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Denney DA, Patel P, Anderson JT. Elevated [CO 2] and temperature augment gas exchange and shift the fitness landscape in a montane forb. THE NEW PHYTOLOGIST 2024; 243:58-71. [PMID: 38655662 DOI: 10.1111/nph.19765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024]
Abstract
Climate change is simultaneously increasing carbon dioxide concentrations ([CO2]) and temperature. These factors could interact to influence plant physiology and performance. Alternatively, increased [CO2] may offset costs associated with elevated temperatures. Furthermore, the interaction between elevated temperature and [CO2] may differentially affect populations from along an elevational gradient and disrupt local adaptation. We conducted a multifactorial growth chamber experiment to examine the interactive effects of temperature and [CO2] on fitness and ecophysiology of diverse accessions of Boechera stricta (Brassicaceae) sourced from a broad elevational gradient in Colorado. We tested whether increased [CO2] would enhance photosynthesis across accessions, and whether warmer conditions would depress the fitness of high-elevation accessions owing to steep reductions in temperature with increasing elevation in this system. Elevational clines in [CO2] are not as evident, making it challenging to predict how locally adapted ecotypes will respond to elevated [CO2]. This experiment revealed that elevated [CO2] increased photosynthesis and intrinsic water use efficiency across all accessions. However, these instantaneous responses to treatments did not translate to changes in fitness. Instead, increased temperatures reduced the probability of reproduction for all accessions. Elevated [CO2] and increased temperatures interacted to shift the adaptive landscape, favoring lower elevation accessions for the probability of survival and fecundity. Our results suggest that elevated temperatures and [CO2] associated with climate change could have severe negative consequences, especially for high-elevation populations.
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Affiliation(s)
- Derek A Denney
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Pratik Patel
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
| | - Jill T Anderson
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
- Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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2
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Soularue JP, Firmat C, Caignard T, Thöni A, Arnoux L, Delzon S, Ronce O, Kremer A. Antagonistic Effects of Assortative Mating on the Evolution of Phenotypic Plasticity along Environmental Gradients. Am Nat 2023; 202:18-39. [PMID: 37384769 PMCID: PMC7614710 DOI: 10.1086/724579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2023]
Abstract
AbstractPrevious theory has shown that assortative mating for plastic traits can maintain genetic divergence across environmental gradients despite high gene flow. Yet these models did not examine how assortative mating affects the evolution of plasticity. We here describe patterns of genetic variation across elevation for plasticity in a trait under assortative mating, using multiple-year observations of budburst date in a common garden of sessile oaks. Despite high gene flow, we found significant spatial genetic divergence for the intercept, but not for the slope, of reaction norms to temperature. We then used individual-based simulations, where both the slope and the intercept of the reaction norm evolve, to examine how assortative mating affects the evolution of plasticity, varying the intensity and distance of gene flow. Our model predicts the evolution of either suboptimal plasticity (reaction norms with a slope shallower than optimal) or hyperplasticity (slopes steeper than optimal) in the presence of assortative mating when optimal plasticity would evolve under random mating. Furthermore, a cogradient pattern of genetic divergence for the intercept of the reaction norm (where plastic and genetic effects are in the same direction) always evolves in simulations with assortative mating, consistent with our observations in the studied oak populations.
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Ong PW, Lin YP, Chen HW, Lo CY, Burlyaeva M, Noble T, Nair RM, Schafleitner R, Vishnyakova M, Bishop-von-Wettberg E, Samsonova M, Nuzhdin S, Ting CT, Lee CR. Environment as a limiting factor of the historical global spread of mungbean. eLife 2023; 12:e85725. [PMID: 37204293 PMCID: PMC10299821 DOI: 10.7554/elife.85725] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/18/2023] [Indexed: 05/20/2023] Open
Abstract
While the domestication process has been investigated in many crops, the detailed route of cultivation range expansion and factors governing this process received relatively little attention. Here, using mungbean (Vigna radiata var. radiata) as a test case, we investigated the genomes of more than 1000 accessions to illustrate climatic adaptation's role in dictating the unique routes of cultivation range expansion. Despite the geographical proximity between South and Central Asia, genetic evidence suggests mungbean cultivation first spread from South Asia to Southeast, East and finally reached Central Asia. Combining evidence from demographic inference, climatic niche modeling, plant morphology, and records from ancient Chinese sources, we showed that the specific route was shaped by the unique combinations of climatic constraints and farmer practices across Asia, which imposed divergent selection favoring higher yield in the south but short-season and more drought-tolerant accessions in the north. Our results suggest that mungbean did not radiate from the domestication center as expected purely under human activity, but instead, the spread of mungbean cultivation is highly constrained by climatic adaptation, echoing the idea that human commensals are more difficult to spread through the south-north axis of continents.
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Affiliation(s)
- Pei-Wen Ong
- Institute of Plant Biology, National Taiwan UniversityTaipeiTaiwan
| | - Ya-Ping Lin
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipeiTaiwan
- World Vegetable CenterTainanTaiwan
| | - Hung-Wei Chen
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipeiTaiwan
| | - Cheng-Yu Lo
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipeiTaiwan
| | - Marina Burlyaeva
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)St. PetersburgRussian Federation
| | - Thomas Noble
- Department of Agriculture and FisheriesWarwickAustralia
| | | | | | - Margarita Vishnyakova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)St. PetersburgRussian Federation
| | - Eric Bishop-von-Wettberg
- Department of Plant and Soil Science and Gund Institute for the Environment, University of VermontBurlingtonUnited States
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic UniversitySaint PetersburgRussian Federation
| | - Maria Samsonova
- Department of Applied Mathematics, Peter the Great St. Petersburg Polytechnic UniversitySaint PetersburgRussian Federation
| | - Sergey Nuzhdin
- University of Southern CaliforniaLos AngelesUnited States
| | - Chau-Ti Ting
- Department of Life Science, National Taiwan UniversityTaipeiTaiwan
| | - Cheng-Ruei Lee
- Institute of Plant Biology, National Taiwan UniversityTaipeiTaiwan
- Institute of Ecology and Evolutionary Biology, National Taiwan UniversityTaipeiTaiwan
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4
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MacTavish R, Anderson JT. Water and nutrient availability exert selection on reproductive phenology. AMERICAN JOURNAL OF BOTANY 2022; 109:1702-1716. [PMID: 36031862 DOI: 10.1002/ajb2.16057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 07/22/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Global change has changed resource availability to plants, which could shift the adaptive landscape. We hypothesize that novel water and nutrient availability combinations alter patterns of natural selection on reproductive phenology in Boechera stricta (Brassicaceae) and influence the evolution of local adaptation. METHODS We conducted a multifactorial greenhouse study using 35 accessions of B. stricta sourced from a broad elevational gradient in the Rocky Mountains. We exposed full siblings to three soil water and two nutrient availability treatment levels, reflecting current and projected future conditions. In addition, we quantified fitness (seed count) and four phenological traits: the timing of first flowering, the duration of flowering, and height and leaf number at flowering. RESULTS Selection favored early flowering and longer duration of flowering, and the genetic correlation between these traits accorded with the direction of selection. In most treatments, we found selection for increased height, but selection on leaf number depended on water availability, with selection favoring more leaves in well-watered conditions and fewer leaves under severe drought. Low-elevation genotypes had the greatest fitness under drought stress, consistent with local adaptation. CONCLUSIONS We found evidence of strong selection on these heritable traits. Furthermore, the direction and strength of selection on size at flowering depended on the variable measured (height vs. leaf number). Finally, selection often favored both early flowering and a longer duration of flowering. Selection on these two components of phenology can be difficult to disentangle due to tight genetic correlations.
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Affiliation(s)
- Rachel MacTavish
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA, 30602, USA
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5
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Ding C, Brouard JS. Assisted migration is plausible for a boreal tree species under climate change: A quantitative and population genetics study of trembling aspen ( Populus tremuloides Michx.) in western Canada. Ecol Evol 2022; 12:e9384. [PMID: 36225831 PMCID: PMC9534759 DOI: 10.1002/ece3.9384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 09/16/2022] [Indexed: 11/14/2022] Open
Abstract
A novel method was tested for improving tree breeding strategies that integrate quantitative and population genetics based on range-wide reciprocal transplant experiments. Five reciprocal common garden tests of Populus tremuloides were investigated including 6450 trees across western Canada focusing on adaptation traits and growth. Both genetic parameters and home-site transplant models were evaluated. We found a genetic trade-off between growth and early spring leaf flush and late fall senescence. Coefficients of phenotypic variation (CVp) of cell lysis (CL), a measure of freezing injury, shrank from 0.28 to 0.10 during acclimation in the fall, and the CVp slope versus the freezing temperature was significantly different from zero (R 2 = 0.33, p = .02). There was more between-population genetic variation in fall phenology than in spring leaf phenology. We suggest that P. tremuloides demonstrated a discrepancy between the ecological optimum and the physiological optimum minimum winter temperature. The sub-optimal growing condition of P. tremuloides is potentially caused by the warmer ecological optimum than the physiological optimum. Assisted migration and breeding of fast growers to reforest cooler plantation sites can improve productivity. Transferring the study populations to less than 4°C of extreme minimum temperature appears safe for reforestation aligning with the historical recolonization direction of the species. This is equivalent to a 5-10° latitudinal northward movement. Fall frost hardiness is an effective criterion for family selection in the range tested in this study.
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Affiliation(s)
- Chen Ding
- Western Gulf Forest Tree Improvement ProgramTexas A&M Forest Service, TAMU SystemCollege StationTexasUSA
| | - Jean S. Brouard
- Isabella Point Forestry Ltd.Salt Spring IslandBritish ColumbiaCanada
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Cooper HF, Best RJ, Andrews LV, Corbin JPM, Garthwaite I, Grady KC, Gehring CA, Hultine KR, Whitham TG, Allan GJ. Evidence of climate-driven selection on tree traits and trait plasticity across the climatic range of a riparian foundation species. Mol Ecol 2022; 31:5024-5040. [PMID: 35947510 DOI: 10.1111/mec.16645] [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: 01/19/2021] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/30/2022]
Abstract
Selection on quantitative traits by heterogeneous climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticities within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood), a foundation riparian distributed throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST -FST analyses to detect selection on traits and trait plasticity. We then explored the environmental drivers of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens, both of which were heritable. 2) Based on QST -FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). These results suggest that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.
