long been recognized as reciprocally influencing each other, with recent research emphasizing how such interactions can occur even on very short (contemporary) time scales. Given that these interactions are mediated by organismal phenotypes, they can be variously shaped by genetic variation, phenotypic plasticity, or both. I here address 8 key questions relevant to the role of plasticity in eco-evolutionary dynamics. Focusing on empirical evidence, especially from natural populations, I offer the following conclusions. 1) Plasticity is--not surprisingly--sometimes adaptive, sometimes maladaptive, and sometimes neutral. 2) Plasticity has costs and limits but these constraints are highly variable, often weak, and hard to detect. 3) Variable environments favor the evolution of increased trait plasticity, which can then buffer fitness/performance (i.e., tolerance). 4) Plasticity sometimes aids colonization of new environments (Baldwin Effect) and responses to in situ environmental change. However, plastic responses are not always necessary or sufficient in these contexts. 5) Plasticity will sometimes promote and sometimes constrain genetic evolution. 6) Plasticity will sometimes help and sometimes hinder ecological speciation but, at present, empirical tests are limited. 7) Plasticity can show considerable evolutionary change in contemporary time, although the rates of this reaction norm evolution are highly variable among taxa and traits. 8) Plasticity appears to have considerable influences on ecological dynamics at the community and ecosystem levels, although many more studies are needed. In summary, plasticity needs to be an integral part of any conceptual framework and empirical investigation of eco-evolutionary dynamics.
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Affiliation(s)
- Andrew P Hendry
- From the Redpath Museum & Department of Biology, 859 Sherbrooke St. W., Montreal, Quebec H3A OC4, Canada.
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45
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Alexandre H, Vrignaud J, Mangin B, Joly S. Genetic architecture of pollination syndrome transition between hummingbird-specialist and generalist species in the genus Rhytidophyllum (Gesneriaceae). PeerJ 2015; 3:e1028. [PMID: 26157613 PMCID: PMC4476130 DOI: 10.7717/peerj.1028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/26/2015] [Indexed: 12/16/2022] Open
Abstract
Adaptation to pollinators is a key factor of diversification in angiosperms. The Caribbean sister genera Rhytidophyllum and Gesneria present an important diversification of floral characters. Most of their species can be divided in two major pollination syndromes. Large-open flowers with pale colours and great amount of nectar represent the generalist syndrome, while the hummingbird-specialist syndrome corresponds to red tubular flowers with a less important nectar volume. Repeated convergent evolution toward the generalist syndrome in this group suggests that such transitions rely on few genes of moderate to large effect. To test this hypothesis, we built a linkage map and performed a QTL detection for divergent pollination syndrome traits by crossing one specimen of the generalist species Rhytidophyllum auriculatum with one specimen of the hummingbird pollinated R. rupincola. Using geometric morphometrics and univariate traits measurements, we found that floral shape among the second-generation hybrids is correlated with morphological variation observed between generalist and hummingbird-specialist species at the genus level. The QTL analysis showed that colour and nectar volume variation between syndromes involve each one major QTL while floral shape has a more complex genetic basis and rely on few genes of moderate effect. Finally, we did not detect any genetic linkage between the QTLs underlying those traits. This genetic independence of traits could have facilitated evolution toward optimal syndromes.
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Affiliation(s)
- Hermine Alexandre
- Institut de Recherche en Biologie Végétale, Université de Montréal , Montreal, QC , Canada
| | - Justine Vrignaud
- Institut de Recherche en Biologie Végétale, Université de Montréal , Montreal, QC , Canada
| | - Brigitte Mangin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM) UMR , Castanet-Tolosan , France ; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM) UMR , Castanet-Tolosan , France
| | - Simon Joly
- Institut de Recherche en Biologie Végétale, Université de Montréal , Montreal, QC , Canada ; Montreal Botanical Garden , Montreal, QC , Canada
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Le Rouzic A, Hansen TF, Gosden TP, Svensson EI. Evolutionary Time-Series Analysis Reveals the Signature of Frequency-Dependent Selection on a Female Mating Polymorphism. Am Nat 2015; 185:E182-96. [DOI: 10.1086/680982] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Piñeros VJ, Rios-Cardenas O, Gutiérrez-Rodríguez C, Mendoza-Cuenca L. Morphological Differentiation in the Damselfish Abudefduf saxatilis Along the Mexican Atlantic Coast is Associated with Environmental Factors and High Connectivity. Evol Biol 2015. [DOI: 10.1007/s11692-015-9314-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Bolstad GH, Hansen TF, Pélabon C, Falahati-Anbaran M, Pérez-Barrales R, Armbruster WS. Genetic constraints predict evolutionary divergence in Dalechampia blossoms. Philos Trans R Soc Lond B Biol Sci 2015; 369:20130255. [PMID: 25002700 PMCID: PMC4084540 DOI: 10.1098/rstb.2013.0255] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
If genetic constraints are important, then rates and direction of evolution should be related to trait evolvability. Here we use recently developed measures of evolvability to test the genetic constraint hypothesis with quantitative genetic data on floral morphology from the Neotropical vine Dalechampia scandens (Euphorbiaceae). These measures were compared against rates of evolution and patterns of divergence among 24 populations in two species in the D. scandens species complex. We found clear evidence for genetic constraints, particularly among traits that were tightly phenotypically integrated. This relationship between evolvability and evolutionary divergence is puzzling, because the estimated evolvabilities seem too large to constitute real constraints. We suggest that this paradox can be explained by a combination of weak stabilizing selection around moving adaptive optima and small realized evolvabilities relative to the observed additive genetic variance.
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Affiliation(s)
- Geir H Bolstad
- Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Thomas F Hansen
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
| | - Christophe Pélabon
- Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Mohsen Falahati-Anbaran
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway School of Biology and Center of Excellence in Phylogeny of Living Organisms, University of Tehran, 14155-6455 Tehran, Iran
| | | | - W Scott Armbruster
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK Institute of Arctic Biology, University of Alaska, Fairbanks AK 99775, USA
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Harrisson KA, Pavlova A, Telonis-Scott M, Sunnucks P. Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl 2014; 7:1008-25. [PMID: 25553064 PMCID: PMC4231592 DOI: 10.1111/eva.12149] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/10/2014] [Indexed: 12/16/2022] Open
Abstract
Genomics promises exciting advances towards the important conservation goal of maximizing evolutionary potential, notwithstanding associated challenges. Here, we explore some of the complexity of adaptation genetics and discuss the strengths and limitations of genomics as a tool for characterizing evolutionary potential in the context of conservation management. Many traits are polygenic and can be strongly influenced by minor differences in regulatory networks and by epigenetic variation not visible in DNA sequence. Much of this critical complexity is difficult to detect using methods commonly used to identify adaptive variation, and this needs appropriate consideration when planning genomic screens, and when basing management decisions on genomic data. When the genomic basis of adaptation and future threats are well understood, it may be appropriate to focus management on particular adaptive traits. For more typical conservations scenarios, we argue that screening genome-wide variation should be a sensible approach that may provide a generalized measure of evolutionary potential that accounts for the contributions of small-effect loci and cryptic variation and is robust to uncertainty about future change and required adaptive response(s). The best conservation outcomes should be achieved when genomic estimates of evolutionary potential are used within an adaptive management framework.
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Affiliation(s)
| | - Alexandra Pavlova
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
| | | | - Paul Sunnucks
- School of Biological Sciences, Monash UniversityMelbourne, Vic., Australia
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