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Affiliation(s)
- Hillary F Cooper
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Rebecca J Best
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Lela V Andrews
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA
| | - Jaclyn P M Corbin
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Iris Garthwaite
- School of Earth and Sustainability, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin C Grady
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Catherine A Gehring
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Kevin R Hultine
- Department of Research, Conservation and Collections, Desert Botanical Garden, Phoenix, AZ, USA
| | - Thomas G Whitham
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
| | - Gerard J Allan
- Department of Biological Science, Northern Arizona University, Flagstaff, AZ, USA.,Center for Adaptable Western Landscapes, Northern Arizona University, Flagstaff, AZ, USA
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Bouteiller XP, Moret F, Ségura R, Klisz M, Martinik A, Monty A, Pino J, van Loo M, Wojda T, Porté AJ, Mariette S. The seeds of invasion: enhanced germination in invasive European populations of black locust (Robinia pseudoacacia L.) compared to native American populations. PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:1006-1017. [PMID: 34546636 DOI: 10.1111/plb.13332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/28/2021] [Indexed: 06/13/2023]
Abstract
Local adaptation and the evolution of phenotypic plasticity may facilitate biological invasions. Both processes can enhance germination and seedling recruitment, which are crucial life-history traits for plants. The rate, timing and speed of germination have recently been documented as playing a major role during the invasion process. Black locust (Robinia pseudoacacia L.) is a North American tree, which has spread widely throughout Europe. A recent study demonstrated that a few populations are the source of European black locust. Thus, invasive populations can be compared to native ones in order to identify genetic-based phenotypic differentiation and the role of phenotypic plasticity can thereby be assessed. A quantitative genetics experiment was performed to evaluate 13 juvenile traits of both native and invasive black locust populations (3000 seeds, 20 populations) subjected to three different thermal treatments (18 °C, 22 °C and 31 °C). The results revealed European populations to have a higher germination rate than the native American populations (88% versus 60%), and even when genetic distance between populations was considered. Moreover, this trait showed lower plasticity to temperature in the invasive range than in the native one. Conversely, other studied traits showed high plasticity to temperature, but they responded in a similar way to temperature increase: the warmer the temperature, the higher the growth rate or germination traits values. The demonstrated genetic differentiation between native and invasive populations testifies to a shift between ranges for the maximum germination percentage. This pattern could be due to human-mediated introduction of black locust.
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Affiliation(s)
| | - F Moret
- BIOGECO, INRAE, Univ. Bordeaux, Cestas, France
| | - R Ségura
- BIOGECO, INRAE, Univ. Bordeaux, Cestas, France
| | - M Klisz
- Department of Silviculture and Genetics, Forest Research Institute, Raszyn, Poland
| | - A Martinik
- Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno, Czech Republic
| | - A Monty
- Gembloux Agro-Bio Tech, Biodiversity and Landscape Unit, University of Liège, Gembloux, Belgium
| | - J Pino
- Centre for Ecological Research and Forestry Applications (CREAF), Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - M van Loo
- Department of Forest Growth, Silviculture and Genetics, Research Centre for Forests (BFW), Vienna, Austria
| | - T Wojda
- Department of Silviculture and Genetics, Forest Research Institute, Raszyn, Poland
| | - A J Porté
- BIOGECO, INRAE, Univ. Bordeaux, Cestas, France
| | - S Mariette
- BIOGECO, INRAE, Univ. Bordeaux, Cestas, France
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8
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Neupane S, Xu S. Adaptive Divergence of Meiotic Recombination Rate in Ecological Speciation. Genome Biol Evol 2021; 12:1869-1881. [PMID: 32857858 PMCID: PMC7594247 DOI: 10.1093/gbe/evaa182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here, we examine the population-level recombination rate variation in two incipient ecological species, the microcrustacean Daphnia pulex (an ephemeral-pond species) and Daphnia pulicaria (a permanent-lake species). The divergence of D. pulicaria from D. pulex involved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate in D. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution.
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Affiliation(s)
| | - Sen Xu
- Department of Biology, University of Texas at Arlington
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9
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Paril JF, Balding DJ, Fournier-Level A. Optimizing sampling design and sequencing strategy for the genomic analysis of quantitative traits in natural populations. Mol Ecol Resour 2021; 22:137-152. [PMID: 34192415 DOI: 10.1111/1755-0998.13458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 05/02/2021] [Accepted: 06/25/2021] [Indexed: 11/27/2022]
Abstract
Mapping the genes underlying ecologically relevant traits in natural populations is fundamental to develop a molecular understanding of species adaptation. Current sequencing technologies enable the characterization of a species' genetic diversity across the landscape or even over its whole range. The relevant capture of the genetic diversity across the landscape is critical for a successful genetic mapping of traits and there are no clear guidelines on how to achieve an optimal sampling and which sequencing strategy to implement. Here we determine, through simulation, the sampling scheme that maximizes the power to map the genetic basis of a complex trait in an outbreeding species across an idealized landscape and draw genomic predictions for the trait, comparing individual and pool sequencing strategies. Our results show that quantitative trait locus detection power and prediction accuracy are higher when more populations over the landscape are sampled and this is more cost-effectively done with pool sequencing than with individual sequencing. Additionally, we recommend sampling populations from areas of high genetic diversity. As progress in sequencing enables the integration of trait-based functional ecology into landscape genomics studies, these findings will guide study designs allowing direct measures of genetic effects in natural populations across the environment.
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Affiliation(s)
- Jefferson F Paril
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - David J Balding
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia.,School of Mathematics and Statistics, The University of Melbourne, Parkville, Victoria, Australia
| | - Alexandre Fournier-Level
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.,Melbourne Integrative Genomics, The University of Melbourne, Parkville, Victoria, Australia
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10
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Chapuis E, Ali N, Noûs C, Besnard G. Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica). Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractCultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.
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Affiliation(s)
- Elodie Chapuis
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | - Nadeen Ali
- CBGP, IRD, CIRAD, INRA, Montpellier SupAgro, University of Montpellier, Montpellier, France
| | | | - Guillaume Besnard
- CNRS, UPS, IRD, UMR5174, EDB, Université Toulouse III Paul Sabatier, Toulouse Cedex, France
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11
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Dumartinet T, Abadie C, Bonnot F, Carreel F, Roussel V, Habas R, Martinez RT, Perez‐Vicente L, Carlier J. Pattern of local adaptation to quantitative host resistance in a major pathogen of a perennial crop. Evol Appl 2020; 13:824-836. [PMID: 32211070 PMCID: PMC7086059 DOI: 10.1111/eva.12904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/10/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired-population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross-inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host-pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used "Cavendish" banana group. These results highlight the need to study specific host-pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.
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Affiliation(s)
- Thomas Dumartinet
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Catherine Abadie
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
- CIRADUMR BGPICapesterre‐Belle‐EauFrance
| | - François Bonnot
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Françoise Carreel
- UMR AGAPUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Véronique Roussel
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Rémy Habas
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | | | | | - Jean Carlier
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
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12
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Siala M, Cassan C, Smaoui S, Kammoun S, Marouane C, Godreuil S, Hachicha S, Mhiri E, Slim L, Gamara D, Messadi-Akrout F, Bañuls AL. A first insight into genetic diversity of Mycobacterium bovis isolated from extrapulmonary tuberculosis patients in South Tunisia assessed by spoligotyping and MIRU VNTR. PLoS Negl Trop Dis 2019; 13:e0007707. [PMID: 31532767 PMCID: PMC6750577 DOI: 10.1371/journal.pntd.0007707] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 08/14/2019] [Indexed: 01/16/2023] Open
Abstract
Introduction In Tunisia, almost 77% of clinically and bacteriologically diagnosed cases of extrapulmonary tuberculosis (EPTB) are zoonotic TB, caused by M. bovis. Although several studies have analyzed bovine TB in cattle in Tunisia, no study has evaluated the risk of transmission to humans in such an endemic country. We aimed to study the genetic diversity of M. bovis human isolates, to ascertain the causes of human EPTB infection by M. bovis and to investigate the distribution and population structure of this species in Tunisia. Materials and methods A total of 110 M. bovis isolates taken from patients with confirmed EPTB were characterized by spoligotyping and MIRU-VNTR typing methods. Results Among the 15 spoligotypes detected in our study, 6 (SB0120, SB0121, SB2025, SB1200, SB1003 and SB0134) were the most prevalent (83.5%) of which SB0120, SB0121 and SB2025 were the most prevailing. MIRU-VNTR typing method showed a high genotypic and genetic diversity. The genetic differentiation based on MIRU-VNTR was significant between populations from South East (Tataouine, Medenine) and Central West (Gafsa, Sidi Bouzid, Kasserine) regions. Of note, 13/15 (86.7%) spoligotypes detected in our study were previously identified in cattle in Tunisia with different frequencies suggesting a peculiar ability of some genotypes to infect humans. Using combined spoligotyping and MIRU-VNTR method, a high clustering rate of 43.9% was obtained. Our results underlined that human EPTB due to M. bovis was more commonly found in female gender and in young patients. Most of our patients, 66.4% (73/110) were raw milk or derivatives consumers, whereas 30.9% (34/110) patients would have contracted EPTB through contact with livestock. The findings suggest that the transmission of Zoonotic TB caused by M. bovis to humans mainly occurred by oral route through raw milk or derivatives. Conclusion Our study showed the urgent need of a better veterinary control with the implementation of effective and comprehensive strategies in order to reach a good protection of animals as well as human health. In South Tunisia, the prevalence of bovine TB is high with Mycobacterium bovis as causative agent and cattle as reservoir of the bacteria. However as previously mentioned in several studies, M. bovis is also responsible for human extrapulmonary tuberculosis (EPTB) cases in South Tunisia. Despite the veterinary and medical problems, M. bovis is still little studied. In this context, this work aimed to study the molecular epidemiology of M. bovis in EPTB patients in south Tunisia in order to determine the main risk factors of transmission. Our results underlined that SB0120, SB0121 and SB2025, previously described in cattle in Tunisia, represent the predominant genotypes. The findings highlighted that human EPTB caused by M. bovis mainly occurred through the consumption of raw milk or derivatives. These data demonstrate the urgent need to implement strategies for preventing and controlling zoonotic TB.
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Affiliation(s)
- Mariam Siala
- Department of Biology, Preparatory Institute for Engineering Studies, Sfax, University of Sfax-Tunisia
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, Sfax, University of Sfax-Tunisia
- * E-mail:
| | - Cécile Cassan
- MIVEGEC, UMR IRD–CNRS—Université de Montpellier, Montpellier, France
| | - Salma Smaoui
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Sana Kammoun
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Chema Marouane
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Sylvain Godreuil
- MIVEGEC, UMR IRD–CNRS—Université de Montpellier, Montpellier, France
- Laboratoire de Bactériologie, CHU de Montpellier, France
| | - Salma Hachicha
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Emna Mhiri
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
- Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A. Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Leila Slim
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
- Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A. Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Dhikrayet Gamara
- Basic Health Care Management, Ministry of Health, Tunis, Tunisia
| | - Férièle Messadi-Akrout
- Department of Mycobacteriology, Regional hygiene care laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia
- Department of Biology B, Faculty of pharmacy, Monastir, University of Monastir, Monastir, Tunisia
| | - Anne-Laure Bañuls
- MIVEGEC, UMR IRD–CNRS—Université de Montpellier, Montpellier, France
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13
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Rifkin JL, Liao IT, Castillo AS, Rausher MD. Multiple aspects of the selfing syndrome of the morning glory Ipomoea lacunosa evolved in response to selection: A Qst-Fst comparison. Ecol Evol 2019; 9:7712-7725. [PMID: 31346434 PMCID: PMC6635925 DOI: 10.1002/ece3.5329] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/17/2019] [Accepted: 05/19/2019] [Indexed: 01/05/2023] Open
Abstract
The frequent transition from outcrossing to selfing in flowering plants is often accompanied by changes in multiple aspects of floral morphology, termed the "selfing syndrome." While the repeated evolution of these changes suggests a role for natural selection, genetic drift may also be responsible. To determine whether selection or drift shaped different aspects of the pollination syndrome and mating system in the highly selfing morning glory Ipomoea lacunosa, we performed multivariate and univariate Qst-Fst comparisons using a wide sample of populations of I. lacunosa and its mixed-mating sister species Ipomoea cordatotriloba. The two species differ in early growth, floral display, inflorescence traits, corolla size, nectar, and pollen number. Our analyses support a role for natural selection driving trait divergence, specifically in corolla size and nectar traits, but not in early growth, display size, inflorescence length, or pollen traits. We also find evidence of selection for reduced herkogamy in I. lacunosa, consistent with selection driving both the transition in mating system and the correlated floral changes. Our research demonstrates that while some aspects of the selfing syndrome evolved in response to selection, others likely evolved due to drift or correlated selection, and the balance between these forces may vary across selfing species.
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Affiliation(s)
| | - Irene T. Liao
- Department of BiologyDuke UniversityDurhamNorth Carolina
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14
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Mathé-Hubert H, Kremmer L, Colinet D, Gatti JL, Van Baaren J, Delava É, Poirié M. Variation in the Venom of Parasitic Wasps, Drift, or Selection? Insights From a Multivariate QST Analysis. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00156] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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15
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Koch EM. The Effects of Demography and Genetics on the Neutral Distribution of Quantitative Traits. Genetics 2019; 211:1371-1394. [PMID: 30782599 PMCID: PMC6456309 DOI: 10.1534/genetics.118.301839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/15/2019] [Indexed: 11/18/2022] Open
Abstract
Neutral models for quantitative trait evolution are useful for identifying phenotypes under selection. These models often assume normally distributed phenotypes. This assumption may be violated when a trait is affected by relatively few variants or when the effects of those variants arise from skewed or heavy tailed distributions. Molecular phenotypes such as gene expression levels may have these properties. To accommodate deviations from normality, models making fewer assumptions about the underlying genetics and patterns of variation are needed. Here, we develop a general neutral model for quantitative trait variation using a coalescent approach. This model allows interpretation of trait distributions in terms of familiar population genetic parameters because it is based on the coalescent. We show how the normal distribution resulting from the infinitesimal limit, where the number of loci grows large as the effect size per mutation becomes small, depends only on expected pairwise coalescent times. We then demonstrate how deviations from normality depend on demography through the distribution of coalescence times as well as through genetic parameters. In particular, population growth events exacerbate deviations while bottlenecks reduce them. We demonstrate the practical applications of this model by showing how to sample from the neutral distribution of [Formula: see text], the ratio of the variance between subpopulations to that in the overall population. We further show it is likely impossible to distinguish sparsity from skewed or heavy tailed mutational effects using only sampled trait values. The model analyzed here greatly expands the parameter space for neutral trait models.
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Affiliation(s)
- Evan M Koch
- Department of Ecology and Evolution, University of Chicago, Illinois 60637
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16
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Luquet E, Rödin Mörch P, Cortázar‐Chinarro M, Meyer‐Lucht Y, Höglund J, Laurila A. Post‐glacial colonization routes coincide with a life‐history breakpoint along a latitudinal gradient. J Evol Biol 2019; 32:356-368. [DOI: 10.1111/jeb.13419] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 01/17/2023]
Affiliation(s)
- Emilien Luquet
- Univ LyonUniversité Claude Bernard Lyon 1CNRSENTPEUMR5023 LEHNA Villeurbanne France
| | - Patrik Rödin Mörch
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Maria Cortázar‐Chinarro
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Yvonne Meyer‐Lucht
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Jacob Höglund
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
| | - Anssi Laurila
- Animal Ecology/Department of Ecology and GeneticsEvolutionary Biology CentreUppsala University Uppsala Sweden
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17
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Born J, Michalski SG. Trait expression and signatures of adaptation in response to nitrogen addition in the common wetland plant Juncus effusus. PLoS One 2019; 14:e0209886. [PMID: 30608976 PMCID: PMC6319709 DOI: 10.1371/journal.pone.0209886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 12/13/2018] [Indexed: 01/16/2023] Open
Abstract
Wetland ecosystems are known to mitigate high nutrient loadings and thus can improve water quality and prevent potential biodiversity loss caused by eutrophication. Plant traits affect wetland processes directly through effects on accumulation or metabolization of substances, and indirectly by affecting microbial transformation processes in the soil. Understanding the causes and consequences of intraspecific variation in plant functional traits and associated ecosystem processes can aid applied ecological approaches such as wetland restoration and construction. Here we investigated molecular variation and phenotypic variation in response to three levels of nitrogen availability for a regional set of populations of the common wetland plant Juncus effusus. We asked whether trait expression reveals signatures of adaptive differentiation by comparing genetic differentiation in quantitative traits and neutral molecular markers (QST—FST comparisons) and relating trait variation to soil conditions of the plant’s origin. Molecular analyses showed that samples clustered into three very distinct genetic lineages with strong population differentiation within and among lineages. Differentiation for quantitative traits was substantial but did not exceed neutral expectations when compared across treatments or for each treatment and lineage separately. However, variation in trait expression could be explained by local soil environmental conditions of sample origin, e.g. for aboveground carbon-to-nitrogen (C:N) ratios, suggesting adaptive differentiation to contribute to trait expression even at regional level.
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Affiliation(s)
- Jennifer Born
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
- * E-mail:
| | - Stefan G. Michalski
- Department of Community Ecology (BZF), Helmholtz Centre for Environmental Research – UFZ, Halle, Germany
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18
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Lobo A, Hansen OK, Hansen JK, Erichsen EO, Jacobsen B, Kjær ED. Local adaptation through genetic differentiation in highly fragmented Tilia cordata populations. Ecol Evol 2018; 8:5968-5976. [PMID: 29988427 PMCID: PMC6024143 DOI: 10.1002/ece3.4131] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 12/30/2022] Open
Abstract
We assessed the level of geographic differentiation of Tilia cordata in Denmark based on tests of 91 trees selected from 12 isolated populations. We used quantitative analysis of spring phenology and population genetic analysis based on SSR markers to infer the likely historical genetic processes within and among populations. High genetic variation within and among populations was observed in spring phenology, which correlated with spring temperatures at the origin of the tested T. cordata trees. The population genetic analysis revealed significant differentiation among the populations, but with no clear sign of isolation by distance. We infer the findings as indications of ongoing fine scale selection in favor of local growth conditions made possible by limited gene flow among the small and fragmented populations. This hypothesis fits well with reports of limited fruiting in the investigated Danish T. cordata populations, while the species is known for its ability to propagate vegetatively by root suckers. Our results suggest that both divergent selection and genetic drift may have played important roles in forming the genetic patterns of T. cordata at its northern distribution limit. However, we also speculate that epigenetic mechanism arising from the original population environment could have created similar patterns in regulating the spring phenology.
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Affiliation(s)
- Albin Lobo
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Ole Kim Hansen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Jon Kehlet Hansen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Eva Ortvald Erichsen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
| | - Birgitte Jacobsen
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
- Present address:
Ministry of Fisheries and HuntingNuukGreenland
| | - Erik Dahl Kjær
- Department of Geosciences and Natural Resource Management (IGN)University of CopenhagenFrederiksberg CDenmark
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19
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Cubry P, Scotti I, Oddou-Muratorio S, Lefèvre F. Generalization of the Q ST framework in hierarchically structured populations: Impacts of inbreeding and dominance. Mol Ecol Resour 2017; 17:e76-e83. [PMID: 28681534 DOI: 10.1111/1755-0998.12693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 05/12/2017] [Accepted: 05/22/2017] [Indexed: 11/30/2022]
Abstract
QST is a differentiation parameter based on the decomposition of the genetic variance of a trait. In the case of additive inheritance and absence of selection, it is analogous to the genic differentiation measured on individual loci, FST . Thus, QST -FST comparison is used to infer selection: selective divergence when QST > FST , or convergence when QST < FST. The definition of Q-statistics was extended to two-level hierarchical population structures with Hardy-Weinberg equilibrium. Here, we generalize the Q-statistics framework to any hierarchical population structure. First, we developed the analytical definition of hierarchical Q-statistics for populations not at Hardy-Weinberg equilibrium. We show that the Q-statistics values obtained with the Hardy-Weinberg definition are lower than their corresponding F-statistics when FIS > 0 (higher when FIS < 0). Then, we used an island model simulation approach to investigate the impact of inbreeding and dominance on the QST -FST framework in a hierarchical population structure. We show that, while differentiation at the lower hierarchical level (QSR ) is a monotonic function of migration, differentiation at the upper level (QRT ) is not. In the case of additive inheritance, we show that inbreeding inflates the variance of QRT , which can increase the frequency of QRT > FRT cases. We also show that dominance drastically reduces Q-statistics below F-statistics for any level of the hierarchy. Therefore, high values of Q-statistics are good indicators of selection, but low values are not in the case of dominance.
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Affiliation(s)
- Philippe Cubry
- INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon Cedex9, France.,IRD, UMR DIADE, Montpellier Cedex 5, France
| | - Ivan Scotti
- INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon Cedex9, France
| | | | - François Lefèvre
- INRA, UR 629 Ecologie des Forêts Méditerranéennes, URFM, Avignon Cedex9, France
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20
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Wadgymar SM, Daws SC, Anderson JT. Integrating viability and fecundity selection to illuminate the adaptive nature of genetic clines. Evol Lett 2017; 1:26-39. [PMID: 30283636 PMCID: PMC6121800 DOI: 10.1002/evl3.3] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/15/2017] [Accepted: 03/20/2017] [Indexed: 12/18/2022] Open
Abstract
Genetically based trait variation across environmental gradients can reflect adaptation to local environments. However, natural populations that appear well-adapted often exhibit directional, not stabilizing, selection on ecologically relevant traits. Temporal variation in the direction of selection could lead to stabilizing selection across multiple episodes of selection, which might be overlooked in short-term studies that evaluate relationships of traits and fitness under only one set of conditions. Furthermore, nonrandom mortality prior to trait expression can bias inferences about trait evolution if viability selection opposes fecundity selection. Here, we leveraged fitness and trait data to test whether phenotypic clines are genetically based and adaptive, whether temporal variation in climate imposes stabilizing selection, and whether viability selection acts on adult phenotypes. We monitored transplants of the subalpine perennial forb, Boechera stricta (Brassicaceae), in common gardens at two elevations over 2-3 years that differed in drought intensity. We quantified viability, and fecundity fitness components for four heritable traits: specific leaf area, integrated water-use efficiency, height at first flower, and flowering phenology. Our results indicate that genetic clines are maintained by selection, but their expression is context dependent, as they do not emerge in all environments. Moreover, selection varied spatially and temporally. Stabilizing selection was most pronounced when we integrated data across years. Finally, viability selection prior to trait expression targeted adult phenotypes (age and size at flowering). Indeed, viability selection for delayed flowering opposed fecundity selection for accelerated flowering; this result demonstrates that neglecting to account for viability selection could lead to inaccurate conclusions that populations are maladapted. Our results suggest that reconciling clinal trait variation with selection requires data collected across multiple spatial scales, time frames, and life-history stages.
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Affiliation(s)
- Susana M Wadgymar
- Department of Genetics and Odum School of Ecology University of Georgia Athens Georgia 30602
| | - S Caroline Daws
- Department of Ecology, Evolution and Behavior University of Minnesota St. Paul Minnesota 55108
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology University of Georgia Athens Georgia 30602
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21
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Evans LM, Kaluthota S, Pearce DW, Allan GJ, Floate K, Rood SB, Whitham TG. Bud phenology and growth are subject to divergent selection across a latitudinal gradient in Populus angustifolia and impact adaptation across the distributional range and associated arthropods. Ecol Evol 2016; 6:4565-81. [PMID: 27386097 PMCID: PMC4931002 DOI: 10.1002/ece3.2222] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/11/2016] [Indexed: 12/12/2022] Open
Abstract
Temperate forest tree species that span large geographical areas and climatic gradients often have high levels of genetic variation. Such species are ideal for testing how neutral demographic factors and climate‐driven selection structure genetic variation within species, and how this genetic variation can affect ecological communities. Here, we quantified genetic variation in vegetative phenology and growth traits in narrowleaf cottonwood, Populus angustifolia, using three common gardens planted with genotypes originating from source populations spanning the species' range along the Rocky Mountains of North America (ca. 1700 km). We present three main findings. First, we found strong evidence of divergent selection (QST > FST) on fall phenology (bud set) with adaptive consequences for frost avoidance. We also found evidence for selection on bud flush duration, tree height, and basal diameter, resulting in population differentiation. Second, we found strong associations with climate variables that were strongly correlated with latitude of origin. More strongly differentiated traits also showed stronger climate correlations, which emphasizes the role that climate has played in divergent selection throughout the range. We found population × garden interaction effects; for some traits, this accounted for more of the variance than either factor alone. Tree height was influenced by the difference in climate of the source and garden locations and declined with increasing transfer distance. Third, growth traits were correlated with dependent arthropod community diversity metrics. Synthesis. Overall, we conclude that climate has influenced genetic variation and structure in phenology and growth traits and leads to local adaptation in P. angustifolia, which can then impact dependent arthropod species. Importantly, relocation of genotypes far northward or southward often resulted in poor growth, likely due to a phenological mismatch with photoperiod, the proximate cue for fall growth cessation. Genotypes moved too far southward suffer from early growth cessation, whereas those moved too far northward are prone to fall frost and winter dieback. In the face of current and forecasted climate change, habitat restoration, forestry, and tree breeding efforts should utilize these findings to better match latitudinal and climatic source environments with management locations for optimal future outcomes.
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Affiliation(s)
- Luke M Evans
- Department of Biological Sciences & Merriam-Powell Center for Environmental Research Northern Arizona University PO Box 5640 Flagstaff Arizona 86011
| | - Sobadini Kaluthota
- Biological Science University of Lethbridge Lethbridge Alberta T1K 3M4 Canada
| | - David W Pearce
- Biological Science University of Lethbridge Lethbridge Alberta T1K 3M4 Canada
| | - Gerard J Allan
- Department of Biological Sciences & Merriam-Powell Center for Environmental Research Northern Arizona University PO Box 5640 Flagstaff Arizona 86011
| | - Kevin Floate
- Lethbridge Research and Development Centre Agriculture and Agri-Food Canada Lethbridge Alberta T1J 4B1 Canada
| | - Stewart B Rood
- Biological Science University of Lethbridge Lethbridge Alberta T1K 3M4 Canada
| | - Thomas G Whitham
- Department of Biological Sciences & Merriam-Powell Center for Environmental Research Northern Arizona University PO Box 5640 Flagstaff Arizona 86011
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22
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Gallien L, Thuiller W, Fort N, Boleda M, Alberto FJ, Rioux D, Lainé J, Lavergne S. Is There Any Evidence for Rapid, Genetically-Based, Climatic Niche Expansion in the Invasive Common Ragweed? PLoS One 2016; 11:e0152867. [PMID: 27116455 PMCID: PMC4846088 DOI: 10.1371/journal.pone.0152867] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 03/21/2016] [Indexed: 01/19/2023] Open
Abstract
Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L.), a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence). Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.
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Affiliation(s)
- Laure Gallien
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
- * E-mail:
| | - Wilfried Thuiller
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
| | - Noémie Fort
- Conservatoire Botanique National Alpin, Domaine de Charance, 05000, Gap, France
| | - Marti Boleda
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
| | - Florian J. Alberto
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
| | - Delphine Rioux
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
| | - Juliette Lainé
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
| | - Sébastien Lavergne
- Laboratoire d’Écologie Alpine (LECA), Univ. Grenoble Alpes, F-38000, Grenoble, France
- Laboratoire d’Écologie Alpine (LECA), CNRS, F-38000, Grenoble, France
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23
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Volis S, Ormanbekova D, Shulgina I. Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions. Mol Ecol 2016; 25:1449-64. [PMID: 26841244 DOI: 10.1111/mec.13565] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/17/2016] [Accepted: 01/26/2016] [Indexed: 02/03/2023]
Abstract
Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean. In a multiyear reciprocal transplant experiment, the plants of desert and Mediterranean origin demonstrated home advantage, and population differentiation in several phenotypic traits related to reproduction exceeded neutral predictions, as determined by comparisons of QST values with theoretical FST distributions. Thus, variation in these traits likely resulted from local adaptation to desert and Mediterranean environments. The two separate common garden experiments conducted with different experimental design revealed that two population comparisons, in contrast to multi-population comparisons, are likely to detect population differences in virtually every trait, but many of these differences reflect effects of local rather than regional environment. We detected a general reduction in neutral (SSR) genetic variation but not in adaptive quantitative trait variation in peripheral desert as compared with Mediterranean core populations. On the other hand, the molecular data indicated intensive gene flow from the Mediterranean core towards desert periphery. Although species range position in our study (edge vs. interior) was confounded with climate (desert vs. Mediterranean), the results suggest that the gene flow from the species core does not have negative consequences for either performance of the peripheral plants or their adaptive potential.
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Affiliation(s)
- S Volis
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - D Ormanbekova
- Department of Agricultural Sciences, University of Bologna, Bologna, 40127, Italy
| | - I Shulgina
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
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24
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Shinn C, Blanchet S, Loot G, Lek S, Grenouillet G. Phenotypic variation as an indicator of pesticide stress in gudgeon: Accounting for confounding factors in the wild. THE SCIENCE OF THE TOTAL ENVIRONMENT 2015; 538:733-742. [PMID: 26327641 DOI: 10.1016/j.scitotenv.2015.08.081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/13/2015] [Accepted: 08/14/2015] [Indexed: 06/04/2023]
Abstract
The response of organisms to environmental stress is currently used in the assessment of ecosystem health. Morphological changes integrate the multiple effects of one or several stress factors upon the development of the exposed organisms. In a natural environment, many factors determine the patterns of morphological differentiation between individuals. However, few studies have sought to distinguish and measure the independent effect of these factors (genetic diversity and structure, spatial structuring of populations, physical-chemical conditions, etc.). Here we investigated the relationship between pesticide levels measured at 11 sites sampled in rivers of the Garonne river basin (SW France) and morphological changes of a freshwater fish species, the gudgeon (Gobio gobio). Each individual sampled was genotyped using 8 microsatellite markers and their phenotype characterized via 17 morphological traits. Our analysis detected a link between population genetic structure (revealed by a Bayesian method) and morphometry (linear discriminant analysis) of the studied populations. We then developed an original method based on general linear models using distance matrices, an extension of the partial Mantel test beyond 3 matrices. This method was used to test the relationship between contamination (toxicity index) and morphometry (PST of morphometric traits), taking into account (1) genetic differentiation between populations (FST), (2) geographical distances between sites, (3) site catchment area, and (4) various physical-chemical parameters for each sampling site. Upon removal of confounding effects, 3 of the 17 morphological traits studied were significantly correlated with pesticide toxicity, suggesting a response of these traits to the anthropogenic stress. These results underline the importance of taking into account the different sources of phenotypic variability between organisms when identifying the stress factors involved. The separation and quantification of the independent effect of such factors provides an interesting outlook regarding the use of these evaluation metrics as indicators of ecosystem health.
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Affiliation(s)
- Cândida Shinn
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier - 4R1, 118 Route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Simon Blanchet
- CR2-CNRS, Laboratoire d'Ecologie Expérimentale du CNRS à Moulis, 09200 Saint Girons, France.
| | - Géraldine Loot
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier - 4R1, 118 Route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Sovan Lek
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier - 4R1, 118 Route de Narbonne, 31062 Toulouse cedex 9, France.
| | - Gaël Grenouillet
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier - 4R1, 118 Route de Narbonne, 31062 Toulouse cedex 9, France.
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Côte J, Bouétard A, Pronost Y, Besnard AL, Coke M, Piquet F, Caquet T, Coutellec MA. Genetic variation of Lymnaea stagnalis tolerance to copper: A test of selection hypotheses and its relevance for ecological risk assessment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2015; 205:209-217. [PMID: 26074162 DOI: 10.1016/j.envpol.2015.05.040] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 06/04/2023]
Abstract
The use of standardized monospecific testing to assess the ecological risk of chemicals implicitly relies on the strong assumption that intraspecific variation in sensitivity is negligible or irrelevant in this context. In this study, we investigated genetic variation in copper sensitivity of the freshwater snail Lymnaea stagnalis, using lineages stemming from eight natural populations or strains found to be genetically differentiated at neutral markers. Copper-induced mortality varied widely among populations, as did the estimated daily death rate and time to 50% mortality (LT50). Population genetic divergence in copper sensitivity was compared to neutral differentiation using the QST-FST approach. No evidence for homogenizing selection could be detected. This result demonstrates that species-level extrapolations from single population studies are highly unreliable. The study provides a simple example of how evolutionary principles could be incorporated into ecotoxicity testing in order to refine ecological risk assessment.
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Affiliation(s)
- Jessica Côte
- INRA, UMR0985 INRA/Agrocampus-Ouest ESE Ecology and Ecosystem Health, Rennes, France
| | - Anthony Bouétard
- INRA, UMR0985 INRA/Agrocampus-Ouest ESE Ecology and Ecosystem Health, Rennes, France
| | | | - Anne-Laure Besnard
- INRA, UMR0985 INRA/Agrocampus-Ouest ESE Ecology and Ecosystem Health, Rennes, France
| | - Maïra Coke
- INRA, Experimental Unit U3E, Rennes, France
| | | | - Thierry Caquet
- INRA, UMR0985 INRA/Agrocampus-Ouest ESE Ecology and Ecosystem Health, Rennes, France
| | - Marie-Agnès Coutellec
- INRA, UMR0985 INRA/Agrocampus-Ouest ESE Ecology and Ecosystem Health, Rennes, France.
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Anderson JT, Perera N, Chowdhury B, Mitchell-Olds T. Microgeographic Patterns of Genetic Divergence and Adaptation across Environmental Gradients in Boechera stricta (Brassicaceae). Am Nat 2015; 186 Suppl 1:S60-73. [PMID: 26656218 DOI: 10.1086/682404] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Abiotic and biotic conditions often vary continuously across the landscape, imposing divergent selection on local populations. We used a provenance trial approach to examine microgeographic variation in local adaptation in Boechera stricta (Brassicaceae), a perennial forb native to the Rocky Mountains. In montane ecosystems, environmental conditions change considerably over short spatial scales, such that neighboring populations can be subject to different selective pressures. Using accessions from southern (Colorado) and northern (Idaho) populations, we characterized spatial variation in genetic similarity via microsatellite markers. We then transplanted genotypes from multiple local populations into common gardens in both regions. Continuous variation in local adaptation emerged for several components of fitness. In Idaho, genotypes from warmer environments (low-elevation or south-facing sites) were poorly adapted to the north-facing garden. In high- and low-elevation Colorado gardens, susceptibility to insect herbivory increased with source elevation. In the high-elevation Colorado garden, germination success peaked for genotypes that evolved at elevations similar to that of the garden and decreased for genotypes from higher and lower elevations. We also found evidence for local maladaptation in survival and fecundity components of fitness in the low-elevation Colorado garden. This approach is a first step in predicting how global change could affect evolutionary dynamics.
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Affiliation(s)
- Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, Georgia 30602
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27
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Sanou A, Tarnagda Z, Kanyala E, Zingué D, Nouctara M, Ganamé Z, Combary A, Hien H, Dembele M, Kabore A, Meda N, Van de Perre P, Neveu D, Bañuls AL, Godreuil S. Mycobacterium bovis in Burkina Faso: epidemiologic and genetic links between human and cattle isolates. PLoS Negl Trop Dis 2014; 8:e3142. [PMID: 25275305 PMCID: PMC4183478 DOI: 10.1371/journal.pntd.0003142] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Accepted: 07/23/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In sub-Saharan Africa, bovine tuberculosis (bTB) is a potential hazard for animals and humans health. The goal of this study was to improve our understanding of bTB epidemiology in Burkina Faso and especially Mycobacterium bovis transmission within and between the bovine and human populations. METHODOLOGY/PRINCIPAL FINDINGS Twenty six M. bovis strains were isolated from 101 cattle carcasses with suspected bTB lesions during routine meat inspections at the Bobo Dioulasso and Ouagadougou slaughterhouses. In addition, 7 M. bovis strains were isolated from 576 patients with pulmonary tuberculosis. Spoligotyping, RDAf1 deletion and MIRU-VNTR typing were used for strains genotyping. The isolation of M. bovis strains was confirmed by spoligotyping and 12 spoligotype signatures were detected. Together, the spoligotyping and MIRU-VNTR data allowed grouping the 33 M. bovis isolates in seven clusters including isolates exclusively from cattle (5) or humans (1) or from both (1). Moreover, these data (genetic analyses and phenetic tree) showed that the M. bovis isolates belonged to the African 1 (Af1) clonal complex (81.8%) and the putative African 5 (Af5) clonal complex (18.2%), in agreement with the results of RDAf1 deletion typing. CONCLUSIONS/SIGNIFICANCE This is the first detailed molecular characterization of M. bovis strains from humans and cattle in Burkina Faso. The distribution of the two Af1 and putative Af5 clonal complexes is comparable to what has been reported in neighbouring countries. Furthermore, the strain genetic profiles suggest that M. bovis circulates across the borders and that the Burkina Faso strains originate from different countries, but have a country-specific evolution. The genetic characterization suggests that, currently, M. bovis transmission occurs mainly between cattle, occasionally between cattle and humans and potentially between humans. This study emphasizes the bTB risk in cattle but also in humans and the difficulty to set up proper disease control strategies in Burkina Faso.
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Affiliation(s)
- Adama Sanou
- MIVEGEC, UMR IRD 224-CNRS 5290-Montpellier Universités 1 et 2, Montpellier, France
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- * E-mail:
| | - Zekiba Tarnagda
- Institut de Recherche en Sciences de la Santé (IRSS), Direction Régionale de l'Ouest (DRO), Bobo Dioulasso, Burkina Faso
- Université de Ouagadougou, Ouagadougou, Burkina Faso
| | | | | | | | | | - Adjima Combary
- Programme National Tuberculose, Ouagadougou, Burkina Faso
| | - Hervé Hien
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- Institut de Recherche en Sciences de la Santé (IRSS), Direction Régionale de l'Ouest (DRO), Bobo Dioulasso, Burkina Faso
| | | | | | - Nicolas Meda
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- Université de Ouagadougou, Ouagadougou, Burkina Faso
| | - Philippe Van de Perre
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France
- Université Montpellier 1, Montpellier, France
- INSERM U 1058, Infection by HIV and by Agents with Mucocutaneous Tropism: From Pathogenesis to Prevention, Montpellier, France
| | - Dorine Neveu
- Université Montpellier 1, Montpellier, France
- INSERM U 1058, Infection by HIV and by Agents with Mucocutaneous Tropism: From Pathogenesis to Prevention, Montpellier, France
| | - Anne Laure Bañuls
- MIVEGEC, UMR IRD 224-CNRS 5290-Montpellier Universités 1 et 2, Montpellier, France
| | - Sylvain Godreuil
- Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie-Virologie, Montpellier, France
- Université Montpellier 1, Montpellier, France
- INSERM U 1058, Infection by HIV and by Agents with Mucocutaneous Tropism: From Pathogenesis to Prevention, Montpellier, France
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28
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Bouétard A, Côte J, Besnard AL, Collinet M, Coutellec MA. Environmental versus anthropogenic effects on population adaptive divergence in the freshwater snail Lymnaea stagnalis. PLoS One 2014; 9:e106670. [PMID: 25207985 PMCID: PMC4160221 DOI: 10.1371/journal.pone.0106670] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 07/07/2014] [Indexed: 12/11/2022] Open
Abstract
Repeated pesticide contaminations of lentic freshwater systems located within agricultural landscapes may affect population evolution in non-target organisms, especially in species with a fully aquatic life cycle and low dispersal ability. The issue of evolutionary impact of pollutants is therefore conceptually important for ecotoxicologists. The impact of historical exposure to pesticides on genetic divergence was investigated in the freshwater gastropod Lymnaea stagnalis, using a set of 14 populations from contrasted environments in terms of pesticide and other anthropogenic pressures. The hypothesis of population adaptive divergence was tested on 11 life-history traits, using Q(ST)-F(ST) comparisons. Despite strong neutral differentiation (mean F(ST) = 0.291), five adult traits or parameters were found to be under divergent selection. Conversely, two early expressed traits showed a pattern consistent with uniform selection or trait canalization, and four adult traits appeared to evolve neutrally. Divergent selection patterns were mostly consistent with a habitat effect, opposing pond to ditch and channel populations. Comparatively, pesticide and other human pressures had little correspondence with evolutionary patterns, despite hatching rate impairment associated with global anthropogenic pressure. Globally, analyses revealed high genetic variation both at neutral markers and fitness-related traits in a species used as model in ecotoxicology, providing empirical support for the need to account for genetic and evolutionary components of population response in ecological risk assessment.
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Affiliation(s)
- Anthony Bouétard
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Jessica Côte
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Anne-Laure Besnard
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Marc Collinet
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
| | - Marie-Agnès Coutellec
- INRA, UMR 0985 ESE, Ecology and Ecosystem Health, INRA – Agrocampus Ouest, CS84215, Rennes Cedex, France
- * E-mail:
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29
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Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, Brunner AM, Schackwitz W, Gunter L, Chen JG, Tuskan GA, DiFazio SP. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet 2014; 46:1089-96. [DOI: 10.1038/ng.3075] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/30/2014] [Indexed: 12/16/2022]
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30
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Gilbert KJ, Whitlock MC. QST-FST comparisons with unbalanced half-sib designs. Mol Ecol Resour 2014; 15:262-7. [PMID: 25042150 DOI: 10.1111/1755-0998.12303] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 07/10/2014] [Accepted: 07/12/2014] [Indexed: 11/28/2022]
Abstract
QST , a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between QST and FST , but that method is limited to balanced data sets with offspring related as half-sibs through shared fathers. We extend this approach (i) to allow for a model more suitable for some plant populations or breeding designs in which offspring are related through mothers (assuming independent fathers for each offspring; half-sibs by dam); and (ii) by explicitly allowing for unbalanced data sets. The resulting approach is made available through the R package QstFstComp.
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Affiliation(s)
- Kimberly J Gilbert
- Department of Zoology, University of British Columbia, 6270 University Blvd., Vancouver, BC, V6T 1Z4, Canada
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31
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Phenotypic divergence of the common toad (Bufo bufo) along an altitudinal gradient: evidence for local adaptation. Heredity (Edinb) 2014; 114:69-79. [PMID: 25074572 DOI: 10.1038/hdy.2014.71] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 06/05/2014] [Accepted: 06/25/2014] [Indexed: 01/31/2023] Open
Abstract
Variation in the environment can induce different patterns of genetic and phenotypic differentiation among populations. Both neutral processes and selection can influence phenotypic differentiation. Altitudinal phenotypic variation is of particular interest in disentangling the interplay between neutral processes and selection in the dynamics of local adaptation processes but remains little explored. We conducted a common garden experiment to study the phenotypic divergence in larval life-history traits among nine populations of the common toad (Bufo bufo) along an altitudinal gradient in France. We further used correlation among population pairwise estimates of quantitative trait (QST) and neutral genetic divergence (FST from neutral microsatellite markers), as well as altitudinal difference, to estimate the relative role of divergent selection and neutral genetic processes in phenotypic divergence. We provided evidence for a neutral genetic differentiation resulting from both isolation by distance and difference in altitude. We found evidence for phenotypic divergence along the altitudinal gradient (faster development, lower growth rate and smaller metamorphic size). The correlation between pairwise QSTs-FSTs and altitude differences suggested that this phenotypic differentiation was most likely driven by altitude-mediated selection rather than by neutral genetic processes. Moreover, we found different divergence patterns for larval traits, suggesting that different selective agents may act on these traits and/or selection on one trait may constrain the evolution on another through genetic correlation. Our study highlighted the need to design more integrative studies on the common toad to unravel the underlying processes of phenotypic divergence and its selective agents in the context of environmental clines.
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32
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Brouillette LC, Mason CM, Shirk RY, Donovan LA. Adaptive differentiation of traits related to resource use in a desert annual along a resource gradient. THE NEW PHYTOLOGIST 2014; 201:1316-1327. [PMID: 24325125 DOI: 10.1111/nph.12628] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/21/2013] [Indexed: 05/15/2023]
Abstract
• Plant resource-use traits are generally hypothesized to be adaptively differentiated for populations distributed along resource gradients. Although nutrient limitations are expected to select for resource-conservative strategies, water limitations may select for either resource-conservative or -acquisitive strategies. We test whether population differentiation reflects local adaptation for traits associated with resource-use strategies in a desert annual (Helianthus anomalus) distributed along a gradient of positively covarying water and nutrient availability. • We compared quantitative trait variation (Q(ST)) with neutral genetic differentiation (F(ST)), in a common garden glasshouse study, for leaf economics spectrum (LES) and related traits: photosynthesis (A(mass), A(area)), leaf nitrogen (N(mass), N(area)), leaf lifetime (LL), leaf mass per area (LMA), leaf water content (LWC), water-use efficiency (WUE, estimated as δ(13)C) and days to first flower (DFF). • Q(ST)-F(ST) differences support adaptive differentiation for Amass , N(mass), N(area), LWC and DFF. The trait combinations associated with drier and lower fertility sites represent correlated trait evolution consistent with the more resource-acquisitive end of the LES. There was no evidence for adaptive differentiation for A(area), LMA and WUE. • These results demonstrate that hot dry environments can selectively favor correlated evolution of traits contributing to a resource-acquisitive and earlier reproduction 'escape' strategy, despite lower fertility.
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Affiliation(s)
- Larry C Brouillette
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
| | - Chase M Mason
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
| | - Rebecca Y Shirk
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
| | - Lisa A Donovan
- Department of Plant Biology, University of Georgia, 2502 Miller Plant Sciences, Athens, GA, 30602, USA
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Lamy JB, Delzon S, Bouche PS, Alia R, Vendramin GG, Cochard H, Plomion C. Limited genetic variability and phenotypic plasticity detected for cavitation resistance in a Mediterranean pine. THE NEW PHYTOLOGIST 2014; 201:874-886. [PMID: 24180459 DOI: 10.1111/nph.12556] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 09/16/2013] [Indexed: 05/04/2023]
Abstract
Resistance to cavitation is a major determinant of plant survival under severe drought and can be used to quantify species adaptive potential. Interspecific variation in this key trait is well defined in woody species, but intraspecific variation (level and structure) resulting from standing genetic variation and phenotypic plasticity has never been determined. Combining for the first time in situ characterization of natural populations and two reciprocal common gardens in dry and wet sites, we estimated variance components (phenotypic, genetic, environmental, and genetic × environmental) of cavitation resistance based on 513 genotypes of a Mediterranean pine, Pinus pinaster. Despite the selected populations being climatically contrasted, phenotypic plasticity in resistance to cavitation remained low and was essentially attributed to family level. Between-population variation in cavitation resistance for both phenotypic and genetic variation was limited. These results strongly suggest that cavitation resistance is buffered against genetic and to a lesser extent environmental variation (canalization) in maritime pine. Consequently, in a drier world, the increasing drought tolerance of Pinus species might be severely constrained by the low level of cavitation resistance variation, resulting in a large-scale loss of productivity.
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Affiliation(s)
- Jean-Baptiste Lamy
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- INRA, UMR 547 PIAF, F-63100, Clermont-Ferrand, France
| | - Sylvain Delzon
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, UMR 1202 BIOGECO, F-33405, Talence, France
| | - Pauline S Bouche
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, UMR 1202 BIOGECO, F-33405, Talence, France
| | - Ricardo Alia
- Departamento de Sistemas y Recursos Forestales, CIFOR - INIA, Carretera de La Coruña km 7.5, 28040, Madrid, Spain
| | - Giovanni Giuseppe Vendramin
- Istituto di Genetica Vegetale, Sezione di Firenze, Consiglio Nazionale delle Ricerche, via Madonna del Piano 10, 50019, Sesto Fiorentino (FI), Italy
| | - Hervé Cochard
- INRA, UMR 547 PIAF, F-63100, Clermont-Ferrand, France
- Clermont Université, Université Blaise Pascal, UMR547 PIAF, BP 10448, F-63000, Clermont-Ferrand, France
| | - Christophe Plomion
- INRA, UMR 1202 BIOGECO, F-33610, Cestas, France
- Univ. Bordeaux, UMR 1202 BIOGECO, F-33405, Talence, France
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Ye Q, Tang F, Wei N, Yao X. Molecular and quantitative trait variation within and among small fragmented populations of the endangered plant species Psilopeganum sinense. ANNALS OF BOTANY 2014; 113:79-86. [PMID: 24265350 PMCID: PMC3864726 DOI: 10.1093/aob/mct255] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 09/11/2013] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Natural selection and genetic drift are important evolutionary forces in determining genetic and phenotypic differentiation in plant populations. The extent to which these two distinct evolutionary forces affect locally adaptive quantitative traits has been well studied in common plant and animal species. However, we know less about how quantitative traits respond to selection pressures and drift in endangered species that have small population sizes and fragmented distributions. To address this question, this study assessed the relative strengths of selection and genetic drift in shaping population differentiation of phenotypic traits in Psilopeganum sinense, a naturally rare and recently endangered plant species. METHODS Population differentiation at five quantitative traits (QST) obtained from a common garden experiment was compared with differentiation at putatively neutral microsatellite markers (FST) in seven populations of P. sinense. QST estimates were derived using a Bayesian hierarchical variance component method. KEY RESULTS Trait-specific QST values were equal to or lower than FST. Neutral genetic diversity was not correlated with quantitative genetic variation within the populations of P. sinense. CONCLUSIONS Despite the prevalent empirical evidence for QST > FST, the results instead suggest a definitive role of stabilizing selection and drift leading to phenotypic differentiation among small populations. Three traits exhibited a significantly lower QST relative to FST, suggesting that populations of P. sinense might have experienced stabilizing selection for the same optimal phenotypes despite large geographical distances between populations and habitat fragmentation. For the other two traits, QST estimates were of the same magnitude as FST, indicating that divergence in these traits could have been achieved by genetic drift alone. The lack of correlation between molecular marker and quantitative genetic variation suggests that sophisticated considerations are required for the inference of conservation measures of P. sinense from neutral genetic markers.
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Affiliation(s)
- Qigang Ye
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Feiyan Tang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, China
| | - Na Wei
- Department of Ecology and Evolutional Biology, The University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Xiaohong Yao
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan 430074, Hubei, China
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Glacial history affected phenotypic differentiation in the alpine plant, Campanula thyrsoides. PLoS One 2013; 8:e73854. [PMID: 24146742 PMCID: PMC3797877 DOI: 10.1371/journal.pone.0073854] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
Numerous widespread Alpine plant species show molecular differentiation among populations from distinct regions. This has been explained as the result of genetic drift during glacial survival in isolated refugia along the border of the European Alps. Since genetic drift may affect molecular markers and phenotypic traits alike, we asked whether phenotypic differentiation mirrors molecular patterns among Alpine plant populations from different regions. Phenotypic traits can be under selection, so we additionally investigated whether part of the phenotypic differentiation can be explained by past selection and/or current adaptation. Using the monocarpic Campanula thyrsoides as our study species, a common garden experiment with plants from 21 populations from four phylogeographic groups located in regions across the Alps and the Jura Mountains was performed to test for differentiation in morphological and phenological traits. Past selection was investigated by comparing phenotypic differentiation among and within regions with molecular differentiation among and within regions. The common garden results indicated regional differentiation among populations for all investigated phenotypic traits, particularly in phenology. Delayed flowering in plants from the South-eastern Alps suggested adaptation to long sub-mediterranean summers and contrasted with earlier flowering of plants experiencing shorter growing seasons in regions with higher elevation to the West. Comparisons between molecular and phenotypic differentiation revealed diversifying selection among regions in height and biomass, which is consistent with adaptation to environmental conditions in glacial refugia. Within regions, past selection acted against strong diversification for most phenotypic traits, causing restricted postglacial adaptation. Evidence consistent with post-glacial adaptation was also given by negative correlation coefficients between several phenotypic traits and elevation of the population's origin. In conclusion, our study suggests that, irrespective of adaptation of plants to their current environment, glacial history can have a strong and long-lasting influence on the phenotypic evolution of Alpine plants.
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DeFaveri J, Merilä J. Evidence for adaptive phenotypic differentiation in Baltic Sea sticklebacks. J Evol Biol 2013; 26:1700-15. [DOI: 10.1111/jeb.12168] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 12/26/2022]
Affiliation(s)
- J. DeFaveri
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki Finland
| | - J. Merilä
- Ecological Genetics Research Unit; Department of Biosciences; University of Helsinki; Helsinki Finland
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Tian-Bi YNT, Jarne P, Konan JNK, Utzinger J, N'Goran EK. Contrasting the distribution of phenotypic and molecular variation in the freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni. Heredity (Edinb) 2013; 110:466-74. [PMID: 23321708 PMCID: PMC3630815 DOI: 10.1038/hdy.2012.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 10/11/2012] [Accepted: 11/26/2012] [Indexed: 11/08/2022] Open
Abstract
Population differentiation was investigated by confronting phenotypic and molecular variation in the highly selfing freshwater snail Biomphalaria pfeifferi, the intermediate host of Schistosoma mansoni. We sampled seven natural populations separated by a few kilometers, and characterized by different habitat regimes (permanent/temporary) and openness (open/closed). A genetic analysis based on five microsatellite markers confirms that B. pfeifferi is a selfer (s≈0.9) and exhibits limited variation within populations. Most pairwise FST were significant indicating marked population structure, though no isolation by distance was detected. Families from the seven populations were monitored under laboratory conditions over two generations (G1 and G2), allowing to record several life-history traits, including growth, fecundity and survival, over 25 weeks. Marked differences were detected among populations for traits expressed early in the life cycle (up to sexual maturity). Age and size at first reproduction had high heritability values, but such a trend was not found for early reproductive traits. In most populations, G1 snails matured later and at a larger size than G2 individuals. Individuals from permanent habitats matured at a smaller size and were more fecund than those from temporary habitats. The mean phenotypic differentiation over all populations (QST) was lower than the mean genetic differentiation (FST), suggesting stabilizing selection. However, no difference was detected between QST and FST for both habitat regime and habitat openness.
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Affiliation(s)
- Y-N T Tian-Bi
- Laboratoire de Génétique, UFR Biosciences, Université Félix Houphouët-Boigny, 22 BP 1106 Abidjan 22, Côte d'Ivoire.
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Lee CR, Mitchell-Olds T. Complex trait divergence contributes to environmental niche differentiation in ecological speciation of Boechera stricta. Mol Ecol 2013; 22:2204-17. [PMID: 23432437 PMCID: PMC3618598 DOI: 10.1111/mec.12250] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 01/10/2013] [Accepted: 01/12/2013] [Indexed: 01/22/2023]
Abstract
Ecological factors may contribute to reproductive isolation if differential local adaptation causes immigrant or hybrid fitness reduction. Because local adaptation results from the interaction between natural selection and adaptive traits, it is crucial to investigate both to understand ecological speciation. Previously, we used niche modelling to identify local water availability as an environmental correlate of incipient ecological speciation between two subspecies in Boechera stricta, a close relative of Arabidopsis. Here, we performed several large-scale glasshouse experiments to investigate the divergence of various physiological, phenological and morphological traits. Although we found no significant difference in physiological traits, the Western subspecies has significantly faster growth rate, larger leaf area, less succulent leaves, delayed reproductive time and longer flowering duration. These trait differences are concordant with previous results that habitats of the Western genotypes have more consistent water availability, while Eastern genotypes inhabit locations with more ephemeral water supplies. In addition, by comparing univariate and multivariate divergence of complex traits (Q(ST)) to the genomewide distribution of SNP FST , we conclude that the aspects of phenology and morphology (but not physiology) are under divergent selection. In addition, we also identified several highly diverged traits without obvious water-related functions.
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Affiliation(s)
- Cheng-Ruei Lee
- Department of Biology, Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.
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Leinonen T, McCairns RJS, O'Hara RB, Merilä J. Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity. Nat Rev Genet 2013; 14:179-90. [PMID: 23381120 DOI: 10.1038/nrg3395] [Citation(s) in RCA: 235] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Comparative studies of the divergence of quantitative traits and neutral molecular markers, known as Q(ST)-F(ST) comparisons, provide a means for researchers to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. The use of Q(ST)-F(ST) comparisons has increased rapidly in the last few years, highlighting the utility of this approach for addressing a wide range of questions that are relevant to evolutionary and ecological genetics. These studies have also provided lessons for the design of future Q(ST)-F(ST) comparisons. Methods based on the Q(ST)-F(ST) approach could also be used to analyse various types of 'omics' data in new and revealing ways.
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Affiliation(s)
- Tuomas Leinonen
- Ecological Genetics Research Unit, Department of Biosciences, PO Box 65, FI-00014 University of Helsinki, Finland
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De Kort H, Vandepitte K, Honnay O. A meta-analysis of the effects of plant traits and geographical scale on the magnitude of adaptive differentiation as measured by the difference between QST and FST. Evol Ecol 2012. [DOI: 10.1007/s10682-012-9624-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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41
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Hübner S, Bdolach E, Ein-Gedy S, Schmid KJ, Korol A, Fridman E. Phenotypic landscapes: phenological patterns in wild and cultivated barley. J Evol Biol 2012; 26:163-74. [PMID: 23176039 DOI: 10.1111/jeb.12043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 09/11/2012] [Accepted: 10/08/2012] [Indexed: 01/31/2023]
Abstract
Phenotypic variation in natural populations is the outcome of the joint effects of environmentally induced adaptations and neutral processes on the genetic architecture of quantitative traits. In this study, we examined the role of adaptation in shaping wild barley phenotypic variation along different environmental gradients. Detailed phenotyping of 164 wild barley (Hordeum spontaneum) accessions from Israel (of the Barley1K collection) and 18 cultivated barley (H. vulgare) varieties was conducted in common garden field trials. Cluster analysis based on phenotypic data indicated that wild barley in this region can be differentiated into three ecotypes in accordance with their ecogeographical distribution: north, coast and desert. Population differentiation (Q(ST) ) for each trait was estimated using a hierarchical Bayesian model and compared to neutral differentiation (F(ST) ) based on 42 microsatellite markers. This analysis indicated that the three clusters diverged in morphological but not in reproductive characteristics. To address the issue of phenotypic variation along environmental gradients, climatic and soil gradients were compared with each of the measured traits given the geographical distance between sampling sites using a partial Mantel test. Flowering time and plant growth were found to be differentially correlated with climatic and soil characteristic gradients, respectively. The H. vulgare varieties were superior to the H. spontaneum accessions in yield components, yet resembled the Mediterranean types in vegetative characteristics and flowering time, which may indicate the geographical origin of domesticated barley.
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Affiliation(s)
- S Hübner
- Department of Evolutionary Biology, University of Haifa, Haifa, Israel
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Lamy JB, Plomion C, Kremer A, Delzon S. Q(ST) < F(ST) As a signature of canalization. Mol Ecol 2012; 21:5646-55. [PMID: 23110372 DOI: 10.1111/mec.12017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 07/27/2012] [Accepted: 07/31/2012] [Indexed: 02/02/2023]
Abstract
A key aim of evolutionary biology - inferring the action of natural selection on wild species - can be achieved by comparing neutral genetic differentiation between populations (F(ST)) with quantitative genetic variation (Q(ST)). Each of the three possible outcomes of comparisons of Q(ST) and F(ST) (Q(ST) > F(ST), Q(ST) = F(ST), Q(ST) < F(ST)) is associated with an inference (diversifying selection, genetic drift, uniform selection, respectively). However, published empirical and theoretical studies have focused on the Q(ST) > F(ST) outcome. We believe that this reflects the absence of a straightforward biological interpretation of the Q(ST) < F(ST) pattern. We here report recent evidence of this neglected evolutionary pattern, provide guidelines to its interpretation as either a canalization phenomenon or a consequence of uniform selection and discuss the significant importance this issue will have for the area of evolutionary biology.
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Kronholm I, Picó FX, Alonso-Blanco C, Goudet J, de Meaux J. Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1. Evolution 2012; 66:2287-302. [PMID: 22759302 DOI: 10.1111/j.1558-5646.2012.01590.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation.
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Affiliation(s)
- Ilkka Kronholm
- Department Genetics and Plant Breeding, Max Planck Institute for Plant Breeding Research, DE-50829 Cologne, Germany
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LE CORRE VALÉRIE, KREMER ANTOINE. The genetic differentiation at quantitative trait loci under local adaptation. Mol Ecol 2012; 21:1548-66. [DOI: 10.1111/j.1365-294x.2012.05479.x] [Citation(s) in RCA: 253] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Volis S. Adaptive genetic differentiation in a predominantly self-pollinating species analyzed by transplanting into natural environment, crossbreeding and Q(ST)-F(ST) test. THE NEW PHYTOLOGIST 2011; 192:237-248. [PMID: 21729087 DOI: 10.1111/j.1469-8137.2011.03799.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
• Both genetic drift and natural selection result in genetic/phenotypic differentiation over space. I analyzed the role of local adaptation in the genetic differentiation of populations of the annual grass Hordeum spontaneum sampled along an aridity gradient. • The study included the introduction of plants having desert vs nondesert origin into natural (desert) environment, analysis of population differentiation in allozymes and random amplified polymorphic DNA (RAPD) markers vs phenotypic traits (Q(ST) -F(ST) comparison), and planting interpopulation hybrids under simulated desert conditions in a glasshouse. • The results of the home advantage test, Q(ST) -F(ST) comparison and crossbreeding were consistent with local adaptation; that is, that differentiation of the desert plants from plants of nondesert origin in phenotypic traits was adaptive, giving them home advantage. Each method used provided additional, otherwise unavailable, information, meaning that they should be viewed as complementary rather than alternative approaches. • Gene flow from adjacent populations (i.e. populations experiencing the desert environment) via seeds (but not pollen) had a positive effect on fitness by enhancing natural selection and counteracting drift. At the same time, the effect of genes from the species distributional core (nondesert plants) by either seed or pollen had a negative fitness effect despite its enriching effect on neutral diversity. The pattern of outbreeding depression observed in interpopulation hybrids (F(1) ) and their segregating progeny (F(2) ) was inconsistent with underdominance, but indicated the presence of additive, dominance and epistatic effects.
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Affiliation(s)
- S Volis
- The Institutes for Applied Research, Ben-Gurion University of the Negev, POB 653, Beer Sheva 84105, Israel
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Decoupling of differentiation between traits and their underlying genes in response to divergent selection. Heredity (Edinb) 2011; 108:375-85. [PMID: 21915150 DOI: 10.1038/hdy.2011.81] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We dissected the relationship between genetic differentiation (Q(ST)) for a trait and its underlying genes (G(STq), differentiation for a quantitative locus) in an evolutionary context, with the aim of identifying the conditions in which these two measurements are decoupled. We used two parameters (θ(B) and θ(W)) scaling the contributions of inter- and intrapopulation allelic covariation between genes controlling the trait of interest. We monitored the changes in θ(B) and θ(W), Q(ST) and G(STq) over successive generations of divergent and stabilizing selection, in simulations for an outcrossing species with extensive gene flow. The dynamics of these parameters are characterized by two phases. Initially, during the earliest generations, differentiation of the trait increases very rapidly and the principal and immediate driver of Q(ST) is θ(B). During subsequent generations, G(STq) increases steadily and makes an equal contribution to Q(ST). These results show that selection first captures beneficial allelic associations at different loci at different populations, and then targets changes in allelic frequencies. The same patterns are observed when environmental change modifies divergent selection, as shown by the very rapid response of θ(B) to the changes of selection regimes. We compare our results with previous experimental findings and consider their relevance to the detection of molecular signatures of natural selection.
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Lamy JB, Bouffier L, Burlett R, Plomion C, Cochard H, Delzon S. Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range. PLoS One 2011; 6:e23476. [PMID: 21858137 PMCID: PMC3155568 DOI: 10.1371/journal.pone.0023476] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 07/19/2011] [Indexed: 11/18/2022] Open
Abstract
Background Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs. Methodology We assessed cavitation resistance (P50), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (FST) and quantitative genetic differentiation (QST), for retrospective identification of the evolutionary forces acting on these traits. Results/Discussion In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h2ns = 0.43±0.18, CVA = 4.4%). QST was significantly lower than FST, indicating uniform selection for P50, rather than genetic drift. Putative mechanisms underlying QST<FST are discussed.
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Affiliation(s)
- Jean-Baptiste Lamy
- INRA, UMR 1202 BIOGECO, F-33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F-33610 Cestas, France
- INRA, UMR 547 PIAF, University of Blaise Pascal, F-63100 Clermont-Ferrand, France
| | - Laurent Bouffier
- INRA, UMR 1202 BIOGECO, F-33610 Cestas, France
- FCBA, Station Sud-Ouest, Domaine de Sivaillan, F-33480 Moulis en Médoc, France
| | - Régis Burlett
- INRA, UMR 1202 BIOGECO, F-33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F-33610 Cestas, France
| | - Christophe Plomion
- INRA, UMR 1202 BIOGECO, F-33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F-33610 Cestas, France
| | - Hervé Cochard
- INRA, UMR 547 PIAF, University of Blaise Pascal, F-63100 Clermont-Ferrand, France
| | - Sylvain Delzon
- INRA, UMR 1202 BIOGECO, F-33610 Cestas, France
- Université de Bordeaux, UMR 1202 BIOGECO, F-33610 Cestas, France
- * E-mail:
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TROKOVIC N, HERCZEG G, SCOTT McCAIRNS RJ, IZZA AB GHANI N, MERILÄ J. Intraspecific divergence in the lateral line system in the nine-spined stickleback (Pungitius pungitius). J Evol Biol 2011; 24:1546-58. [DOI: 10.1111/j.1420-9101.2011.02286.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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KAWAKAMI TAKESHI, MORGAN THEODOREJ, NIPPERT JESSEB, OCHELTREE TROYW, KEITH ROSE, DHAKAL PREETI, UNGERER MARKC. Natural selection drives clinal life history patterns in the perennial sunflower species, Helianthus maximiliani. Mol Ecol 2011; 20:2318-28. [DOI: 10.1111/j.1365-294x.2011.05105.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Alberto F, Bouffier L, Louvet JM, Lamy JB, Delzon S, Kremer A. Adaptive responses for seed and leaf phenology in natural populations of sessile oak along an altitudinal gradient. J Evol Biol 2011; 24:1442-54. [PMID: 21507119 DOI: 10.1111/j.1420-9101.2011.02277.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We assessed the adaptive potential of seed and leaf phenology in 10 natural populations of sessile oak (Quercus petraea) sampled along two altitudinal transects using common garden experiments. Population differentiation for both phenological traits was observed with high-altitude populations germinating and flushing later than low altitude ones. However, high genetic variation and heritability values were also maintained within populations, despite slightly decreasing for dates of leaf unfolding with increasing altitude. We suggest that biotic and abiotic fluctuating selection pressures within populations and high gene flow are the main mechanisms maintaining high genetic variation for these fitness related traits. Moreover, changes in selection intensity and/or selection pressures along the altitudinal gradient can explain the reduction in genetic variation observed for leaf phenology. We anticipate that the maintenance of high genetic variation will be a valuable resource for future adaptation of sessile oak populations undergoing an upslope shift caused by climate change.
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Affiliation(s)
- F Alberto
- INRA, UMR1202 Biodiversité Gènes et Communautés, Cestas, France
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